Citrus Sinensis ID: 042593

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350--
Protein Sequence
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHcccccccccccEEHHHHHHHHcccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHcccccccEEEHHHHHHHHHcccccHHHHHcccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHcccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccEEEEHHHHHHHHHHcHHcccccccccHHHHHHHHHcccccHHHHHHHHHccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccHHHcccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHccccccccEHHHHHHHHHHHcccHHHHHHHHHHcccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEEEHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHccccccccEHHHHHHHHHHHcccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
FLVYKQLQQIYihshsplpplfdsftySFLIRTCvtlsypnlgtQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLkdssklfdelpernlVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAaceytepseiTILAVLPAIwkngevrncqlihgygekrgfnafDIHVSNCLidtyakcgcifsasklfedtsvdrknLVSWTTIISGFAMHGMGKEAVENFERMqkvglkpnrswrigeeGLKFFDKMVEECevlpdikhygCLIDILERAGRLEQAEevasgipsqitnVVVWRTGFLRLLINsyffspitlnsqrlffFPAALYALTQILgfkplfrkessdg
Flexible Loop (DISEMBL)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLfedtsvdrKNLVSWTTIISGFAMHGMGKEAVENFERMQkvglkpnrswriGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEvasgipsqitnvVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG
Low Complexity Region (SEG)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG
Disordered region (IsUnstruct)
*LVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLF*******
Disordered Region (DISOPRED)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSD*
Disordered Region (DISEMBL)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG
Disordered Region (DISPRO)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESS**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG
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	352	2.2.26 [Sep-21-2011]
Q680Z7	504	Pentatricopeptide repeat-	yes	no	0.855	0.597	0.485	2e-84
Q9SIL5	534	Pentatricopeptide repeat-	no	no	0.792	0.522	0.363	3e-52
Q9FMA1	530	Pentatricopeptide repeat-	no	no	0.778	0.516	0.361	4e-48
A8MQA3	595	Pentatricopeptide repeat-	no	no	0.755	0.447	0.372	2e-46
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.778	0.441	0.327	5e-41
Q8LK93	603	Pentatricopeptide repeat-	no	no	0.758	0.442	0.341	2e-40
Q9SZT8	632	Pentatricopeptide repeat-	no	no	0.815	0.454	0.324	9e-40
Q9FX24	581	Pentatricopeptide repeat-	no	no	0.775	0.469	0.337	1e-39
Q9SN39	871	Pentatricopeptide repeat-	no	no	0.730	0.295	0.320	2e-39
Q9FNN7	511	Pentatricopeptide repeat-	no	no	0.846	0.583	0.313	3e-39

>sp|Q680Z7|PPR24_ARATH Pentatricopeptide repeat-containing protein At1g09220, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E25 PE=2 SV=1

 Score =  312 bits (800), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 164/338 (48%), Positives = 217/338 (64%), Gaps = 37/338 (10%)

Query: 1   FLVYKQLQQI-YIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFS--KVGFQS 57
           + +Y QLQ++ ++  H+   P FDSFTY FL++      +P+L   +       K+GF+S
Sbjct: 97  YFLYDQLQRLHFLSDHNKSLPPFDSFTYLFLLKASSNPRFPSLLLGIGLHGLTLKLGFES 156

Query: 58  HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGL----------------- 100
           HVYV TAL  MY+  G + D+ K+FDE+PERN VTWNV+ITGL                 
Sbjct: 157 HVYVQTALVGMYLVGGNMIDAHKVFDEMPERNPVTWNVMITGLTNLGDFEKALCFLEKMP 216

Query: 101 ----VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQ 156
               V WT IIDGY+R+++  EA+ LF RM AC+  +P+EITILA+LPA+W  G+++ C 
Sbjct: 217 NRTVVSWTTIIDGYARVDKPKEAILLFSRMVACDAIKPNEITILAILPAVWNLGDLKMCG 276

Query: 157 LIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFA 216
            +H Y  KRGF   DI V+N LID YAKCGCI SA K F +    RKNLVSWTT+IS FA
Sbjct: 277 SVHAYVGKRGFVPCDIRVTNSLIDAYAKCGCIQSAFKFFIEIPNGRKNLVSWTTMISAFA 336

Query: 217 MHGMGKEAVENFERMQKVGLKPNRSWRIG------------EEGLKFFDKMVEECEVLPD 264
           +HGMGKEAV  F+ M+++GLKPNR   I             EE L+FF+ MV E ++ PD
Sbjct: 337 IHGMGKEAVSMFKDMERLGLKPNRVTMISVLNACSHGGLAEEEFLEFFNTMVNEYKITPD 396

Query: 265 IKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWR 302
           +KHYGCL+D+L R GRLE+AE++A  IP +    VVWR
Sbjct: 397 VKHYGCLVDMLRRKGRLEEAEKIALEIPIE-EKAVVWR 433

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIL5|PP165_ARATH Pentatricopeptide repeat-containing protein At2g20540 OS=Arabidopsis thaliana GN=PCMP-E78 PE=2 SV=1

 Score =  205 bits (522), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 117/322 (36%), Positives = 179/322 (55%), Gaps = 43/322 (13%)

Query: 3   VYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVN 62
           +YKQL    +     LP   D FT+ F+ ++C +L    LG Q+H    K G + HV   
Sbjct: 95  IYKQL----LRKSFELP---DRFTFPFMFKSCASLGSCYLGKQVHGHLCKFGPRFHVVTE 147

Query: 63  TALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITG---------------------LV 101
            AL DMY+    L D+ K+FDE+ ER++++WN +++G                     +V
Sbjct: 148 NALIDMYMKFDDLVDAHKVFDEMYERDVISWNSLLSGYARLGQMKKAKGLFHLMLDKTIV 207

Query: 102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGY 161
            WT +I GY+ +    EA+  FR M      EP EI++++VLP+  + G +   + IH Y
Sbjct: 208 SWTAMISGYTGIGCYVEAMDFFREMQLAG-IEPDEISLISVLPSCAQLGSLELGKWIHLY 266

Query: 162 GEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMG 221
            E+RGF      V N LI+ Y+KCG I  A +LF    ++ K+++SW+T+ISG+A HG  
Sbjct: 267 AERRGFLK-QTGVCNALIEMYSKCGVISQAIQLF--GQMEGKDVISWSTMISGYAYHGNA 323

Query: 222 KEAVENFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKHYGC 270
             A+E F  MQ+  +KPN    +G           +EGL++FD M ++ ++ P I+HYGC
Sbjct: 324 HGAIETFNEMQRAKVKPNGITFLGLLSACSHVGMWQEGLRYFDMMRQDYQIEPKIEHYGC 383

Query: 271 LIDILERAGRLEQAEEVASGIP 292
           LID+L RAG+LE+A E+   +P
Sbjct: 384 LIDVLARAGKLERAVEITKTMP 405

Arabidopsis thaliana (taxid: 3702)

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

 Score =  192 bits (487), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 113/313 (36%), Positives = 170/313 (54%), Gaps = 39/313 (12%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D+FT+ F+++  V +S    G Q+H      GF S V+V T L  MY S G L D+ K+F
Sbjct: 115 DTFTFPFVLKIAVRVSDVWFGRQIHGQVVVFGFDSSVHVVTGLIQMYFSCGGLGDARKMF 174

Query: 83  DELPERNLVTWNVIITGL-----------------------VKWTGIIDGYSRMNRSNEA 119
           DE+  +++  WN ++ G                        V WT +I GY++  R++EA
Sbjct: 175 DEMLVKDVNVWNALLAGYGKVGEMDEARSLLEMMPCWVRNEVSWTCVISGYAKSGRASEA 234

Query: 120 LALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI 179
           + +F+RM   E  EP E+T+LAVL A    G +   + I  Y + RG N   + ++N +I
Sbjct: 235 IEVFQRMLM-ENVEPDEVTLLAVLSACADLGSLELGERICSYVDHRGMNR-AVSLNNAVI 292

Query: 180 DTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN 239
           D YAK G I  A  +FE   V+ +N+V+WTTII+G A HG G EA+  F RM K G++PN
Sbjct: 293 DMYAKSGNITKALDVFE--CVNERNVVTWTTIIAGLATHGHGAEALAMFNRMVKAGVRPN 350

Query: 240 RSWRIG-----------EEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA 288
               I            + G + F+ M  +  + P+I+HYGC+ID+L RAG+L +A+EV 
Sbjct: 351 DVTFIAILSACSHVGWVDLGKRLFNSMRSKYGIHPNIEHYGCMIDLLGRAGKLREADEVI 410

Query: 289 SGIPSQITNVVVW 301
             +P +  N  +W
Sbjct: 411 KSMPFK-ANAAIW 422

Arabidopsis thaliana (taxid: 3702)

>sp|A8MQA3|PP330_ARATH Pentatricopeptide repeat-containing protein At4g21065 OS=Arabidopsis thaliana GN=PCMP-H28 PE=2 SV=2

 Score =  186 bits (472), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 109/293 (37%), Positives = 172/293 (58%), Gaps = 27/293 (9%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D+ TY FLI+   T++   LG  +H+V  + GF S +YV  +L  +Y + G +  + K+F
Sbjct: 120 DTHTYPFLIKAVTTMADVRLGETIHSVVIRSGFGSLIYVQNSLLHLYANCGDVASAYKVF 179

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
           D++PE++LV WN           +I+G++   +  EALAL+  M + +  +P   TI+++
Sbjct: 180 DKMPEKDLVAWN----------SVINGFAENGKPEEALALYTEMNS-KGIKPDGFTIVSL 228

Query: 143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
           L A  K G +   + +H Y  K G    ++H SN L+D YA+CG +  A  LF D  VD 
Sbjct: 229 LSACAKIGALTLGKRVHVYMIKVGLTR-NLHSSNVLLDLYARCGRVEEAKTLF-DEMVD- 285

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKV-GLKPNRSWRIG-----------EEGLK 250
           KN VSWT++I G A++G GKEA+E F+ M+   GL P     +G           +EG +
Sbjct: 286 KNSVSWTSLIVGLAVNGFGKEAIELFKYMESTEGLLPCEITFVGILYACSHCGMVKEGFE 345

Query: 251 FFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           +F +M EE ++ P I+H+GC++D+L RAG++++A E    +P Q  NVV+WRT
Sbjct: 346 YFRRMREEYKIEPRIEHFGCMVDLLARAGQVKKAYEYIKSMPMQ-PNVVIWRT 397

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJY7|PP449_ARATH Pentatricopeptide repeat-containing protein At5g66520 OS=Arabidopsis thaliana GN=PCMP-H61 PE=2 SV=1

 Score =  168 bits (426), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 102/311 (32%), Positives = 162/311 (52%), Gaps = 37/311 (11%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           +++T+  L++ C  LS     TQ+HA  +K+G+++ VY   +L + Y   G  K +  LF
Sbjct: 114 NAYTFPSLLKACSNLSAFEETTQIHAQITKLGYENDVYAVNSLINSYAVTGNFKLAHLLF 173

Query: 83  DELPERNLVTWNVIITGLVK---------------------WTGIIDGYSRMNRSNEALA 121
           D +PE + V+WN +I G VK                     WT +I GY + + + EAL 
Sbjct: 174 DRIPEPDDVSWNSVIKGYVKAGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQ 233

Query: 122 LFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT 181
           LF  M   +  EP  +++   L A  + G +   + IH Y  K      D  +   LID 
Sbjct: 234 LFHEMQNSD-VEPDNVSLANALSACAQLGALEQGKWIHSYLNKTRIR-MDSVLGCVLIDM 291

Query: 182 YAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN-- 239
           YAKCG +  A ++F++  + +K++ +WT +ISG+A HG G+EA+  F  MQK+G+KPN  
Sbjct: 292 YAKCGEMEEALEVFKN--IKKKSVQAWTALISGYAYHGHGREAISKFMEMQKMGIKPNVI 349

Query: 240 ---------RSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASG 290
                        + EEG   F  M  +  + P I+HYGC++D+L RAG L++A+     
Sbjct: 350 TFTAVLTACSYTGLVEEGKLIFYSMERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQE 409

Query: 291 IPSQITNVVVW 301
           +P +  N V+W
Sbjct: 410 MPLK-PNAVIW 419

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LK93|PP145_ARATH Pentatricopeptide repeat-containing protein At2g02980 OS=Arabidopsis thaliana GN=PCMP-H26 PE=2 SV=2

 Score =  166 bits (421), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 100/293 (34%), Positives = 159/293 (54%), Gaps = 26/293 (8%)

Query: 21  LFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSK 80
           L D++T+  L++ C        G QLH +  K+G   +VYV   L +MY     +  +  
Sbjct: 126 LPDNYTFPSLLKACAVAKALEEGRQLHCLSMKLGLDDNVYVCPTLINMYTECEDVDSARC 185

Query: 81  LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITIL 140
           +FD + E  +V +N +ITG          Y+R NR NEAL+LFR M   +Y +P+EIT+L
Sbjct: 186 VFDRIVEPCVVCYNAMITG----------YARRNRPNEALSLFREMQG-KYLKPNEITLL 234

Query: 141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSV 200
           +VL +    G +   + IH Y +K  F  + + V+  LID +AKCG +  A  +FE   +
Sbjct: 235 SVLSSCALLGSLDLGKWIHKYAKKHSFCKY-VKVNTALIDMFAKCGSLDDAVSIFE--KM 291

Query: 201 DRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGL 249
             K+  +W+ +I  +A HG  ++++  FERM+   ++P+    +G           EEG 
Sbjct: 292 RYKDTQAWSAMIVAYANHGKAEKSMLMFERMRSENVQPDEITFLGLLNACSHTGRVEEGR 351

Query: 250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWR 302
           K+F +MV +  ++P IKHYG ++D+L RAG LE A E    +P   T  ++WR
Sbjct: 352 KYFSQMVSKFGIVPSIKHYGSMVDLLSRAGNLEDAYEFIDKLPISPTP-MLWR 403

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZT8|PP354_ARATH Pentatricopeptide repeat-containing protein At4g37380, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H48 PE=3 SV=1

 Score =  164 bits (415), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 109/336 (32%), Positives = 173/336 (51%), Gaps = 49/336 (14%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           FL+Y QL        S + P  + FT+S L+++C T S    G  +H    K G     Y
Sbjct: 115 FLLYVQLLS------SEINP--NEFTFSSLLKSCSTKS----GKLIHTHVLKFGLGIDPY 162

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIIT---------------------G 99
           V T L D+Y   G +  + K+FD +PER+LV+   +IT                      
Sbjct: 163 VATGLVDVYAKGGDVVSAQKVFDRMPERSLVSSTAMITCYAKQGNVEAARALFDSMCERD 222

Query: 100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
           +V W  +IDGY++    N+AL LF+++ A    +P EIT++A L A  + G +   + IH
Sbjct: 223 IVSWNVMIDGYAQHGFPNDALMLFQKLLAEGKPKPDEITVVAALSACSQIGALETGRWIH 282

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
            + +       ++ V   LID Y+KCG +  A  +F DT   RK++V+W  +I+G+AMHG
Sbjct: 283 VFVKSSRIR-LNVKVCTGLIDMYSKCGSLEEAVLVFNDTP--RKDIVAWNAMIAGYAMHG 339

Query: 220 MGKEAVENFERMQKV-GLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKH 267
             ++A+  F  MQ + GL+P     IG            EG++ F+ M +E  + P I+H
Sbjct: 340 YSQDALRLFNEMQGITGLQPTDITFIGTLQACAHAGLVNEGIRIFESMGQEYGIKPKIEH 399

Query: 268 YGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           YGCL+ +L RAG+L++A E    + +   + V+W +
Sbjct: 400 YGCLVSLLGRAGQLKRAYETIKNM-NMDADSVLWSS 434

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FX24|PPR71_ARATH Pentatricopeptide repeat-containing protein At1g34160 OS=Arabidopsis thaliana GN=PCMP-H68 PE=2 SV=2

 Score =  163 bits (413), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 105/311 (33%), Positives = 170/311 (54%), Gaps = 38/311 (12%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D+ T SF ++ C      +   QLH   ++ G  +   + T L D Y   G L  + KLF
Sbjct: 108 DALTCSFTLKACARALCSSAMDQLHCQINRRGLSADSLLCTTLLDAYSKNGDLISAYKLF 167

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
           DE+P R++ +WN +I GLV            NR++EA+ L++RM   E    SE+T++A 
Sbjct: 168 DEMPVRDVASWNALIAGLVSG----------NRASEAMELYKRMET-EGIRRSEVTVVAA 216

Query: 143 LPAIWKNGEVRNCQLI-HGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD 201
           L A    G+V+  + I HGY         ++ VSN  ID Y+KCG +  A ++FE  +  
Sbjct: 217 LGACSHLGDVKEGENIFHGYSND------NVIVSNAAIDMYSKCGFVDKAYQVFEQFT-G 269

Query: 202 RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN-----------RSWRIGEEGLK 250
           +K++V+W T+I+GFA+HG    A+E F++++  G+KP+           R   + E GL 
Sbjct: 270 KKSVVTWNTMITGFAVHGEAHRALEIFDKLEDNGIKPDDVSYLAALTACRHAGLVEYGLS 329

Query: 251 FFDKMVEECE-VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL 309
            F+ M   C+ V  ++KHYGC++D+L RAGRL +A ++   + S I + V+W++    LL
Sbjct: 330 VFNNMA--CKGVERNMKHYGCVVDLLSRAGRLREAHDIICSM-SMIPDPVLWQS----LL 382

Query: 310 INSYFFSPITL 320
             S  +S + +
Sbjct: 383 GASEIYSDVEM 393

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN39|PP320_ARATH Pentatricopeptide repeat-containing protein At4g18750, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H45 PE=2 SV=1

 Score =  163 bits (413), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 90/281 (32%), Positives = 151/281 (53%), Gaps = 24/281 (8%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D +T + ++  C      + G ++H    +      ++V+ AL DMY   G ++++  +F
Sbjct: 396 DVYTVTAVLNCCARYRLLDEGKRVHEWIKENDLGFDIFVSNALMDMYAKCGSMQEAELVF 455

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
            E+  +++++WN II G          YS+   +NEAL+LF  +   +   P E T+  V
Sbjct: 456 SEMRVKDIISWNTIIGG----------YSKNCYANEALSLFNLLLEEKRFSPDERTVACV 505

Query: 143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
           LPA          + IHGY  + G+ + D HV+N L+D YAKCG +  A  LF+D  +  
Sbjct: 506 LPACASLSAFDKGREIHGYIMRNGYFS-DRHVANSLVDMYAKCGALLLAHMLFDD--IAS 562

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKF 251
           K+LVSWT +I+G+ MHG GKEA+  F +M++ G++ +    +            +EG +F
Sbjct: 563 KDLVSWTVMIAGYGMHGFGKEAIALFNQMRQAGIEADEISFVSLLYACSHSGLVDEGWRF 622

Query: 252 FDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP 292
           F+ M  EC++ P ++HY C++D+L R G L +A      +P
Sbjct: 623 FNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIENMP 663

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FNN7|PP371_ARATH Pentatricopeptide repeat-containing protein At5g08510 OS=Arabidopsis thaliana GN=PCMP-E20 PE=2 SV=1

 Score =  162 bits (410), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 109/348 (31%), Positives = 175/348 (50%), Gaps = 50/348 (14%)

Query: 1   FLVYKQLQQIYIHSHSPLPPL-------FDSF-----TYSFLIRTCVTLSYPNLGTQLHA 48
           FL  K +Q  Y+H H P   +       FD       T++F+     + S       LH+
Sbjct: 48  FLYNKLIQAYYVH-HQPHESIVLYNLLSFDGLRPSHHTFNFIFAASASFSSARPLRLLHS 106

Query: 49  VFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITG--------- 99
            F + GF+S  +  T L   Y  LG L  + ++FDE+ +R++  WN +ITG         
Sbjct: 107 QFFRSGFESDSFCCTTLITAYAKLGALCCARRVFDEMSKRDVPVWNAMITGYQRRGDMKA 166

Query: 100 ------------LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIW 147
                       +  WT +I G+S+    +EAL +F  M   +  +P+ IT+++VLPA  
Sbjct: 167 AMELFDSMPRKNVTSWTTVISGFSQNGNYSEALKMFLCMEKDKSVKPNHITVVSVLPACA 226

Query: 148 KNGEVRNCQLIHGYGEKRGFNAFD-IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLV 206
             GE+   + + GY  + GF  FD I+V N  I+ Y+KCG I  A +LFE+   +++NL 
Sbjct: 227 NLGELEIGRRLEGYARENGF--FDNIYVCNATIEMYSKCGMIDVAKRLFEELG-NQRNLC 283

Query: 207 SWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKFFDKM 255
           SW ++I   A HG   EA+  F +M + G KP+    +G            +G + F  M
Sbjct: 284 SWNSMIGSLATHGKHDEALTLFAQMLREGEKPDAVTFVGLLLACVHGGMVVKGQELFKSM 343

Query: 256 VEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
            E  ++ P ++HYGC+ID+L R G+L++A ++   +P +  + VVW T
Sbjct: 344 EEVHKISPKLEHYGCMIDLLGRVGKLQEAYDLIKTMPMK-PDAVVWGT 390

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	352
449459636	495	PREDICTED: pentatricopeptide repeat-cont	0.812	0.577	0.522	2e-89
224123708	337	predicted protein [Populus trichocarpa]	0.670	0.700	0.604	6e-85
356506146	503	PREDICTED: pentatricopeptide repeat-cont	0.843	0.590	0.476	4e-84
356554965	517	PREDICTED: pentatricopeptide repeat-cont	0.846	0.576	0.468	6e-84
302144057	627	unnamed protein product [Vitis vinifera]	0.849	0.476	0.510	9e-83
147860607	610	hypothetical protein VITISV_027522 [Viti	0.849	0.490	0.510	1e-82
225444407	470	PREDICTED: pentatricopeptide repeat-cont	0.849	0.636	0.504	1e-82
334182414	504	pentatricopeptide repeat-containing prot	0.855	0.597	0.485	1e-82
255568986	337	pentatricopeptide repeat-containing prot	0.670	0.700	0.585	1e-82
147772248	538	hypothetical protein VITISV_033453 [Viti	0.849	0.555	0.507	6e-82

>gi|449459636|ref|XP_004147552.1| PREDICTED: pentatricopeptide repeat-containing protein At1g09220, mitochondrial-like [Cucumis sativus] gi|449484988|ref|XP_004157038.1| PREDICTED: pentatricopeptide repeat-containing protein At1g09220, mitochondrial-like [Cucumis sativus]

 Score =  335 bits (858), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 166/318 (52%), Positives = 215/318 (67%), Gaps = 32/318 (10%)

Query: 18  LPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKD 77
           +PP +D+F YSFL+ +C  L     G QLHA+  K+GF SHVYV TA+  MY + GFL D
Sbjct: 109 IPPSYDTFAYSFLLHSCADLELIGPGFQLHALTFKLGFPSHVYVQTAVLRMYAASGFLLD 168

Query: 78  SSKLFDELPERNLVTWNVIITGLVK---------------------WTGIIDGYSRMNRS 116
           + K+FDE+P+R+ VTWNV+ITGLVK                     WT IIDGY+R+NR 
Sbjct: 169 AMKVFDEMPDRSSVTWNVLITGLVKFGELKRARDVFDQMPMRTVVSWTAIIDGYTRLNRH 228

Query: 117 NEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSN 176
            EA  LF RM A    EP+E+T+L + PAI   G ++ CQ +H Y EK+GF   D+ ++N
Sbjct: 229 EEAAGLFWRMVAHFGMEPNEVTLLTIFPAISNLGALKLCQSVHAYAEKKGFKVSDVRIAN 288

Query: 177 CLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGL 236
            LID YAKCGCI SASK+FE+ S + KNLVSWT+IISGF MHGMGKEA+E+FE M+K G 
Sbjct: 289 SLIDCYAKCGCINSASKVFEEMSAEIKNLVSWTSIISGFTMHGMGKEAMESFEIMEKEGH 348

Query: 237 KPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAE 285
           +PNR   +            EEGL+FF+KMV E ++ PDI HYG LID+L RAGR+E+AE
Sbjct: 349 EPNRVTFLSIVSACSHGGLVEEGLEFFEKMVAEYQIKPDIMHYGSLIDMLGRAGRIEEAE 408

Query: 286 EVASGIPSQITNVVVWRT 303
           ++A  IP +I +VV+WRT
Sbjct: 409 KIALEIPKEIASVVIWRT 426

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123708|ref|XP_002319146.1| predicted protein [Populus trichocarpa] gi|222857522|gb|EEE95069.1| predicted protein [Populus trichocarpa]

 Score =  320 bits (820), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 162/268 (60%), Positives = 193/268 (72%), Gaps = 32/268 (11%)

Query: 68  MYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW---------------------TGI 106
           MY+S G L D+  LFDE+P+RN+VTWNV+ITGLVKW                     TGI
Sbjct: 1   MYLSSGVLGDAMILFDEMPKRNVVTWNVMITGLVKWGKLEFASSLFDEMPEKNVVSWTGI 60

Query: 107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRG 166
           IDGY R N+ +E L+LFRRM  CE  +P+EITILA+LPAI   GE+++C LIHGY EKRG
Sbjct: 61  IDGYIRNNKYSEGLSLFRRMVVCEGIKPTEITILAILPAISNMGELKSCSLIHGYAEKRG 120

Query: 167 FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVE 226
           FNAFDI V+N +ID Y+KCGCI SA K FED SV+RKNLVSWT+IISGFAMHGM KEAVE
Sbjct: 121 FNAFDIRVANSIIDCYSKCGCIASAFKFFEDISVERKNLVSWTSIISGFAMHGMWKEAVE 180

Query: 227 NFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKHYGCLIDIL 275
            FERM+K GLKPNR   +            +EGL+ F KMV E  VLPDIKHYGC++D+L
Sbjct: 181 YFERMEKAGLKPNRVTFLSVLNACSHGGLVDEGLRCFYKMVNEHGVLPDIKHYGCVVDML 240

Query: 276 ERAGRLEQAEEVASGIPSQITNVVVWRT 303
            R GRLE+AE +A  IPS+I NVV+WRT
Sbjct: 241 GRTGRLEEAENMALEIPSEIVNVVIWRT 268

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356506146|ref|XP_003521848.1| PREDICTED: pentatricopeptide repeat-containing protein At1g09220, mitochondrial-like [Glycine max]

 Score =  317 bits (813), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 160/336 (47%), Positives = 218/336 (64%), Gaps = 39/336 (11%)

Query: 1   FLVYKQLQQIYIHSHSPLP-PLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV 59
           F  Y Q      H H+ L  P  D+F+++FL       +Y + GTQLHA+  KVGFQ HV
Sbjct: 105 FFTYTQ------HCHTFLTYPSLDTFSFAFLCHASANPNYTHFGTQLHALVFKVGFQFHV 158

Query: 60  YVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW---------------- 103
           YV T L  MY S G L +++++F E+  RNLV+WNV ITGL+KW                
Sbjct: 159 YVKTGLLQMYSSSGLLVEAAQVFYEMQHRNLVSWNVFITGLIKWGEVELACSVFNQMPAR 218

Query: 104 -----TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLI 158
                T +IDGY+R N+  +AL LFR+M   +  EP+E+T+L + PAI   G ++ CQ +
Sbjct: 219 SVVSWTLVIDGYTRRNQPIKALTLFRKMIEVDGIEPTEVTLLTIFPAIANIGCIKICQSV 278

Query: 159 HGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMH 218
           H Y EKRGFNAFD+ ++N L+D YAKCGCI S S+ F++    R+NLVSWT+ ISGFAM+
Sbjct: 279 HVYVEKRGFNAFDVRITNALLDLYAKCGCIASMSRFFQEIPDQRRNLVSWTSTISGFAMN 338

Query: 219 GMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKH 267
           GMG+EA+E+FE M+K GL+PN    +G           EEG+ FF KMV++  ++PDIKH
Sbjct: 339 GMGREALESFESMEKTGLRPNHVTFLGVLSACSHGGLVEEGINFFVKMVKDWCLVPDIKH 398

Query: 268 YGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           YGC+ID+L RAGRLE+AE+VA  +P ++ N V+WRT
Sbjct: 399 YGCVIDMLGRAGRLEEAEKVALQVPHEVANAVMWRT 434

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356554965|ref|XP_003545811.1| PREDICTED: pentatricopeptide repeat-containing protein At1g09220, mitochondrial-like [Glycine max]

 Score =  317 bits (812), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 157/335 (46%), Positives = 217/335 (64%), Gaps = 37/335 (11%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           F  Y Q   I++       P  D+F+++FL       +Y + GTQLHA+  KVGFQ  VY
Sbjct: 119 FFTYTQHCHIFLTY-----PSLDTFSFAFLCHASANPNYTHFGTQLHALIFKVGFQFQVY 173

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK------------------ 102
           V T L  MY S G L +++++F E+  RNLV+WNV ITGL+K                  
Sbjct: 174 VQTRLLQMYSSSGLLVEAAQVFYEMQHRNLVSWNVFITGLIKLGEVELACSVFNQMPARS 233

Query: 103 ---WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
              WT +IDGY+R N+  +AL LFR+M   +  EP+E+T+L + PAI   G ++ CQ +H
Sbjct: 234 VVSWTLVIDGYTRRNQPIKALTLFRKMIEVDGIEPTEVTLLTIFPAIANIGCIKICQSVH 293

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
           GY EKRGFNAFD+ ++N L+D YAKCGCI S S+ F++    R+NLVSWT+ ISGFAM+G
Sbjct: 294 GYVEKRGFNAFDVRITNALLDLYAKCGCIASVSRFFQEIPDQRRNLVSWTSTISGFAMNG 353

Query: 220 MGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKHY 268
           MG+EA+E+FE M+K GL+PN    +G           EEG+ FF KMV++  ++PDIKHY
Sbjct: 354 MGREALESFESMEKAGLRPNHVTFLGVLSACSHGGLVEEGINFFVKMVKDWCLVPDIKHY 413

Query: 269 GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           GC+ID+L RAGRLE+AE++A  +P ++ N V+WRT
Sbjct: 414 GCVIDMLGRAGRLEEAEKIALQVPHEVANAVMWRT 448

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302144057|emb|CBI23162.3| unnamed protein product [Vitis vinifera]

 Score =  313 bits (801), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 171/335 (51%), Positives = 220/335 (65%), Gaps = 36/335 (10%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           FL+++ L+   +H   P P  FDSF++SFL++ C  L +   G QLHA+  K+GF+ HVY
Sbjct: 71  FLLFRHLR---LHHVYP-PLSFDSFSFSFLLKACANLQHREGGLQLHALTLKLGFEFHVY 126

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW----------------- 103
           V+T L ++Y + G   ++ ++FDE+P RN VTWNV ITGL KW                 
Sbjct: 127 VHTVLLNVYAACGAFLEAKQVFDEMPVRNSVTWNVFITGLAKWGELHLACSLLDEMPRPT 186

Query: 104 ----TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
               T IIDGY+RMN+  +ALALF  M   E  +P+EIT+LA+ PAI   G +  CQLIH
Sbjct: 187 VVSWTTIIDGYTRMNQPKQALALFLTMFLDEGIKPTEITLLAIFPAISNLGALEICQLIH 246

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
            YGEK G NA DI +   L+DTYAKCGCI SAS +F + +   +NLVSWT+IIS FAMHG
Sbjct: 247 TYGEKSGLNASDIRIRTSLLDTYAKCGCIESASGVFGEIAAKGRNLVSWTSIISAFAMHG 306

Query: 220 MGKEAVENFERMQKVGLKPNR-----------SWRIGEEGLKFFDKMVEECEVLPDIKHY 268
           M KEA+ENFERMQK  LKPNR              + EEGLK F KMV EC++ PD+KHY
Sbjct: 307 MAKEALENFERMQKECLKPNRITFLSVLNACSHGGLVEEGLKLFTKMVNECQISPDVKHY 366

Query: 269 GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           GCLID+L RAGRL++AE++A  IP  + NVV+WRT
Sbjct: 367 GCLIDMLGRAGRLDEAEKMALEIPDYVVNVVIWRT 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860607|emb|CAN79717.1| hypothetical protein VITISV_027522 [Vitis vinifera]

 Score =  313 bits (801), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 171/335 (51%), Positives = 220/335 (65%), Gaps = 36/335 (10%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           FL+++ L+   +H   P P  FDSF++SFL++ C  L +   G QLHA+  K+GF+ HVY
Sbjct: 71  FLLFRHLR---LHHVYP-PLSFDSFSFSFLLKACANLQHREGGLQLHALTLKLGFEFHVY 126

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW----------------- 103
           V+T L ++Y + G   ++ ++FDE+P RN VTWNV ITGL KW                 
Sbjct: 127 VHTVLLNVYAACGAFLEAKQVFDEMPVRNSVTWNVFITGLAKWGELHLACSLLDEMPRPT 186

Query: 104 ----TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
               T IIDGY+RMN+  +ALALF  M   E  +P+EIT+LA+ PAI   G +  CQLIH
Sbjct: 187 VVSWTTIIDGYTRMNQPKQALALFLTMFLDEGIKPTEITLLAIFPAISNLGALEICQLIH 246

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
            YGEK G NA DI +   L+DTYAKCGCI SAS +F + +   +NLVSWT+IIS FAMHG
Sbjct: 247 TYGEKSGLNASDIRIRTSLLDTYAKCGCIESASGVFGEIAAKGRNLVSWTSIISAFAMHG 306

Query: 220 MGKEAVENFERMQKVGLKPNR-----------SWRIGEEGLKFFDKMVEECEVLPDIKHY 268
           M KEA+ENFERMQK  LKPNR              + EEGLK F KMV EC++ PD+KHY
Sbjct: 307 MAKEALENFERMQKECLKPNRITFLSVLNACSHGGLVEEGLKLFTKMVNECQISPDVKHY 366

Query: 269 GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           GCLID+L RAGRL++AE++A  IP  + NVV+WRT
Sbjct: 367 GCLIDMLGRAGRLDEAEKMALEIPDYVVNVVIWRT 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444407|ref|XP_002265471.1| PREDICTED: pentatricopeptide repeat-containing protein At1g09220, mitochondrial-like [Vitis vinifera]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 169/335 (50%), Positives = 220/335 (65%), Gaps = 36/335 (10%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           FL+++ L+  +++     P  FDSF++SFL++ C  L +   G QLHA+  K+GF+ HVY
Sbjct: 71  FLLFRHLRLHHVYP----PLSFDSFSFSFLLKACANLQHREGGLQLHALTLKLGFEFHVY 126

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW----------------- 103
           V+T L ++Y + G   ++ ++FDE+P RN VTWNV ITGL KW                 
Sbjct: 127 VHTVLLNVYAACGAFLEAKQVFDEMPVRNSVTWNVFITGLAKWGELHLACSLLDEMPRPT 186

Query: 104 ----TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
               T IIDGY+RMN+  +ALALF  M   E  +P+EIT+LA+ PAI   G +  CQLIH
Sbjct: 187 VVSWTTIIDGYTRMNQPKQALALFLTMFLDEGIKPTEITLLAIFPAISNLGALEICQLIH 246

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
            YGEK G NA DI +   L+DTYAKCGCI SAS +F + +   +NLVSWT+IIS FAMHG
Sbjct: 247 TYGEKSGLNASDIRIRTSLLDTYAKCGCIESASGVFGEIAAKGRNLVSWTSIISAFAMHG 306

Query: 220 MGKEAVENFERMQKVGLKPNR-----------SWRIGEEGLKFFDKMVEECEVLPDIKHY 268
           M KEA+ENFERMQK  LKPNR              + EEGLK F KMV EC++ PD+KHY
Sbjct: 307 MAKEALENFERMQKECLKPNRITFLSVLNACSHGGLVEEGLKLFTKMVNECQISPDVKHY 366

Query: 269 GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           GCLID+L RAGRL++AE++A  IP  + NVV+WRT
Sbjct: 367 GCLIDMLGRAGRLDEAEKMALEIPDYVVNVVIWRT 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334182414|ref|NP_172393.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75116771|sp|Q680Z7.1|PPR24_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g09220, mitochondrial; Flags: Precursor gi|51969004|dbj|BAD43194.1| hypothetical protein [Arabidopsis thaliana] gi|51969582|dbj|BAD43483.1| hypothetical protein [Arabidopsis thaliana] gi|51969876|dbj|BAD43630.1| hypothetical protein [Arabidopsis thaliana] gi|62318861|dbj|BAD93927.1| hypothetical protein [Arabidopsis thaliana] gi|332190294|gb|AEE28415.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 164/338 (48%), Positives = 217/338 (64%), Gaps = 37/338 (10%)

Query: 1   FLVYKQLQQI-YIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFS--KVGFQS 57
           + +Y QLQ++ ++  H+   P FDSFTY FL++      +P+L   +       K+GF+S
Sbjct: 97  YFLYDQLQRLHFLSDHNKSLPPFDSFTYLFLLKASSNPRFPSLLLGIGLHGLTLKLGFES 156

Query: 58  HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGL----------------- 100
           HVYV TAL  MY+  G + D+ K+FDE+PERN VTWNV+ITGL                 
Sbjct: 157 HVYVQTALVGMYLVGGNMIDAHKVFDEMPERNPVTWNVMITGLTNLGDFEKALCFLEKMP 216

Query: 101 ----VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQ 156
               V WT IIDGY+R+++  EA+ LF RM AC+  +P+EITILA+LPA+W  G+++ C 
Sbjct: 217 NRTVVSWTTIIDGYARVDKPKEAILLFSRMVACDAIKPNEITILAILPAVWNLGDLKMCG 276

Query: 157 LIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFA 216
            +H Y  KRGF   DI V+N LID YAKCGCI SA K F +    RKNLVSWTT+IS FA
Sbjct: 277 SVHAYVGKRGFVPCDIRVTNSLIDAYAKCGCIQSAFKFFIEIPNGRKNLVSWTTMISAFA 336

Query: 217 MHGMGKEAVENFERMQKVGLKPNRSWRIG------------EEGLKFFDKMVEECEVLPD 264
           +HGMGKEAV  F+ M+++GLKPNR   I             EE L+FF+ MV E ++ PD
Sbjct: 337 IHGMGKEAVSMFKDMERLGLKPNRVTMISVLNACSHGGLAEEEFLEFFNTMVNEYKITPD 396

Query: 265 IKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWR 302
           +KHYGCL+D+L R GRLE+AE++A  IP +    VVWR
Sbjct: 397 VKHYGCLVDMLRRKGRLEEAEKIALEIPIE-EKAVVWR 433

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568986|ref|XP_002525463.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223535276|gb|EEF36953.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 157/268 (58%), Positives = 191/268 (71%), Gaps = 32/268 (11%)

Query: 68  MYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW---------------------TGI 106
           MY++ GFL ++   FDE+PE+N VTWNV+ITGLVKW                     TGI
Sbjct: 1   MYLASGFLGNALLAFDEMPEKNSVTWNVMITGLVKWGKLEFARSFFDDMPEKNVVSWTGI 60

Query: 107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRG 166
           IDGY RMNR  E LALFRRM + E   PSEITILA+LPAI   GE++NC LIH   EKRG
Sbjct: 61  IDGYVRMNRITEGLALFRRMVSFEGIAPSEITILAILPAISGIGELQNCGLIHCLVEKRG 120

Query: 167 FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVE 226
           FN+ DI V+N +IDTYAKCGCI SAS+ FE+ SV+RKNLVSWT+IISGFAMHGMG+EAV+
Sbjct: 121 FNSSDIRVTNSIIDTYAKCGCIVSASRFFEEISVERKNLVSWTSIISGFAMHGMGQEAVK 180

Query: 227 NFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDIKHYGCLIDIL 275
            FE M++ GLKPNR   +             EG +FF+KMV +  +LPDIKHYGCL+D+L
Sbjct: 181 RFENMERTGLKPNRVTFLSVLNACSHGGLVAEGHEFFEKMVNQYSILPDIKHYGCLVDML 240

Query: 276 ERAGRLEQAEEVASGIPSQITNVVVWRT 303
            R GRLE+AE++A GIPS+I N V+WRT
Sbjct: 241 GRTGRLEEAEKLALGIPSEIVNAVIWRT 268

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772248|emb|CAN78346.1| hypothetical protein VITISV_033453 [Vitis vinifera]

 Score =  310 bits (794), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 170/335 (50%), Positives = 221/335 (65%), Gaps = 36/335 (10%)

Query: 1   FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY 60
           FL+++ L+   +H   P P  FDSF++SFL++ C  L +   G QLHA+  K+GF+ HVY
Sbjct: 71  FLLFRHLR---LHHVYP-PLSFDSFSFSFLLKACANLQHREGGLQLHALTLKLGFEFHVY 126

Query: 61  VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW----------------- 103
           V+T L ++Y + G   ++ ++FDE+P RN VTWNV ITGL KW                 
Sbjct: 127 VHTVLLNVYAACGAFLEAKQVFDEMPVRNSVTWNVFITGLAKWGELHLARSLLDEMPMPT 186

Query: 104 ----TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH 159
               T IIDGY+RMN+  +ALALF  M   E  +P+EIT+LA+ PAI   G +  CQLIH
Sbjct: 187 VVSWTTIIDGYTRMNQPKQALALFLTMFLDEGIKPTEITLLAIFPAISNLGALEICQLIH 246

Query: 160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHG 219
            YGEK G NA DI +   L+DTYAKCGCI SAS++F +     +NLVSWT+IIS FAMHG
Sbjct: 247 TYGEKSGLNASDIRIRTSLLDTYAKCGCIESASRVFGEIDAKSRNLVSWTSIISAFAMHG 306

Query: 220 MGKEAVENFERMQKVGLKPNR-----------SWRIGEEGLKFFDKMVEECEVLPDIKHY 268
           M KEA+ENFERMQK  LKPNR              + EEGLKFF KMV + ++ PD+KHY
Sbjct: 307 MAKEALENFERMQKECLKPNRITFLSVLNACSHGGLVEEGLKFFTKMVNKYQISPDVKHY 366

Query: 269 GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           GCLID+L RAGRL++AE++A  IP+ + NVV+WRT
Sbjct: 367 GCLIDMLGRAGRLDEAEKMALEIPNYVVNVVIWRT 401

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	352
TAIR|locus:4010713895	595	AT4G21065 "AT4G21065" [Arabido	0.755	0.447	0.372	3.1e-44
TAIR|locus:2010012	474	AT1G13410 "AT1G13410" [Arabido	0.713	0.529	0.341	1.8e-39
TAIR|locus:2085874	472	MEF20 "AT3G18970" [Arabidopsis	0.735	0.548	0.343	2.1e-38
TAIR|locus:2056740	603	OTP85 "ORGANELLE TRANSCRIPT PR	0.752	0.439	0.340	4.8e-38
TAIR|locus:2027589	611	PGN "AT1G56570" [Arabidopsis t	0.718	0.414	0.339	8.1e-37
TAIR|locus:2151694	550	AT5G37570 "AT5G37570" [Arabido	0.551	0.352	0.317	9.9e-37
TAIR|locus:2095487	504	AT3G28660 "AT3G28660" [Arabido	0.721	0.503	0.310	1.3e-36
TAIR|locus:2124137	871	DOT4 "DEFECTIVELY ORGANIZED TR	0.752	0.304	0.313	1.4e-36
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.769	0.507	0.341	2.1e-36
TAIR|locus:2049736	500	AT2G37320 "AT2G37320" [Arabido	0.829	0.584	0.306	4.4e-36

TAIR|locus:4010713895 AT4G21065 "AT4G21065" [Arabidopsis thaliana (taxid:3702)]

 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 109/293 (37%), Positives = 172/293 (58%)

Query:    23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
             D+ TY FLI+   T++   LG  +H+V  + GF S +YV  +L  +Y + G +  + K+F
Sbjct:   120 DTHTYPFLIKAVTTMADVRLGETIHSVVIRSGFGSLIYVQNSLLHLYANCGDVASAYKVF 179

Query:    83 DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
             D++PE++LV WN           +I+G++   +  EALAL+  M + +  +P   TI+++
Sbjct:   180 DKMPEKDLVAWN----------SVINGFAENGKPEEALALYTEMNS-KGIKPDGFTIVSL 228

Query:   143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
             L A  K G +   + +H Y  K G    ++H SN L+D YA+CG +  A  LF D  VD 
Sbjct:   229 LSACAKIGALTLGKRVHVYMIKVGLTR-NLHSSNVLLDLYARCGRVEEAKTLF-DEMVD- 285

Query:   203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKV-GLKPNRSWRIG-----------EEGLK 250
             KN VSWT++I G A++G GKEA+E F+ M+   GL P     +G           +EG +
Sbjct:   286 KNSVSWTSLIVGLAVNGFGKEAIELFKYMESTEGLLPCEITFVGILYACSHCGMVKEGFE 345

Query:   251 FFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
             +F +M EE ++ P I+H+GC++D+L RAG++++A E    +P Q  NVV+WRT
Sbjct:   346 YFRRMREEYKIEPRIEHFGCMVDLLARAGQVKKAYEYIKSMPMQ-PNVVIWRT 397

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2010012 AT1G13410 "AT1G13410" [Arabidopsis thaliana (taxid:3702)]

 Score = 421 (153.3 bits), Expect = 1.8e-39, P = 1.8e-39
 Identities = 95/278 (34%), Positives = 156/278 (56%)

Query:    39 YPNLGTQLHA--VFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVI 96
             Y  +G  L A  +F ++  +  +  NT L + Y ++G ++   ++FD++PERN+ +WN  
Sbjct:   100 YIEMGNMLEARSLFDQMPCRDVMSWNTVL-EGYANIGDMEACERVFDDMPERNVFSWN-- 156

Query:    97 ITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQ 156
                     G+I GY++  R +E L  F+RM       P++ T+  VL A  K G     +
Sbjct:   157 --------GLIKGYAQNGRVSEVLGSFKRMVDEGSVVPNDATMTLVLSACAKLGAFDFGK 208

Query:   157 LIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFA 216
              +H YGE  G+N  D++V N LID Y KCG I  A ++F+   + R++L+SW T+I+G A
Sbjct:   209 WVHKYGETLGYNKVDVNVKNALIDMYGKCGAIEIAMEVFK--GIKRRDLISWNTMINGLA 266

Query:   217 MHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKFFDKMVEECEVLPDI 265
              HG G EA+  F  M+  G+ P++   +G           E+GL +F+ M  +  ++P+I
Sbjct:   267 AHGHGTEALNLFHEMKNSGISPDKVTFVGVLCACKHMGLVEDGLAYFNSMFTDFSIMPEI 326

Query:   266 KHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
             +H GC++D+L RAG L QA E  + +P +  + V+W T
Sbjct:   327 EHCGCVVDLLSRAGFLTQAVEFINKMPVK-ADAVIWAT 363

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2085874 MEF20 "AT3G18970" [Arabidopsis thaliana (taxid:3702)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 98/285 (34%), Positives = 156/285 (54%)

Query:    26 TYSFLIRTCV---TLSYPNLGTQLHAVFSKVGF--QSHVYVNTALGDMYVSLGFLKDSSK 80
             T+ F++  C    + S   +G  +H +  K+GF  +S + + T L   Y   G L+ + K
Sbjct:   110 TFVFVLGACARSASSSALRVGRIVHGMVKKLGFLYESEL-IGTTLLHFYAKNGDLRYARK 168

Query:    81 LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC-EYTEPSEITI 139
             +FDE+PER  VTWN +I G              + + +A+ LFRR + C     P++ T+
Sbjct:   169 VFDEMPERTSVTWNAMIGGYCSHKD-----KGNHNARKAMVLFRRFSCCGSGVRPTDTTM 223

Query:   140 LAVLPAIWKNGEVRNCQLIHGYGEKRGFNA-FDIHVSNCLIDTYAKCGCIFSASKLFEDT 198
             + VL AI + G +    L+HGY EK GF    D+ +   L+D Y+KCGC+ +A  +FE  
Sbjct:   224 VCVLSAISQTGLLEIGSLVHGYIEKLGFTPEVDVFIGTALVDMYSKCGCLNNAFSVFELM 283

Query:   199 SVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR--------SWR-IG--EE 247
              V  KN+ +WT++ +G A++G G E      RM + G+KPN         ++R IG  EE
Sbjct:   284 KV--KNVFTWTSMATGLALNGRGNETPNLLNRMAESGIKPNEITFTSLLSAYRHIGLVEE 341

Query:   248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP 292
             G++ F  M     V P I+HYGC++D+L +AGR+++A +    +P
Sbjct:   342 GIELFKSMKTRFGVTPVIEHYGCIVDLLGKAGRIQEAYQFILAMP 386

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2056740 OTP85 "ORGANELLE TRANSCRIPT PROCESSING 85" [Arabidopsis thaliana (taxid:3702)]

 Score = 409 (149.0 bits), Expect = 4.8e-38, P = 4.8e-38
 Identities = 99/291 (34%), Positives = 158/291 (54%)

Query:    23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
             D++T+  L++ C        G QLH +  K+G   +VYV   L +MY     +  +  +F
Sbjct:   128 DNYTFPSLLKACAVAKALEEGRQLHCLSMKLGLDDNVYVCPTLINMYTECEDVDSARCVF 187

Query:    83 DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
             D + E  +V +N +ITG          Y+R NR NEAL+LFR M   +Y +P+EIT+L+V
Sbjct:   188 DRIVEPCVVCYNAMITG----------YARRNRPNEALSLFREMQG-KYLKPNEITLLSV 236

Query:   143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
             L +    G +   + IH Y +K  F  + + V+  LID +AKCG +  A  +FE   +  
Sbjct:   237 LSSCALLGSLDLGKWIHKYAKKHSFCKY-VKVNTALIDMFAKCGSLDDAVSIFE--KMRY 293

Query:   203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKF 251
             K+  +W+ +I  +A HG  ++++  FERM+   ++P+    +G           EEG K+
Sbjct:   294 KDTQAWSAMIVAYANHGKAEKSMLMFERMRSENVQPDEITFLGLLNACSHTGRVEEGRKY 353

Query:   252 FDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWR 302
             F +MV +  ++P IKHYG ++D+L RAG LE A E    +P   T ++ WR
Sbjct:   354 FSQMVSKFGIVPSIKHYGSMVDLLSRAGNLEDAYEFIDKLPISPTPML-WR 403

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2027589 PGN "AT1G56570" [Arabidopsis thaliana (taxid:3702)]

 Score = 399 (145.5 bits), Expect = 8.1e-37, P = 8.1e-37
 Identities = 95/280 (33%), Positives = 161/280 (57%)

Query:    25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDE 84
             +  +  +R   ++     G Q+HA   K GFQS++ V  ++ D+Y   G+L ++   F E
Sbjct:   214 YCITIAVRASASIDSVTTGKQIHASVIKRGFQSNLPVMNSILDLYCRCGYLSEAKHYFHE 273

Query:    85 LPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLP 144
             + +++L+TWN +I+ L +           + S+EAL +F+R  +  +  P+  T  +++ 
Sbjct:   274 MEDKDLITWNTLISELER-----------SDSSEALLMFQRFESQGFV-PNCYTFTSLVA 321

Query:   145 AIWKNGEVRNC-QLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK 203
             A   N    NC Q +HG   +RGFN  ++ ++N LID YAKCG I  + ++F +  VDR+
Sbjct:   322 AC-ANIAALNCGQQLHGRIFRRGFNK-NVELANALIDMYAKCGNIPDSQRVFGEI-VDRR 378

Query:   204 NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR--------SWR---IGEEGLKFF 252
             NLVSWT+++ G+  HG G EAVE F++M   G++P+R        + R   + E+GLK+F
Sbjct:   379 NLVSWTSMMIGYGSHGYGAEAVELFDKMVSSGIRPDRIVFMAVLSACRHAGLVEKGLKYF 438

Query:   253 DKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP 292
             + M  E  + PD   Y C++D+L RAG++ +A E+   +P
Sbjct:   439 NVMESEYGINPDRDIYNCVVDLLGRAGKIGEAYELVERMP 478

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009651 "response to salt stress" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0009749 "response to glucose stimulus" evidence=IMP

GO:0050832 "defense response to fungus" evidence=IMP

TAIR|locus:2151694 AT5G37570 "AT5G37570" [Arabidopsis thaliana (taxid:3702)]

 Score = 288 (106.4 bits), Expect = 9.9e-37, Sum P(2) = 9.9e-37
 Identities = 67/211 (31%), Positives = 117/211 (55%)

Query:   103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYG 162
             W+ +I GY++  + NEA  +F  M A +  +P E  ++ ++ A  + G    C+ +  Y 
Sbjct:   272 WSALILGYAQNGQPNEAFKVFSEMCA-KNVKPDEFIMVGLMSACSQMGCFELCEKVDSYL 330

Query:   163 EKRGFNAFDIH-VSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMG 221
              +R  N F  H V   LID  AKCG +  A+KLFE+  + +++LVS+ +++ G A+HG G
Sbjct:   331 HQR-MNKFSSHYVVPALIDMNAKCGHMDRAAKLFEE--MPQRDLVSYCSMMEGMAIHGCG 387

Query:   222 KEAVENFERMQKVGLKPNR-----------SWRIGEEGLKFFDKMVEECEVLPDIKHYGC 270
              EA+  FE+M   G+ P+              R+ EEGL++F+ M ++  +L    HY C
Sbjct:   388 SEAIRLFEKMVDEGIVPDEVAFTVILKVCGQSRLVEEGLRYFELMRKKYSILASPDHYSC 447

Query:   271 LIDILERAGRLEQAEEVASGIPSQITNVVVW 301
             ++++L R G+L++A E+   +P +  +   W
Sbjct:   448 IVNLLSRTGKLKEAYELIKSMPFE-AHASAW 477

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2095487 AT3G28660 "AT3G28660" [Arabidopsis thaliana (taxid:3702)]

 Score = 358 (131.1 bits), Expect = 1.3e-36, Sum P(2) = 1.3e-36
 Identities = 87/280 (31%), Positives = 148/280 (52%)

Query:    26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVG-FQSHVYVNTALGDMYVSLGFLKDSSKLFDE 84
             T+ FLI  C+   + ++G Q+H    K G F S  +V T +  +YV    L D+ K+FDE
Sbjct:   118 TFHFLIVACLKACFFSVGKQIHCWVVKNGVFLSDGHVQTGVLRIYVEDKLLFDARKVFDE 177

Query:    85 LPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLP 144
             +P+ ++V W+V++          +GY R    +E L +F+ M      EP E ++   L 
Sbjct:   178 IPQPDVVKWDVLM----------NGYVRCGLGSEGLEVFKEMLV-RGIEPDEFSVTTALT 226

Query:   145 AIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN 204
             A  + G +   + IH + +K+ +   D+ V   L+D YAKCGCI +A ++FE   + R+N
Sbjct:   227 ACAQVGALAQGKWIHEFVKKKRWIESDVFVGTALVDMYAKCGCIETAVEVFE--KLTRRN 284

Query:   205 LVSWTTIISGFAMHGMGKEAVENFERMQKV-GLKPNRSWRIG-----------EEGLKFF 252
             + SW  +I G+A +G  K+A    +R+++  G+KP+    +G           EEG    
Sbjct:   285 VFSWAALIGGYAAYGYAKKATTCLDRIEREDGIKPDSVVLLGVLAACAHGGFLEEGRTML 344

Query:   253 DKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP 292
             + M     + P  +HY C++D++ RAGRL+ A ++   +P
Sbjct:   345 ENMEARYGITPKHEHYSCIVDLMCRAGRLDDALDLIEKMP 384

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2124137 DOT4 "DEFECTIVELY ORGANIZED TRIBUTARIES 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 403 (146.9 bits), Expect = 1.4e-36, P = 1.4e-36
 Identities = 91/290 (31%), Positives = 154/290 (53%)

Query:    23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
             D +T + ++  C      + G ++H    +      ++V+ AL DMY   G ++++  +F
Sbjct:   396 DVYTVTAVLNCCARYRLLDEGKRVHEWIKENDLGFDIFVSNALMDMYAKCGSMQEAELVF 455

Query:    83 DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
              E+  +++++WN II           GYS+   +NEAL+LF  +   +   P E T+  V
Sbjct:   456 SEMRVKDIISWNTII----------GGYSKNCYANEALSLFNLLLEEKRFSPDERTVACV 505

Query:   143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
             LPA          + IHGY  + G+ + D HV+N L+D YAKCG +  A  LF+D  +  
Sbjct:   506 LPACASLSAFDKGREIHGYIMRNGYFS-DRHVANSLVDMYAKCGALLLAHMLFDD--IAS 562

Query:   203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG-----------EEGLKF 251
             K+LVSWT +I+G+ MHG GKEA+  F +M++ G++ +    +            +EG +F
Sbjct:   563 KDLVSWTVMIAGYGMHGFGKEAIALFNQMRQAGIEADEISFVSLLYACSHSGLVDEGWRF 622

Query:   252 FDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVW 301
             F+ M  EC++ P ++HY C++D+L R G L +A      +P    +  +W
Sbjct:   623 FNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIENMPIP-PDATIW 671

GO:0009507 "chloroplast" evidence=ISM

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010588 "cotyledon vascular tissue pattern formation" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2054789 MEF21 "mitochondrial editing factor 21" [Arabidopsis thaliana (taxid:3702)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 103/302 (34%), Positives = 165/302 (54%)

Query:    12 IHSH-SPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYV 70
             +H H     P F   T + LI   + + + +L    H VF ++  +  +  N+ L   Y 
Sbjct:   131 VHGHLCKFGPRFHVVTENALID--MYMKFDDL-VDAHKVFDEMYERDVISWNSLLSG-YA 186

Query:    71 SLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE 130
              LG +K +  LF  + ++ +V+W  +I+G   +TGI   Y       EA+  FR M    
Sbjct:   187 RLGQMKKAKGLFHLMLDKTIVSWTAMISG---YTGI-GCYV------EAMDFFREMQLAG 236

Query:   131 YTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS 190
               EP EI++++VLP+  + G +   + IH Y E+RGF      V N LI+ Y+KCG I  
Sbjct:   237 I-EPDEISLISVLPSCAQLGSLELGKWIHLYAERRGFLK-QTGVCNALIEMYSKCGVISQ 294

Query:   191 ASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIG----- 245
             A +LF    ++ K+++SW+T+ISG+A HG    A+E F  MQ+  +KPN    +G     
Sbjct:   295 AIQLFGQ--MEGKDVISWSTMISGYAYHGNAHGAIETFNEMQRAKVKPNGITFLGLLSAC 352

Query:   246 ------EEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVV 299
                   +EGL++FD M ++ ++ P I+HYGCLID+L RAG+LE+A E+   +P +  +  
Sbjct:   353 SHVGMWQEGLRYFDMMRQDYQIEPKIEHYGCLIDVLARAGKLERAVEITKTMPMK-PDSK 411

Query:   300 VW 301
             +W
Sbjct:   412 IW 413

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2049736 AT2G37320 "AT2G37320" [Arabidopsis thaliana (taxid:3702)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 98/320 (30%), Positives = 171/320 (53%)

Query:    22 FDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKL 81
             FD++  S  +R+C        G+  H +  K GF S VY+ ++L  +Y   G ++++ K+
Sbjct:   118 FDAYGLSSAVRSCGLNRDFRTGSGFHCLALKGGFISDVYLGSSLVVLYRDSGEVENAYKV 177

Query:    82 FDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILA 141
             F+E+PERN+V+W          T +I G+++  R +  L L+ +M     ++P++ T  A
Sbjct:   178 FEEMPERNVVSW----------TAMISGFAQEWRVDICLKLYSKMRKST-SDPNDYTFTA 226

Query:   142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD 201
             +L A   +G +   + +H      G  ++ +H+SN LI  Y KCG +  A ++F+  S  
Sbjct:   227 LLSACTGSGALGQGRSVHCQTLHMGLKSY-LHISNSLISMYCKCGDLKDAFRIFDQFS-- 283

Query:   202 RKNLVSWTTIISGFAMHGMGKEAVENFERMQ-KVGLKPNRSWRIG-----------EEGL 249
              K++VSW ++I+G+A HG+  +A+E FE M  K G KP+    +G           +EG 
Sbjct:   284 NKDVVSWNSMIAGYAQHGLAMQAIELFELMMPKSGTKPDAITYLGVLSSCRHAGLVKEGR 343

Query:   250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL 309
             KFF+ M E   + P++ HY CL+D+L R G L++A E+   +P +  N V+W +      
Sbjct:   344 KFFNLMAEH-GLKPELNHYSCLVDLLGRFGLLQEALELIENMPMK-PNSVIWGSLLFSCR 401

Query:   310 INSYFFSPITLNSQRLFFFP 329
             ++   ++ I    +RL   P
Sbjct:   402 VHGDVWTGIRAAEERLMLEP 421

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	352
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-43
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-35
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-33
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-28
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-27
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-22
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-18
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-11
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-07
pfam01535	31	pfam01535, PPR, PPR repeat	8e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	4e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.003

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

 Score =  158 bits (402), Expect = 4e-43
 Identities = 91/303 (30%), Positives = 155/303 (51%), Gaps = 39/303 (12%)

Query: 3   VYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVN 62
            Y  ++Q    + SP     D  T + ++  C  L   ++G +LH +  + G  S+V V 
Sbjct: 376 TYALMEQ---DNVSP-----DEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVA 427

Query: 63  TALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMN-RSNEALA 121
            AL +MY     +  + ++F  +PE+++++W  II GL           R+N R  EAL 
Sbjct: 428 NALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGL-----------RLNNRCFEALI 476

Query: 122 LFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT 181
            FR+M      +P+ +T++A L A  + G +   + IH +  + G   FD  + N L+D 
Sbjct: 477 FFRQMLL--TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI-GFDGFLPNALLDL 533

Query: 182 YAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN-- 239
           Y +CG +  A   F   +   K++VSW  +++G+  HG G  AVE F RM + G+ P+  
Sbjct: 534 YVRCGRMNYAWNQF---NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEV 590

Query: 240 ----------RSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVAS 289
                     RS  +  +GL++F  M E+  + P++KHY C++D+L RAG+L +A    +
Sbjct: 591 TFISLLCACSRSGMV-TQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFIN 649

Query: 290 GIP 292
            +P
Sbjct: 650 KMP 652

Length = 857

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

 Score =  134 bits (340), Expect = 5e-35
 Identities = 85/275 (30%), Positives = 130/275 (47%), Gaps = 35/275 (12%)

Query: 26  TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDEL 85
           T+  ++R    L     G QLH    K G     +V+ AL DMY   G ++D+  +FD +
Sbjct: 226 TFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGM 285

Query: 86  PERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM-----AACEYTEPSEITIL 140
           PE+  V WN ++ G          Y+    S EAL L+  M     +  ++T    I I 
Sbjct: 286 PEKTTVAWNSMLAG----------YALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIF 335

Query: 141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSV 200
           + L        + + +  H    + GF   DI  +  L+D Y+K G +  A  +F+   +
Sbjct: 336 SRL------ALLEHAKQAHAGLIRTGF-PLDIVANTALVDLYSKWGRMEDARNVFD--RM 386

Query: 201 DRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN-----------RSWRIGEEGL 249
            RKNL+SW  +I+G+  HG G +AVE FERM   G+ PN           R   + E+G 
Sbjct: 387 PRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGW 446

Query: 250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQA 284
           + F  M E   + P   HY C+I++L R G L++A
Sbjct: 447 EIFQSMSENHRIKPRAMHYACMIELLGREGLLDEA 481

Length = 697

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

 Score =  129 bits (327), Expect = 4e-33
 Identities = 89/316 (28%), Positives = 146/316 (46%), Gaps = 33/316 (10%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D +T+  ++RTC  +     G ++HA   + GF+  V V  AL  MYV  G +  +  +F
Sbjct: 186 DVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF 245

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
           D +P R+ ++WN +I+          GY       E L LF  M      +P  +TI +V
Sbjct: 246 DRMPRRDCISWNAMIS----------GYFENGECLEGLELFFTMRELS-VDPDLMTITSV 294

Query: 143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
           + A    G+ R  + +HGY  K GF A D+ V N LI  Y   G    A K+F  + ++ 
Sbjct: 295 ISACELLGDERLGREMHGYVVKTGF-AVDVSVCNSLIQMYLSLGSWGEAEKVF--SRMET 351

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR----SWRIGEEGLKFFDKMVEE 258
           K+ VSWT +ISG+  +G+  +A+E +  M++  + P+     S       L   D  V+ 
Sbjct: 352 KDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKL 411

Query: 259 CEVLPDIKHY------GCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINS 312
            E+               LI++  +   +++A EV   IP +  +V+ W +    L +N+
Sbjct: 412 HELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK--DVISWTSIIAGLRLNN 469

Query: 313 YFFSPITLNSQRLFFF 328
             F       + L FF
Sbjct: 470 RCF-------EALIFF 478

Length = 857

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

 Score =  114 bits (288), Expect = 4e-28
 Identities = 69/217 (31%), Positives = 114/217 (52%), Gaps = 15/217 (6%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D  T + +I  C  L    LG ++H    K GF   V V  +L  MY+SLG   ++ K+F
Sbjct: 287 DLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVF 346

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
             +  ++ V+W  +I+G  K  G+ D         +AL  +  M   +   P EITI +V
Sbjct: 347 SRMETKDAVSWTAMISGYEK-NGLPD---------KALETYALMEQ-DNVSPDEITIASV 395

Query: 143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
           L A    G++     +H   E++G  ++ + V+N LI+ Y+KC CI  A ++F   ++  
Sbjct: 396 LSACACLGDLDVGVKLHELAERKGLISYVV-VANALIEMYSKCKCIDKALEVFH--NIPE 452

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN 239
           K+++SWT+II+G  ++    EA+  F +M  + LKPN
Sbjct: 453 KDVISWTSIIAGLRLNNRCFEALIFFRQM-LLTLKPN 488

Length = 857

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

 Score =  113 bits (284), Expect = 2e-27
 Identities = 83/299 (27%), Positives = 130/299 (43%), Gaps = 46/299 (15%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
            + TY  L+  C+ L        ++      GF+   Y+   +  M+V  G L D+ +LF
Sbjct: 122 PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLF 181

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
           DE+PERNL +W  II GLV                EA ALFR M   + ++    T + +
Sbjct: 182 DEMPERNLASWGTIIGGLVD----------AGNYREAFALFREMWE-DGSDAEPRTFVVM 230

Query: 143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR 202
           L A    G  R  Q +H    K G    D  VS  LID Y+KCG I  A  +F+   +  
Sbjct: 231 LRASAGLGSARAGQQLHCCVLKTGVVG-DTFVSCALIDMYSKCGDIEDARCVFD--GMPE 287

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKF-FDKMVEECEV 261
           K  V+W ++++G+A+HG  +EA+  +  M+  G+  +          +F F  M+     
Sbjct: 288 KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSID----------QFTFSIMIRIFSR 337

Query: 262 LPDIKHYG-------------------CLIDILERAGRLEQAEEVASGIPSQITNVVVW 301
           L  ++H                      L+D+  + GR+E A  V   +P    N++ W
Sbjct: 338 LALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP--RKNLISW 394

Length = 697

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

 Score = 99.2 bits (247), Expect = 1e-22
 Identities = 75/300 (25%), Positives = 129/300 (43%), Gaps = 44/300 (14%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGD----MYVSLGFLKDS 78
           D   Y  L R C        G+++ +        SH  +   LG+    M+V  G L  +
Sbjct: 85  DEDAYVALFRLCEWKRAVEEGSRVCSRALS----SHPSLGVRLGNAMLSMFVRFGELVHA 140

Query: 79  SKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE-----YTE 133
             +F ++PER+L +WNV          ++ GY++    +EAL L+ RM         YT 
Sbjct: 141 WYVFGKMPERDLFSWNV----------LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTF 190

Query: 134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASK 193
           P  +     +P + +  EV    +  G+         D+ V N LI  Y KCG + SA  
Sbjct: 191 PCVLRTCGGIPDLARGREVHAHVVRFGFEL-------DVDVVNALITMYVKCGDVVSARL 243

Query: 194 LFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN---------RSWRI 244
           +F+   + R++ +SW  +ISG+  +G   E +E F  M+++ + P+             +
Sbjct: 244 VFD--RMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELL 301

Query: 245 GEEGL-KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRT 303
           G+E L +     V +     D+     LI +    G   +AE+V S + ++  + V W  
Sbjct: 302 GDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK--DAVSWTA 359

Length = 857

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

 Score = 86.5 bits (214), Expect = 1e-18
 Identities = 44/123 (35%), Positives = 64/123 (52%), Gaps = 11/123 (8%)

Query: 23  DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF 82
           D FT+S +IR    L+      Q HA   + GF   +  NTAL D+Y   G ++D+  +F
Sbjct: 324 DQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVF 383

Query: 83  DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAV 142
           D +P +NL++WN +I           GY    R  +A+ +F RM A E   P+ +T LAV
Sbjct: 384 DRMPRKNLISWNALIA----------GYGNHGRGTKAVEMFERMIA-EGVAPNHVTFLAV 432

Query: 143 LPA 145
           L A
Sbjct: 433 LSA 435

Length = 697

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

 Score = 65.3 bits (159), Expect = 1e-11
 Identities = 53/199 (26%), Positives = 88/199 (44%), Gaps = 17/199 (8%)

Query: 114 NRSNEALALFRRM-AACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI 172
            R  EAL LF  + A C +T P+  T  A++ A      +R  + ++ + E  GF   D 
Sbjct: 101 GRHREALELFEILEAGCPFTLPAS-TYDALVEACIALKSIRCVKAVYWHVESSGFEP-DQ 158

Query: 173 HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERM- 231
           ++ N ++  + KCG +  A +LF++  +  +NL SW TII G    G  +EA   F  M 
Sbjct: 159 YMMNRVLLMHVKCGMLIDARRLFDE--MPERNLASWGTIIGGLVDAGNYREAFALFREMW 216

Query: 232 QKVGLKPNRSWRI-----GEEGLKFFDKMVEECEV---LPDIKHYGC-LIDILERAGRLE 282
           +       R++ +        G     + +  C +   +       C LID+  + G +E
Sbjct: 217 EDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIE 276

Query: 283 QAEEVASGIPSQITNVVVW 301
            A  V  G+P +    V W
Sbjct: 277 DARCVFDGMPEK--TTVAW 293

Length = 697

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

 Score = 46.2 bits (111), Expect = 3e-07
 Identities = 14/37 (37%), Positives = 25/37 (67%)

Query: 203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN 239
            ++V++ T+I G+   G  +EA++ F  M+K G+KPN
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPN 37

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

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

 Score = 39.0 bits (92), Expect = 8e-05
 Identities = 11/31 (35%), Positives = 22/31 (70%)

Query: 206 VSWTTIISGFAMHGMGKEAVENFERMQKVGL 236
           V++ ++ISG+   G  +EA+E F+ M++ G+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 12/34 (35%), Positives = 23/34 (67%)

Query: 206 VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN 239
           V++ T+I G    G  +EA+E F+ M++ G++P+
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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

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

 Score = 34.7 bits (81), Expect = 0.003
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 10/38 (26%)

Query: 89  NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM 126
           ++VT+N +I          DGY +  +  EAL LF  M
Sbjct: 2   DVVTYNTLI----------DGYCKKGKVEEALKLFNEM 29

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	352
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	99.86
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.84
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.83
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.82
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.73
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.71
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.66
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.63
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.62
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.62
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.55
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.54
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.54
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.54
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.53
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.52
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.5
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.45
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.45
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.44
PF13041	50	PPR_2: PPR repeat family	99.44
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.43
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.42
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.42
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.4
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.39
PRK14574	822	hmsH outer membrane protein; Provisional	99.39
PF13041	50	PPR_2: PPR repeat family	99.37
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.37
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.35
KOG1126	638	consensus DNA-binding cell division cycle control	99.35
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.33
PRK14574	822	hmsH outer membrane protein; Provisional	99.32
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.29
KOG2076	895	consensus RNA polymerase III transcription factor	99.27
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.27
KOG1129	478	consensus TPR repeat-containing protein [General f	99.25
KOG1126	638	consensus DNA-binding cell division cycle control	99.24
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.23
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.23
PRK12370	553	invasion protein regulator; Provisional	99.19
PRK12370	553	invasion protein regulator; Provisional	99.13
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.12
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.12
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.11
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.08
KOG2076	895	consensus RNA polymerase III transcription factor	99.07
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.06
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.05
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.98
PF12854	34	PPR_1: PPR repeat	98.98
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.97
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.97
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.96
KOG2003	840	consensus TPR repeat-containing protein [General f	98.95
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.95
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.94
KOG2003	840	consensus TPR repeat-containing protein [General f	98.93
PRK11189	296	lipoprotein NlpI; Provisional	98.91
PRK11189	296	lipoprotein NlpI; Provisional	98.9
PF12854	34	PPR_1: PPR repeat	98.89
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.85
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.84
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.84
KOG1129	478	consensus TPR repeat-containing protein [General f	98.83
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.83
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.77
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.76
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.72
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.7
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.7
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.61
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.6
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.57
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.56
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.56
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.55
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.49
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.48
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.48
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.46
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.45
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.45
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.44
PLN02789	320	farnesyltranstransferase	98.43
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.42
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.41
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.39
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.39
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.36
PLN02789	320	farnesyltranstransferase	98.36
KOG1125	579	consensus TPR repeat-containing protein [General f	98.35
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.33
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.32
PRK15359	144	type III secretion system chaperone protein SscB;	98.32
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.31
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.3
KOG1125	579	consensus TPR repeat-containing protein [General f	98.3
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.27
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.27
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.27
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.25
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.24
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.22
PRK15359	144	type III secretion system chaperone protein SscB;	98.2
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.17
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.15
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.15
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.14
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.13
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.12
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.1
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.1
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.07
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.06
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.03
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.03
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.02
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.01
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.01
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.99
PRK04841	903	transcriptional regulator MalT; Provisional	97.97
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.9
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.9
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.89
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.86
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.85
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.82
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.81
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.8
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.8
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.8
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.77
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.77
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.76
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.76
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.76
PRK04841	903	transcriptional regulator MalT; Provisional	97.76
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.76
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	97.76
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.74
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.72
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.72
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.72
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.71
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.69
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.69
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.67
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.63
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.62
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	97.62
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.57
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.55
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.55
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.52
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	97.44
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.43
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.41
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.41
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.4
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.38
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.37
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.37
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.35
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.31
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.26
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.24
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.22
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.21
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.17
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.16
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	97.14
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.1
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.1
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.09
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.07
KOG0553	304	consensus TPR repeat-containing protein [General f	97.0
KOG0553	304	consensus TPR repeat-containing protein [General f	96.99
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.96
PF12688	120	TPR_5: Tetratrico peptide repeat	96.96
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.89
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.89
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.85
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.83
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.78
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.77
PRK10803	263	tol-pal system protein YbgF; Provisional	96.73
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.69
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.68
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.68
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.66
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.64
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.6
PRK10803	263	tol-pal system protein YbgF; Provisional	96.53
PF13371	73	TPR_9: Tetratricopeptide repeat	96.51
PF12688	120	TPR_5: Tetratrico peptide repeat	96.49
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.47
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.42
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.38
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.34
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.25
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.05
PF13371	73	TPR_9: Tetratricopeptide repeat	96.05
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.02
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	95.99
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.84
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.82
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.81
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.71
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.64
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	95.63
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.63
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.62
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.62
KOG3941	406	consensus Intermediate in Toll signal transduction	95.61
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.54
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.52
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.51
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.5
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.5
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.49
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.45
PRK15331	165	chaperone protein SicA; Provisional	95.38
KOG3941	406	consensus Intermediate in Toll signal transduction	95.31
COG4105	254	ComL DNA uptake lipoprotein [General function pred	95.31
COG3898	531	Uncharacterized membrane-bound protein [Function u	95.31
KOG2041	1189	consensus WD40 repeat protein [General function pr	95.26
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.14
PF13512	142	TPR_18: Tetratricopeptide repeat	95.04
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.99
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.76
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	94.67
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.58
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.41
COG3898	531	Uncharacterized membrane-bound protein [Function u	94.33
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.3
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.27
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.23
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	94.19
PRK15331	165	chaperone protein SicA; Provisional	94.13
COG1747	711	Uncharacterized N-terminal domain of the transcrip	93.99
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.91
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	93.9
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	93.82
COG0457	291	NrfG FOG: TPR repeat [General function prediction	93.79
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.72
PF13428	44	TPR_14: Tetratricopeptide repeat	93.72
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.69
PF13428	44	TPR_14: Tetratricopeptide repeat	93.67
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.61
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.58
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.56
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.35
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	93.21
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	93.08
KOG4555	175	consensus TPR repeat-containing protein [Function	92.69
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	92.1
PF13929	292	mRNA_stabil: mRNA stabilisation	91.95
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	91.92
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.9
COG3118	304	Thioredoxin domain-containing protein [Posttransla	91.74
PF13431	34	TPR_17: Tetratricopeptide repeat	91.67
COG4105	254	ComL DNA uptake lipoprotein [General function pred	91.37
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.24
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	91.1
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.07
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	90.71
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	90.69
KOG2610	491	consensus Uncharacterized conserved protein [Funct	90.6
COG3118	304	Thioredoxin domain-containing protein [Posttransla	90.52
KOG2610	491	consensus Uncharacterized conserved protein [Funct	90.5
KOG4555	175	consensus TPR repeat-containing protein [Function	90.26
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	89.76
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.67
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	89.45
COG1747	711	Uncharacterized N-terminal domain of the transcrip	89.27
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.16
PF13431	34	TPR_17: Tetratricopeptide repeat	89.13
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	89.13
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	88.9
PF13512	142	TPR_18: Tetratricopeptide repeat	88.75
KOG1585	308	consensus Protein required for fusion of vesicles	88.66
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.36
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	88.08
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.02
KOG1941	518	consensus Acetylcholine receptor-associated protei	87.82
PF13929	292	mRNA_stabil: mRNA stabilisation	87.59
COG5159	421	RPN6 26S proteasome regulatory complex component [	87.55
COG0457	291	NrfG FOG: TPR repeat [General function prediction	87.1
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	86.97
PRK11906	458	transcriptional regulator; Provisional	86.7
KOG1585	308	consensus Protein required for fusion of vesicles	86.56
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	86.36
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	85.47
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	85.44
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	85.2
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	84.71
COG4455	273	ImpE Protein of avirulence locus involved in tempe	84.45
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	84.28
PHA02875	413	ankyrin repeat protein; Provisional	84.2
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	84.14
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	84.06
PRK11906	458	transcriptional regulator; Provisional	84.05
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	83.99
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	83.71
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	83.7
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	83.06
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	82.67
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	82.41
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	81.92

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=9e-52  Score=398.02  Aligned_cols=290  Identities=16%  Similarity=0.215  Sum_probs=227.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC----CCchhHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE----RNLVTWNVIIT   98 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~~i~   98 (352)
                      |..+|+.+|.+|++.|+++.|.++|+.|.+.|+.||..+|+.||.+|++.|++++|.++|++|.+    ||..+      
T Consensus       436 d~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvT------  509 (1060)
T PLN03218        436 TLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHT------  509 (1060)
T ss_pred             CHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHH------
Confidence            99999999999999999999999999999999999999999999999999999999999999984    88888      


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHh--cCCCCCchhhHH
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEK--RGFNAFDIHVSN  176 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~  176 (352)
                          |+.+|.+|++.|++++|.++|++| ...|+.||..||+.+|.+|++.|++++|.+++++|.+  .|+.| +..+|+
T Consensus       510 ----ynaLI~gy~k~G~~eeAl~lf~~M-~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~P-D~vTyn  583 (1060)
T PLN03218        510 ----FGALIDGCARAGQVAKAFGAYGIM-RSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDP-DHITVG  583 (1060)
T ss_pred             ----HHHHHHHHHHCcCHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCC-cHHHHH
Confidence                777777777777777777777777 6667777777777777777777777777777777765  45666 777777


Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh----------
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI----------  244 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~----------  244 (352)
                      ++|.+|++.|++++|.++|++|.+.  .|+..+||++|.+|++.|++++|.++|++|.+.|+.||..+|.          
T Consensus       584 aLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G  663 (1060)
T PLN03218        584 ALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG  663 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Confidence            7777777777777777777777655  5677777777777777777777777777777777777776666          


Q ss_pred             -hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhhHHHHHHHHhcccccCccccc
Q 042593          245 -GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVWRTGFLRLLINSYFFSPITLN  321 (352)
Q Consensus       245 -~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~  321 (352)
                       .++|.++++.|.+. |+.||..+|+.||.+|+++|++++|.++|++|...  .||..+||+||.+|++.|++++|++++
T Consensus       664 ~~eeA~~l~~eM~k~-G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf  742 (1060)
T PLN03218        664 DLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVL  742 (1060)
T ss_pred             CHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence             67777777777776 77777777777777777777777777777777544  677777777777777777777777777


Q ss_pred             ccch
Q 042593          322 SQRL  325 (352)
Q Consensus       322 ~~~~  325 (352)
                      .+|.
T Consensus       743 ~eM~  746 (1060)
T PLN03218        743 SEMK  746 (1060)
T ss_pred             HHHH
Confidence            7664

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=4.5e-51  Score=393.23  Aligned_cols=305  Identities=17%  Similarity=0.183  Sum_probs=293.4

Q ss_pred             hhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593            2 LVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus         2 ~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      ++|+.|.+     .|+.|   |..+|+.+|.+|++.|+++.|.++|+.|.+.|+.||..+|+.+|.+|++.|++++|.++
T Consensus       458 ~lf~~M~~-----~Gl~p---D~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~l  529 (1060)
T PLN03218        458 RVLRLVQE-----AGLKA---DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGA  529 (1060)
T ss_pred             HHHHHHHH-----cCCCC---CHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHH
Confidence            68999999     99999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCCC----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhc-cCCCCChhhHHHHHHHHHhCCChhhHH
Q 042593           82 FDELPE----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC-EYTEPSEITILAVLPAIWKNGEVRNCQ  156 (352)
Q Consensus        82 ~~~m~~----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~p~~~t~~~ll~~~~~~~~~~~a~  156 (352)
                      |++|.+    ||..+          ||.+|.+|++.|++++|.++|++|... .|+.||..||++++.+|++.|++++|.
T Consensus       530 f~~M~~~Gv~PD~vT----------YnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~  599 (1060)
T PLN03218        530 YGIMRSKNVKPDRVV----------FNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAK  599 (1060)
T ss_pred             HHHHHHcCCCCCHHH----------HHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHH
Confidence            999964    88888          999999999999999999999999432 678999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          157 LIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ++|++|.+.|+.| +..+|+.+|.+|++.|++++|.++|++|...  .||..+|+++|.+|++.|++++|.+++++|.+.
T Consensus       600 elf~~M~e~gi~p-~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~  678 (1060)
T PLN03218        600 EVYQMIHEYNIKG-TPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQ  678 (1060)
T ss_pred             HHHHHHHHcCCCC-ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence            9999999999999 9999999999999999999999999999876  799999999999999999999999999999999


Q ss_pred             CCCCCcchhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhh
Q 042593          235 GLKPNRSWRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVW  301 (352)
Q Consensus       235 ~~~p~~~~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~  301 (352)
                      |+.||..+|.           .++|.++|++|... |+.||..+|+.||.+|++.|++++|.++|++|...  .||..+|
T Consensus       679 G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~-g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty  757 (1060)
T PLN03218        679 GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY  757 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            9999999988           89999999999998 99999999999999999999999999999999876  8999999


Q ss_pred             HHHHHHHHhcccccCcccccccchh
Q 042593          302 RTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       302 ~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      ++++.+|.+.|++++|.+++.++..
T Consensus       758 ~sLL~a~~k~G~le~A~~l~~~M~k  782 (1060)
T PLN03218        758 SILLVASERKDDADVGLDLLSQAKE  782 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999864

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

Probab=100.00  E-value=1e-50  Score=386.63  Aligned_cols=322  Identities=27%  Similarity=0.470  Sum_probs=291.4

Q ss_pred             hhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593            2 LVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus         2 ~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      ++|++|.+     .|+.|   |..+|+.++.+|++.|+.+.+.+++..+.+.|+.||..+||+||++|++.|++++|.++
T Consensus       210 ~lf~~M~~-----~g~~p---~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~v  281 (697)
T PLN03081        210 ALFREMWE-----DGSDA---EPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCV  281 (697)
T ss_pred             HHHHHHHH-----hCCCC---ChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHH
Confidence            56777877     77778   88888888888888888888888888888888888889999999999999999999999


Q ss_pred             hccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHH
Q 042593           82 FDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGY  161 (352)
Q Consensus        82 ~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  161 (352)
                      |++|.++|.++          ||.+|.+|++.|++++|+++|++| ...|+.||..||++++.+|++.|++++|.++++.
T Consensus       282 f~~m~~~~~vt----------~n~li~~y~~~g~~~eA~~lf~~M-~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~  350 (697)
T PLN03081        282 FDGMPEKTTVA----------WNSMLAGYALHGYSEEALCLYYEM-RDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAG  350 (697)
T ss_pred             HHhCCCCChhH----------HHHHHHHHHhCCCHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            99999999998          999999999999999999999999 8899999999999999999999999999999999


Q ss_pred             HHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          162 GEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       162 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      |.+.|+.+ +..+|++||++|++.|++++|.++|++|.  .||+.+||+||.+|+++|+.++|.++|++|.+.|+.||..
T Consensus       351 m~~~g~~~-d~~~~~~Li~~y~k~G~~~~A~~vf~~m~--~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~  427 (697)
T PLN03081        351 LIRTGFPL-DIVANTALVDLYSKWGRMEDARNVFDRMP--RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHV  427 (697)
T ss_pred             HHHhCCCC-CeeehHHHHHHHHHCCCHHHHHHHHHhCC--CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHH
Confidence            99999999 99999999999999999999999999994  6899999999999999999999999999999999999999


Q ss_pred             hhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHh
Q 042593          242 WRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLI  310 (352)
Q Consensus       242 ~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~  310 (352)
                      ||.           .++|.++|+.|.+.+|+.|+..+|+.++++|++.|++++|.+++++|... |+..+|++|+.+|..
T Consensus       428 T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~-p~~~~~~~Ll~a~~~  506 (697)
T PLN03081        428 TFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFK-PTVNMWAALLTACRI  506 (697)
T ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCC-CCHHHHHHHHHHHHH
Confidence            998           99999999999987799999999999999999999999999999998765 999999999999999


Q ss_pred             cccccCcccccccchhhhhhHHHHhhhhhcccccccccCCCC
Q 042593          311 NSYFFSPITLNSQRLFFFPAALYALTQILGFKPLFRKESSDG  352 (352)
Q Consensus       311 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  352 (352)
                      +|+++.|..+.++.+...|..      ...|+.+...|++.|
T Consensus       507 ~g~~~~a~~~~~~l~~~~p~~------~~~y~~L~~~y~~~G  542 (697)
T PLN03081        507 HKNLELGRLAAEKLYGMGPEK------LNNYVVLLNLYNSSG  542 (697)
T ss_pred             cCCcHHHHHHHHHHhCCCCCC------CcchHHHHHHHHhCC
Confidence            999999988877765443321      233444555555443

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

Probab=100.00  E-value=1.6e-50  Score=385.29  Aligned_cols=301  Identities=27%  Similarity=0.397  Sum_probs=290.1

Q ss_pred             ChhhHHHHHHhhccC-CCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHH
Q 042593            1 FLVYKQLQQIYIHSH-SPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSS   79 (352)
Q Consensus         1 ~~~~~~M~~~~~~~~-g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~   79 (352)
                      +++|++|..     . +..|   |..+|+.++.+|++.++++.+.+++..|.+.|+.||..+||.|+++|++.|++++|.
T Consensus       107 l~~f~~m~~-----~~~~~~---~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~  178 (697)
T PLN03081        107 LELFEILEA-----GCPFTL---PASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDAR  178 (697)
T ss_pred             HHHHHHHHh-----cCCCCC---CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHH
Confidence            368999987     4 4678   999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHH
Q 042593           80 KLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH  159 (352)
Q Consensus        80 ~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~  159 (352)
                      ++|++|.+||..+          ||.++.+|++.|++++|+++|++| ...|+.||..||+.++.+|++.|+.+.+.+++
T Consensus       179 ~lf~~m~~~~~~t----------~n~li~~~~~~g~~~~A~~lf~~M-~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~  247 (697)
T PLN03081        179 RLFDEMPERNLAS----------WGTIIGGLVDAGNYREAFALFREM-WEDGSDAEPRTFVVMLRASAGLGSARAGQQLH  247 (697)
T ss_pred             HHHhcCCCCCeee----------HHHHHHHHHHCcCHHHHHHHHHHH-HHhCCCCChhhHHHHHHHHhcCCcHHHHHHHH
Confidence            9999999999999          999999999999999999999999 78899999999999999999999999999999


Q ss_pred             HHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Q 042593          160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN  239 (352)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~  239 (352)
                      ..+.+.|+.+ +..+|++||++|++.|++++|.++|++|  ..+|+.+||++|.+|++.|+.++|.++|++|.+.|+.||
T Consensus       248 ~~~~~~g~~~-d~~~~n~Li~~y~k~g~~~~A~~vf~~m--~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd  324 (697)
T PLN03081        248 CCVLKTGVVG-DTFVSCALIDMYSKCGDIEDARCVFDGM--PEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSID  324 (697)
T ss_pred             HHHHHhCCCc-cceeHHHHHHHHHHCCCHHHHHHHHHhC--CCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence            9999999999 9999999999999999999999999999  568999999999999999999999999999999999999


Q ss_pred             cchhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHH
Q 042593          240 RSWRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRL  308 (352)
Q Consensus       240 ~~~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~  308 (352)
                      ..||.           .++|.++++.|.+. |+.||..+|+.||++|+++|++++|.++|++|...  |..+||+||.+|
T Consensus       325 ~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~-g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~--d~~t~n~lI~~y  401 (697)
T PLN03081        325 QFTFSIMIRIFSRLALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK--NLISWNALIAGY  401 (697)
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHHHHh-CCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCC--CeeeHHHHHHHH
Confidence            99998           89999999999999 99999999999999999999999999999999864  999999999999


Q ss_pred             HhcccccCcccccccchh
Q 042593          309 LINSYFFSPITLNSQRLF  326 (352)
Q Consensus       309 ~~~g~~~~a~~~~~~~~~  326 (352)
                      +++|+.++|++++.+|..
T Consensus       402 ~~~G~~~~A~~lf~~M~~  419 (697)
T PLN03081        402 GNHGRGTKAVEMFERMIA  419 (697)
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            999999999999999863

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.5e-49  Score=386.97  Aligned_cols=301  Identities=28%  Similarity=0.483  Sum_probs=290.5

Q ss_pred             ChhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHH
Q 042593            1 FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSK   80 (352)
Q Consensus         1 ~~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~   80 (352)
                      +++|++|.+     .|+.|   |..||+.++++|+..++++.+.+++..|.+.|+.||..+||+||.+|++.|++++|.+
T Consensus       172 ~~~f~~M~~-----~g~~P---d~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~  243 (857)
T PLN03077        172 LCLYHRMLW-----AGVRP---DVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARL  243 (857)
T ss_pred             HHHHHHHHH-----cCCCC---ChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHH
Confidence            368899998     89999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHH
Q 042593           81 LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHG  160 (352)
Q Consensus        81 ~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  160 (352)
                      +|++|.+||.++          ||.+|.+|++.|++++|+++|++| ...|+.||..||+.++.+|++.|+.+.+.+++.
T Consensus       244 lf~~m~~~d~~s----------~n~li~~~~~~g~~~eAl~lf~~M-~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~  312 (857)
T PLN03077        244 VFDRMPRRDCIS----------WNAMISGYFENGECLEGLELFFTM-RELSVDPDLMTITSVISACELLGDERLGREMHG  312 (857)
T ss_pred             HHhcCCCCCcch----------hHHHHHHHHhCCCHHHHHHHHHHH-HHcCCCCChhHHHHHHHHHHhcCChHHHHHHHH
Confidence            999999999999          999999999999999999999999 888999999999999999999999999999999


Q ss_pred             HHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          161 YGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       161 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                      .+.+.|+.| +..+|+.||.+|++.|++++|.++|++|  ..||+.+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus       313 ~~~~~g~~~-d~~~~n~Li~~y~k~g~~~~A~~vf~~m--~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~  389 (857)
T PLN03077        313 YVVKTGFAV-DVSVCNSLIQMYLSLGSWGEAEKVFSRM--ETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDE  389 (857)
T ss_pred             HHHHhCCcc-chHHHHHHHHHHHhcCCHHHHHHHHhhC--CCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCc
Confidence            999999999 9999999999999999999999999999  4789999999999999999999999999999999999999


Q ss_pred             chhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHH
Q 042593          241 SWRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL  309 (352)
Q Consensus       241 ~~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~  309 (352)
                      .|+.           .+.+.++++.|.+. |+.|+..+|+.||++|+++|++++|.++|++|.+.  |..+|+++|.+|.
T Consensus       390 ~t~~~ll~a~~~~g~~~~a~~l~~~~~~~-g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~--d~vs~~~mi~~~~  466 (857)
T PLN03077        390 ITIASVLSACACLGDLDVGVKLHELAERK-GLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK--DVISWTSIIAGLR  466 (857)
T ss_pred             eeHHHHHHHHhccchHHHHHHHHHHHHHh-CCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCC--CeeeHHHHHHHHH
Confidence            9998           89999999999999 99999999999999999999999999999999876  9999999999999


Q ss_pred             hcccccCcccccccchh
Q 042593          310 INSYFFSPITLNSQRLF  326 (352)
Q Consensus       310 ~~g~~~~a~~~~~~~~~  326 (352)
                      +.|+.++|+.++.++..
T Consensus       467 ~~g~~~eA~~lf~~m~~  483 (857)
T PLN03077        467 LNNRCFEALIFFRQMLL  483 (857)
T ss_pred             HCCCHHHHHHHHHHHHh
Confidence            99999999999999864

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=9.8e-49  Score=381.19  Aligned_cols=298  Identities=28%  Similarity=0.433  Sum_probs=285.3

Q ss_pred             ChhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHH
Q 042593            1 FLVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSK   80 (352)
Q Consensus         1 ~~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~   80 (352)
                      +++|++|.+     .|+.|   |..||+.++.+|++.|+++.+.+++..|.+.|+.||..+||.||.+|++.|++++|.+
T Consensus       273 l~lf~~M~~-----~g~~P---d~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~  344 (857)
T PLN03077        273 LELFFTMRE-----LSVDP---DLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEK  344 (857)
T ss_pred             HHHHHHHHH-----cCCCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHH
Confidence            368999999     89999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHH
Q 042593           81 LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHG  160 (352)
Q Consensus        81 ~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  160 (352)
                      +|++|.+||..+          ||.+|.+|++.|++++|+++|++| ...|+.||..||+.++.+|++.|+++.|.++++
T Consensus       345 vf~~m~~~d~~s----------~n~li~~~~~~g~~~~A~~lf~~M-~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~  413 (857)
T PLN03077        345 VFSRMETKDAVS----------WTAMISGYEKNGLPDKALETYALM-EQDNVSPDEITIASVLSACACLGDLDVGVKLHE  413 (857)
T ss_pred             HHhhCCCCCeee----------HHHHHHHHHhCCCHHHHHHHHHHH-HHhCCCCCceeHHHHHHHHhccchHHHHHHHHH
Confidence            999999999999          999999999999999999999999 888999999999999999999999999999999


Q ss_pred             HHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          161 YGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       161 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                      .+.+.|+.+ +..+|++||++|++.|++++|.++|++|  ..+|+.+||++|.+|+++|+.++|..+|++|.. ++.||.
T Consensus       414 ~~~~~g~~~-~~~~~n~Li~~y~k~g~~~~A~~vf~~m--~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~  489 (857)
T PLN03077        414 LAERKGLIS-YVVVANALIEMYSKCKCIDKALEVFHNI--PEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNS  489 (857)
T ss_pred             HHHHhCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHhC--CCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCH
Confidence            999999999 9999999999999999999999999999  468999999999999999999999999999986 699999


Q ss_pred             chhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHH
Q 042593          241 SWRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL  309 (352)
Q Consensus       241 ~~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~  309 (352)
                      .|+.           .+.+.+++..+.+. |+.+|..++++||++|+++|++++|.++|+++ .  +|..+||++|.+|+
T Consensus       490 ~t~~~lL~a~~~~g~l~~~~~i~~~~~~~-g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~--~d~~s~n~lI~~~~  565 (857)
T PLN03077        490 VTLIAALSACARIGALMCGKEIHAHVLRT-GIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-E--KDVVSWNILLTGYV  565 (857)
T ss_pred             hHHHHHHHHHhhhchHHHhHHHHHHHHHh-CCCccceechHHHHHHHHcCCHHHHHHHHHhc-C--CChhhHHHHHHHHH
Confidence            9998           78899999999998 99999999999999999999999999999998 3  59999999999999


Q ss_pred             hcccccCcccccccch
Q 042593          310 INSYFFSPITLNSQRL  325 (352)
Q Consensus       310 ~~g~~~~a~~~~~~~~  325 (352)
                      ++|+.++|++++.+|.
T Consensus       566 ~~G~~~~A~~lf~~M~  581 (857)
T PLN03077        566 AHGKGSMAVELFNRMV  581 (857)
T ss_pred             HcCCHHHHHHHHHHHH
Confidence            9999999999999886

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.86  E-value=1.7e-19  Score=161.57  Aligned_cols=289  Identities=16%  Similarity=0.116  Sum_probs=222.5

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchh-HHHHHHHHHhHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVT-WNVIITGLVKWT  104 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~-~~~~i~~~~~~~  104 (352)
                      .......+...|++++|...|+.+.+.+ +.+..++..+...+...|++++|..+++.+.. ++... .....     +.
T Consensus        38 ~y~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~-----~~  111 (389)
T PRK11788         38 DYFKGLNFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLA-----LQ  111 (389)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHH-----HH
Confidence            3333445667889999999999998875 45667888899999999999999999988765 32211 11111     78


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc---hhhHHHHHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD---IHVSNCLIDT  181 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~li~~  181 (352)
                      .+...|.+.|++++|..+|+++ .... +++..++..++..+.+.|++++|...++.+.+.+..+..   ...+..+...
T Consensus       112 ~La~~~~~~g~~~~A~~~~~~~-l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~  189 (389)
T PRK11788        112 ELGQDYLKAGLLDRAEELFLQL-VDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQ  189 (389)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH-HcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHH
Confidence            8888999999999999999999 4332 346778899999999999999999999998877644311   2245667788


Q ss_pred             HHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHhHH
Q 042593          182 YAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEEGL  249 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~a~  249 (352)
                      +.+.|++++|.+.|+++.+..| +...+..+...+.+.|++++|.+.++++.+.+......++.           .++|.
T Consensus       190 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  269 (389)
T PRK11788        190 ALARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGL  269 (389)
T ss_pred             HHhCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHH
Confidence            8899999999999998876544 45677788889999999999999999988753222111111           88888


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHh---cccccCcccccccchh
Q 042593          250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLI---NSYFFSPITLNSQRLF  326 (352)
Q Consensus       250 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~---~g~~~~a~~~~~~~~~  326 (352)
                      ..++++.+.   .|+...+..++..+.+.|++++|..+++++....|+..+++.++..+..   .|+..+++.++++++.
T Consensus       270 ~~l~~~~~~---~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~  346 (389)
T PRK11788        270 EFLRRALEE---YPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVG  346 (389)
T ss_pred             HHHHHHHHh---CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHH
Confidence            888888765   4666777899999999999999999999887667888899988888775   5588899988887764

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.84  E-value=1.4e-18  Score=155.73  Aligned_cols=253  Identities=10%  Similarity=0.002  Sum_probs=204.8

Q ss_pred             HHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC---hhhHHHH
Q 042593           66 GDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS---EITILAV  142 (352)
Q Consensus        66 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~t~~~l  142 (352)
                      ...+...|++++|...|+++.+.++....+       +..+...+...|++++|..+++.+.. .+..++   ..++..+
T Consensus        42 g~~~~~~~~~~~A~~~~~~al~~~p~~~~~-------~~~la~~~~~~g~~~~A~~~~~~~l~-~~~~~~~~~~~~~~~L  113 (389)
T PRK11788         42 GLNFLLNEQPDKAIDLFIEMLKVDPETVEL-------HLALGNLFRRRGEVDRAIRIHQNLLS-RPDLTREQRLLALQEL  113 (389)
T ss_pred             HHHHHhcCChHHHHHHHHHHHhcCcccHHH-------HHHHHHHHHHcCcHHHHHHHHHHHhc-CCCCCHHHHHHHHHHH
Confidence            345668899999999999998744333222       88899999999999999999999944 332222   2468889


Q ss_pred             HHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC------HhhHHHHHHHHH
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN------LVSWTTIISGFA  216 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~------~~~~~~li~~~~  216 (352)
                      ...+.+.|+++.|..+++++.+....  +..+++.++.++.+.|++++|.+.++.+....|+      ...+..+...+.
T Consensus       114 a~~~~~~g~~~~A~~~~~~~l~~~~~--~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  191 (389)
T PRK11788        114 GQDYLKAGLLDRAEELFLQLVDEGDF--AEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQAL  191 (389)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHcCCcc--hHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence            99999999999999999999876432  7789999999999999999999999998765432      224567788899


Q ss_pred             cCCCHHHHHHHHHHHHhcCCCCCcc-hhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHH
Q 042593          217 MHGMGKEAVENFERMQKVGLKPNRS-WRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQA  284 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~p~~~-~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  284 (352)
                      +.|++++|...++++.+..  |+.. .+.           .++|..+++++... +......++..++.+|.+.|+.++|
T Consensus       192 ~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~p~~~~~~~~~l~~~~~~~g~~~~A  268 (389)
T PRK11788        192 ARGDLDAARALLKKALAAD--PQCVRASILLGDLALAQGDYAAAIEALERVEEQ-DPEYLSEVLPKLMECYQALGDEAEG  268 (389)
T ss_pred             hCCCHHHHHHHHHHHHhHC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-ChhhHHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999998754  3322 111           89999999999875 3222346788999999999999999


Q ss_pred             HHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          285 EEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       285 ~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      ...++++....|+...+..++..+...|++++|+..+.+.+...|..
T Consensus       269 ~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~  315 (389)
T PRK11788        269 LEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSL  315 (389)
T ss_pred             HHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCH
Confidence            99999987666677778999999999999999999999998877755

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

Probab=99.83  E-value=4.5e-18  Score=168.12  Aligned_cols=299  Identities=12%  Similarity=0.012  Sum_probs=184.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +..++..+...+...|++++|.+.|+.+.+.. +.+...+..+...+...|++++|.+.|+++.+  | +..++..+...
T Consensus       464 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  542 (899)
T TIGR02917       464 NASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGL  542 (899)
T ss_pred             CcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH
Confidence            55567777777777777777777777666543 33445555566666666666666666666543  1 22222211111


Q ss_pred             HH------------------------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhH
Q 042593          100 LV------------------------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNC  155 (352)
Q Consensus       100 ~~------------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a  155 (352)
                      +.                        .+..+...+...|++++|..+++++ ... .+.+..+|..+..++.+.|++++|
T Consensus       543 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~-~~~-~~~~~~~~~~l~~~~~~~~~~~~A  620 (899)
T TIGR02917       543 YLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEA-ADA-APDSPEAWLMLGRAQLAAGDLNKA  620 (899)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHH-HHc-CCCCHHHHHHHHHHHHHcCCHHHH
Confidence            11                        2455666666667777777777666 322 133455677777777777777777


Q ss_pred             HHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          156 QLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...++.+.+....  +...+..+..++.+.|++++|.+.|+++....| +..++..+...+...|++++|.++++.+.+.
T Consensus       621 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  698 (899)
T TIGR02917       621 VSSFKKLLALQPD--SALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQ  698 (899)
T ss_pred             HHHHHHHHHhCCC--ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            7777777665432  556666777777777777777777777655533 4666677777777777777777777777665


Q ss_pred             CCCCCcchhh----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHH
Q 042593          235 GLKPNRSWRI----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRT  303 (352)
Q Consensus       235 ~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~  303 (352)
                      +.........          .++|...++++...   .|+..++..+..++.+.|+.++|.+.++.+... +.+..++..
T Consensus       699 ~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~  775 (899)
T TIGR02917       699 HPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR---APSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRTA  775 (899)
T ss_pred             CcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh---CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            4221111111          66677777776654   244456666677777777777777777666555 555666677


Q ss_pred             HHHHHHhcccccCcccccccchhhhh
Q 042593          304 GFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       304 li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                      +...|...|++++|++.+.+.+...|
T Consensus       776 la~~~~~~g~~~~A~~~~~~~~~~~p  801 (899)
T TIGR02917       776 LAELYLAQKDYDKAIKHYRTVVKKAP  801 (899)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHhCC
Confidence            77777777777777777777665544

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=99.82  E-value=7e-18  Score=166.75  Aligned_cols=282  Identities=12%  Similarity=0.050  Sum_probs=144.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +..++..+...+.+.|+.++|..+++.+.+.+ +.+...+..++..|.+.|++++|..+++++.+  | +...       
T Consensus       532 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-------  603 (899)
T TIGR02917       532 NLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEA-------  603 (899)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHH-------
Confidence            45566666666666666666666666665544 34455556666666666666666666666543  1 2223       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                         |..+..++...|++++|...|+++....  +.+...+..+..++.+.|++++|..+++.+.+....  +...+..+.
T Consensus       604 ---~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~l~  676 (899)
T TIGR02917       604 ---WLMLGRAQLAAGDLNKAVSSFKKLLALQ--PDSALALLLLADAYAVMKNYAKAITSLKRALELKPD--NTEAQIGLA  676 (899)
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC--CHHHHHHHH
Confidence               5555555666666666666666552211  123334555555555566666666666555544322  445555555


Q ss_pred             HHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHh
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEE  247 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~  247 (352)
                      ..+...|++++|.++++.+.... .+...+..+...+...|++++|...|+++.+.+..+  .+..           .++
T Consensus       677 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~  754 (899)
T TIGR02917       677 QLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSS--QNAIKLHRALLASGNTAE  754 (899)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCc--hHHHHHHHHHHHCCCHHH
Confidence            55555555555555555554432 234445555555555555555555555555443222  1111           444


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      |...++++.+.  .+.+...+..+...|.+.|+.++|.+.|+++... +.+..+++.+...+...|+ .+|+..+.+.
T Consensus       755 A~~~~~~~l~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~  829 (899)
T TIGR02917       755 AVKTLEAWLKT--HPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKA  829 (899)
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHH
Confidence            44444444442  2223444444444455555555555555444433 3344444444444444444 3344444433

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.73  E-value=3.2e-15  Score=141.32  Aligned_cols=288  Identities=10%  Similarity=-0.010  Sum_probs=205.6

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGL  100 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~  100 (352)
                      ...+..++.+....|+++.|...++.+.+.. |.+...+..+...+...|++++|...+++..+  |+ ...        
T Consensus        76 ~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a--------  146 (656)
T PRK15174         76 RDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQI--------  146 (656)
T ss_pred             hhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHH--------
Confidence            4445556666677888888888888888765 45667777888888888888888888888765  43 233        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                        +..+...+...|++++|...+.++....   |+.. .+..+ ..+.+.|++++|...++.+.+....+ +...+..+.
T Consensus       147 --~~~la~~l~~~g~~~eA~~~~~~~~~~~---P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~-~~~~~~~l~  219 (656)
T PRK15174        147 --FALHLRTLVLMDKELQAISLARTQAQEV---PPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALE-RQESAGLAV  219 (656)
T ss_pred             --HHHHHHHHHHCCChHHHHHHHHHHHHhC---CCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCc-chhHHHHHH
Confidence              7777888888888888888888773322   2222 23222 34677888888888888877664333 444555567


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHH----HHHHHHHHHhcCCCCCcchhh----------
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKE----AVENFERMQKVGLKPNRSWRI----------  244 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~----a~~~~~~m~~~~~~p~~~~~~----------  244 (352)
                      .++.+.|++++|...++......| +...+..+...+...|++++    |...+++..+.  .|+.....          
T Consensus       220 ~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~  297 (656)
T PRK15174        220 DTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRIVTLYADALIRT  297 (656)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHC
Confidence            788888899999888888766644 56777788888888888875    78888888774  45533222          


Q ss_pred             --hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchh-hHHHHHHHHhcccccCccccc
Q 042593          245 --GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVV-WRTGFLRLLINSYFFSPITLN  321 (352)
Q Consensus       245 --~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~-~~~li~~~~~~g~~~~a~~~~  321 (352)
                        .++|...+++.... . +-+...+..+..++.+.|++++|...++.+....|+... +..+...+...|++++|+..+
T Consensus       298 g~~~eA~~~l~~al~l-~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l  375 (656)
T PRK15174        298 GQNEKAIPLLQQSLAT-H-PDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVF  375 (656)
T ss_pred             CCHHHHHHHHHHHHHh-C-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHH
Confidence              78888888887764 2 224556777888888999999999998887766444433 334566788899999999888


Q ss_pred             ccchhhhhhH
Q 042593          322 SQRLFFFPAA  331 (352)
Q Consensus       322 ~~~~~~~~~~  331 (352)
                      .+.+...|..
T Consensus       376 ~~al~~~P~~  385 (656)
T PRK15174        376 EHYIQARASH  385 (656)
T ss_pred             HHHHHhChhh
Confidence            8877655543

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

Probab=99.71  E-value=6.1e-16  Score=135.91  Aligned_cols=295  Identities=12%  Similarity=0.035  Sum_probs=200.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      -..+|..+.+.+-..|+++.|+.+++.+++.. +-....|..+..++...|+.+.|...|.+..+  |+.....+-+.-+
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnL  193 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNL  193 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHH
Confidence            46789999999999999999999999999876 45678999999999999999999999988775  4333222111111


Q ss_pred             H-------------------------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhh
Q 042593          101 V-------------------------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRN  154 (352)
Q Consensus       101 ~-------------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~  154 (352)
                      .                         .|+.|...+-..|+.-.|+..|++..+   +.|+- ..|-.+.+.|...+.++.
T Consensus       194 lka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvk---ldP~f~dAYiNLGnV~ke~~~~d~  270 (966)
T KOG4626|consen  194 LKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVK---LDPNFLDAYINLGNVYKEARIFDR  270 (966)
T ss_pred             HHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhc---CCCcchHHHhhHHHHHHHHhcchH
Confidence            1                         577777777778888888888887744   34443 367777777777777777


Q ss_pred             HHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          155 CQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       155 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      |...|.+.....  |....++..+...|-..|+++.|++.+++.....|+ ...|+.|..++-..|++.+|++.|+....
T Consensus       271 Avs~Y~rAl~lr--pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~  348 (966)
T KOG4626|consen  271 AVSCYLRALNLR--PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALR  348 (966)
T ss_pred             HHHHHHHHHhcC--CcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHH
Confidence            777777665543  325666666666777777777777777777666665 56677777777777777777777777666


Q ss_pred             cCCCCCcchhh----------hHhHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhh
Q 042593          234 VGLKPNRSWRI----------GEEGLKFFDKMVEECEVLPD-IKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVW  301 (352)
Q Consensus       234 ~~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~  301 (352)
                      ....--....+          .++|..+|.+..+-   .|. ....+.|...|-.+|+.++|...+++..+. +.-..++
T Consensus       349 l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v---~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~  425 (966)
T KOG4626|consen  349 LCPNHADAMNNLGNIYREQGKIEEATRLYLKALEV---FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADAL  425 (966)
T ss_pred             hCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh---ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHH
Confidence            43222122222          56666666665532   232 345566666666666666666666666555 2233466


Q ss_pred             HHHHHHHHhcccccCcccccccchh
Q 042593          302 RTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       302 ~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      +.+...|-..|+...|++...+++.
T Consensus       426 ~NmGnt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  426 SNMGNTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             HhcchHHHHhhhHHHHHHHHHHHHh
Confidence            6666666666666666666666554

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.66  E-value=7.7e-14  Score=132.00  Aligned_cols=287  Identities=8%  Similarity=-0.093  Sum_probs=227.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +..-...++..+.+.|+++.|+.+++...... +-+......++.+....|++++|...|+++.+  |+ ...       
T Consensus        41 ~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a-------  112 (656)
T PRK15174         41 NEQNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPED-------  112 (656)
T ss_pred             cccCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHH-------
Confidence            44556677888999999999999999998876 33455666677788889999999999999876  43 333       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                         |..+...+.+.|++++|...+++...   +.|+ ...+..+...+...|+.++|...++.+......  +...+..+
T Consensus       113 ---~~~la~~l~~~g~~~~Ai~~l~~Al~---l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~--~~~a~~~~  184 (656)
T PRK15174        113 ---VLLVASVLLKSKQYATVADLAEQAWL---AFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPP--RGDMIATC  184 (656)
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC--CHHHHHHH
Confidence               77888899999999999999999944   2344 557888999999999999999999988776554  33444333


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCC--CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDR--KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------  244 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------  244 (352)
                       ..+...|++++|...++.+....  ++...+..+..++...|++++|...+++..+..  |+.....            
T Consensus       185 -~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~--p~~~~~~~~Lg~~l~~~G~  261 (656)
T PRK15174        185 -LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG--LDGAALRRSLGLAYYQSGR  261 (656)
T ss_pred             -HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCC
Confidence             34788999999999999976553  344455566778999999999999999998754  4432221            


Q ss_pred             hH----hHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCccc
Q 042593          245 GE----EGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPIT  319 (352)
Q Consensus       245 ~~----~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~  319 (352)
                      .+    +|...+++.... . +.+...+..+...+.+.|++++|...+++.... +.+...+..+...+...|++++|+.
T Consensus       262 ~~eA~~~A~~~~~~Al~l-~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~  339 (656)
T PRK15174        262 SREAKLQAAEHWRHALQF-N-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASD  339 (656)
T ss_pred             chhhHHHHHHHHHHHHhh-C-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            33    478899988864 2 235678899999999999999999999988777 5566788889999999999999999


Q ss_pred             ccccchhhhhh
Q 042593          320 LNSQRLFFFPA  330 (352)
Q Consensus       320 ~~~~~~~~~~~  330 (352)
                      .+.+.+...|.
T Consensus       340 ~l~~al~~~P~  350 (656)
T PRK15174        340 EFVQLAREKGV  350 (656)
T ss_pred             HHHHHHHhCcc
Confidence            99888765554

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

Probab=99.63  E-value=6.3e-16  Score=131.93  Aligned_cols=260  Identities=15%  Similarity=0.036  Sum_probs=113.5

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHHhC-CCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHH
Q 042593           29 FLIRTCVTLSYPNLGTQLHAVFSKVG-FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        29 ~ll~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li  107 (352)
                      .+...+.+.|++++|+++++...... -+.|...|..+...+...++.+.|.+.++++.+.+......       +..++
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~-------~~~l~   85 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQD-------YERLI   85 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-------ccccc
Confidence            55788889999999999996655443 24455666677777888999999999999998744332222       66666


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      .. ...+++++|.+++.+..+ .  .++...+..++..+.+.++++++..+++.+....-.+.+...|..+...+.+.|+
T Consensus        86 ~l-~~~~~~~~A~~~~~~~~~-~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~  161 (280)
T PF13429_consen   86 QL-LQDGDPEEALKLAEKAYE-R--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGD  161 (280)
T ss_dssp             ------------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCH
T ss_pred             cc-cccccccccccccccccc-c--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCC
Confidence            66 789999999999987733 2  2566677888899999999999999999987654333378889999999999999


Q ss_pred             hHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChh
Q 042593          188 IFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIK  266 (352)
Q Consensus       188 ~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~  266 (352)
                      .++|++.+++.....| |....+.++..+...|+.+++.++++...+.                          .+.|+.
T Consensus       162 ~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~--------------------------~~~~~~  215 (280)
T PF13429_consen  162 PDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKA--------------------------APDDPD  215 (280)
T ss_dssp             HHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH---------------------------HTSCC
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHH--------------------------CcCHHH
Confidence            9999999999877766 5788999999999999999999999988774                          234667


Q ss_pred             hHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          267 HYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       267 ~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      .+..+..+|...|+.++|...+++.... +.|+.....+...+...|+.++|.++..+.+
T Consensus       216 ~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  216 LWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT----------------
T ss_pred             HHHHHHHHhccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            7888999999999999999999997765 5688888889999999999999999988865

>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=99.62  E-value=3e-13  Score=127.97  Aligned_cols=289  Identities=11%  Similarity=-0.088  Sum_probs=219.8

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      +......+.+.|+++.|+..|+..++.  .|+...|..+..+|.+.|++++|++.+++..+.++....+       |..+
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a-------~~~~  200 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKA-------LNRR  200 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHH-------HHHH
Confidence            456677888999999999999998864  4788899999999999999999999999987633322122       8888


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCC---------------------------CCC-hhhHHHHHHH-------------
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYT---------------------------EPS-EITILAVLPA-------------  145 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~---------------------------~p~-~~t~~~ll~~-------------  145 (352)
                      ..+|...|++++|+.-|.......+.                           .|. ...+..+...             
T Consensus       201 a~a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  280 (615)
T TIGR00990       201 ANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGL  280 (615)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhh
Confidence            89999999999998766543111110                           011 0000000000             


Q ss_pred             -----------------------HHhCCChhhHHHHHHHHHhcC-CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          146 -----------------------IWKNGEVRNCQLIHGYGEKRG-FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       146 -----------------------~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                                             ....+++++|...++...+.+ ..|.....++.+..++...|++++|...|++....
T Consensus       281 ~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l  360 (615)
T TIGR00990       281 EDSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL  360 (615)
T ss_pred             hcccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence                                   012256788899999888765 23435677888899999999999999999998766


Q ss_pred             CCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHhcCCCCChhhH
Q 042593          202 RKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEECEVLPDIKHY  268 (352)
Q Consensus       202 ~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~~~~~p~~~~~  268 (352)
                      .|+ ...|..+...+...|++++|...|++..+..  |+.....            .++|...|++.++.  .+.+...+
T Consensus       361 ~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~  436 (615)
T TIGR00990       361 DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN--SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSH  436 (615)
T ss_pred             CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHH
Confidence            665 6688888999999999999999999988753  4432222            89999999998864  23356778


Q ss_pred             HHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhh
Q 042593          269 GCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       269 ~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      ..+..++.+.|++++|...+++.... +.+...|+.+...+...|++++|+..+.+.+...
T Consensus       437 ~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~  497 (615)
T TIGR00990       437 IQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELE  497 (615)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            88999999999999999999988766 5567899999999999999999999888876543

>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=99.62  E-value=1.3e-13  Score=130.56  Aligned_cols=188  Identities=11%  Similarity=-0.052  Sum_probs=154.8

Q ss_pred             cCCcchHHHHHHHHHHhC-CCC-chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcC
Q 042593           37 LSYPNLGTQLHAVFSKVG-FQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMN  114 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~-~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~  114 (352)
                      .+++++|.+.|+...+.+ ..| +...++.+...+...|++++|+..|++..+.++.....       |..+...+...|
T Consensus       307 ~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~-------~~~la~~~~~~g  379 (615)
T TIGR00990       307 DESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQS-------YIKRASMNLELG  379 (615)
T ss_pred             hhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHH-------HHHHHHHHHHCC
Confidence            367888999999988765 223 45678888999999999999999999987633322222       778888899999


Q ss_pred             CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHH
Q 042593          115 RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKL  194 (352)
Q Consensus       115 ~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  194 (352)
                      ++++|...|++.....  +-+..++..+...+...|++++|...+++..+....  +...+..+..++.+.|++++|...
T Consensus       380 ~~~eA~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~--~~~~~~~la~~~~~~g~~~eA~~~  455 (615)
T TIGR00990       380 DPDKAEEDFDKALKLN--SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPD--FIFSHIQLGVTQYKEGSIASSMAT  455 (615)
T ss_pred             CHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCcc--CHHHHHHHHHHHHHCCCHHHHHHH
Confidence            9999999999984432  234568888999999999999999999999887543  677888899999999999999999


Q ss_pred             HHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          195 FEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       195 ~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      |++.....| +...|+.+...+...|++++|...|++..+..
T Consensus       456 ~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~  497 (615)
T TIGR00990       456 FRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELE  497 (615)
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            999876655 57889999999999999999999999988753

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.55  E-value=3.6e-12  Score=128.57  Aligned_cols=289  Identities=10%  Similarity=0.050  Sum_probs=196.1

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc---hhHHHHHHHHHhH--
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL---VTWNVIITGLVKW--  103 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~---~~~~~~i~~~~~~--  103 (352)
                      ...+...|++++|...|+...+.. +.+...+..|..++.+.|++++|+..|++..+  |+.   ..|..++.....|  
T Consensus       276 G~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        276 GLAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            456678899999999999999865 45788899999999999999999999998765  332   2233333211112  


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH-----
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL-----  178 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-----  178 (352)
                      ......+.+.|++++|...|++.....  +.+...+..+...+...|++++|.+.+++..+....  +...+..+     
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~--P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~--~~~a~~~L~~l~~  430 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVD--NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG--NTNAVRGLANLYR  430 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHH
Confidence            223456778999999999999984432  134456777888899999999999999998876433  33333222     


Q ss_pred             -------------------------------------HHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCC
Q 042593          179 -------------------------------------IDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGM  220 (352)
Q Consensus       179 -------------------------------------i~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~  220 (352)
                                                           ...+...|++++|.+.|++..+..| +...+..+...|.+.|+
T Consensus       431 ~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~  510 (1157)
T PRK11447        431 QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQ  510 (1157)
T ss_pred             hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence                                                 2344567889999999988776655 56777888889999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHh------------------------------
Q 042593          221 GKEAVENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEE------------------------------  258 (352)
Q Consensus       221 ~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~------------------------------  258 (352)
                      +++|...++++.+..  |+.....            .++|...++.+...                              
T Consensus       511 ~~~A~~~l~~al~~~--P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~  588 (1157)
T PRK11447        511 RSQADALMRRLAQQK--PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGK  588 (1157)
T ss_pred             HHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCC
Confidence            999999999987643  3322111            33343333322110                              


Q ss_pred             -------c-CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          259 -------C-EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       259 -------~-~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                             . ..+.+...+..+...+.+.|+.++|...+++.... +.+...+..+...|...|++++|++.+.+.+.
T Consensus       589 ~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~  665 (1157)
T PRK11447        589 EAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPA  665 (1157)
T ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence                   0 11233445555666677777777777777766655 55566677777777777777777766665543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.54  E-value=4e-12  Score=128.24  Aligned_cols=291  Identities=10%  Similarity=0.008  Sum_probs=191.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCC-chhhH------------HHHHHHHHhcCChhHHHHHhccCCCCC
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQS-HVYVN------------TALGDMYVSLGFLKDSSKLFDELPERN   89 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~------------~~li~~~~~~g~~~~a~~~~~~m~~~~   89 (352)
                      +...+..+..++.+.|++++|+..|+...+..-.. ....+            ..+...+.+.|++++|+..|++..+.+
T Consensus       302 ~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~  381 (1157)
T PRK11447        302 DSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVD  381 (1157)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            56778888888889999999999998887754211 11111            122445677888888888888876522


Q ss_pred             chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHH----------------------------
Q 042593           90 LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITIL----------------------------  140 (352)
Q Consensus        90 ~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~----------------------------  140 (352)
                      +....+       +..+...+...|++++|++.|++..+..   |+ ...+.                            
T Consensus       382 P~~~~a-------~~~Lg~~~~~~g~~~eA~~~y~~aL~~~---p~~~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~  451 (1157)
T PRK11447        382 NTDSYA-------VLGLGDVAMARKDYAAAERYYQQALRMD---PGNTNAVRGLANLYRQQSPEKALAFIASLSASQRRS  451 (1157)
T ss_pred             CCCHHH-------HHHHHHHHHHCCCHHHHHHHHHHHHHhC---CCCHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHH
Confidence            211111       6667778888888888888888874422   22 11221                            


Q ss_pred             --------------HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CH
Q 042593          141 --------------AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NL  205 (352)
Q Consensus       141 --------------~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~  205 (352)
                                    .+...+...|++++|...+++..+....  +...+..+..+|.+.|++++|...++++....| +.
T Consensus       452 ~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~--~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~  529 (1157)
T PRK11447        452 IDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPG--SVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDP  529 (1157)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCH
Confidence                          1223345678888888888888876543  667777888888999999999999888765544 33


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcC--------------------------------------CCCCcchhh---
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVG--------------------------------------LKPNRSWRI---  244 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--------------------------------------~~p~~~~~~---  244 (352)
                      ..+..+...+...++.++|...++.+....                                      ..|+.....   
T Consensus       530 ~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~L  609 (1157)
T PRK11447        530 EQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTL  609 (1157)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHH
Confidence            333333333444444444444443321100                                      112221111   


Q ss_pred             ---------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccc
Q 042593          245 ---------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYF  314 (352)
Q Consensus       245 ---------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~  314 (352)
                               .++|...|++..+.  -+.+...+..++..|...|+.++|.+.++..... +.+...+..+...+...|++
T Consensus       610 a~~~~~~g~~~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~  687 (1157)
T PRK11447        610 ADWAQQRGDYAAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDT  687 (1157)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCH
Confidence                     78888888888864  2335677888888888889999998888877665 44556677777888888888


Q ss_pred             cCcccccccchhh
Q 042593          315 FSPITLNSQRLFF  327 (352)
Q Consensus       315 ~~a~~~~~~~~~~  327 (352)
                      ++|++++++.+..
T Consensus       688 ~eA~~~~~~al~~  700 (1157)
T PRK11447        688 AAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHHHHHHHHhhh
Confidence            8888888877653

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

Probab=99.54  E-value=1e-12  Score=116.07  Aligned_cols=264  Identities=13%  Similarity=0.076  Sum_probs=207.7

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI  137 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  137 (352)
                      -..+|+.+.+.+-..|++++|+.+++.+.+.++....+       |..+..++...|+.+.|.+.|.+..+   +.|+..
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel~p~fida-------~inla~al~~~~~~~~a~~~~~~alq---lnP~l~  184 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIELKPKFIDA-------YINLAAALVTQGDLELAVQCFFEALQ---LNPDLY  184 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcCchhhHH-------HhhHHHHHHhcCCCcccHHHHHHHHh---cCcchh
Confidence            35689999999999999999999999987633322222       88889999999999999999988844   456655


Q ss_pred             h-HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHH
Q 042593          138 T-ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGF  215 (352)
Q Consensus       138 t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~  215 (352)
                      . .+.+-+-+...|++++|...|.+..+....  -...|+.|...+...|+...|++.|++..+..|+ ...|-.|-..|
T Consensus       185 ca~s~lgnLlka~Grl~ea~~cYlkAi~~qp~--fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~  262 (966)
T KOG4626|consen  185 CARSDLGNLLKAEGRLEEAKACYLKAIETQPC--FAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVY  262 (966)
T ss_pred             hhhcchhHHHHhhcccchhHHHHHHHHhhCCc--eeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHH
Confidence            3 334444555678899999888888877543  5778889999999999999999999988777775 57788888889


Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHHcCChh
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEECEVLPD-IKHYGCLIDILERAGRLE  282 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  282 (352)
                      ...+.+++|...|.+...  ..|+.....            .+.|++.+++.++.   .|+ ...|+.|..++...|++.
T Consensus       263 ke~~~~d~Avs~Y~rAl~--lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~---~P~F~~Ay~NlanALkd~G~V~  337 (966)
T KOG4626|consen  263 KEARIFDRAVSCYLRALN--LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL---QPNFPDAYNNLANALKDKGSVT  337 (966)
T ss_pred             HHHhcchHHHHHHHHHHh--cCCcchhhccceEEEEeccccHHHHHHHHHHHHhc---CCCchHHHhHHHHHHHhccchH
Confidence            999999999999888766  456543332            88888888887753   554 568889999999999999


Q ss_pred             HHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhHHHHhhhh
Q 042593          283 QAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQI  338 (352)
Q Consensus       283 ~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  338 (352)
                      +|+..++..... +....+.+.|...|...|++++|..++...+..+|-...+++++
T Consensus       338 ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNL  394 (966)
T KOG4626|consen  338 EAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNL  394 (966)
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhH
Confidence            999998887766 55667888888889999999999998888888777666555543

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

Probab=99.54  E-value=3.9e-14  Score=120.87  Aligned_cols=231  Identities=16%  Similarity=0.090  Sum_probs=114.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      |...|..+...+-..++++.|.+.++.+...+ +-++..+..++.. ...+++++|.+++++.-+  ++...        
T Consensus        43 ~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~~~~~--------  112 (280)
T PF13429_consen   43 DPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQDGDPEEALKLAEKAYERDGDPRY--------  112 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccc-ccccccccccccc-cccccccccccccccccccccccch--------
Confidence            44444445556667899999999999999877 3477788888888 789999999999987754  44444        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        +...+..+.+.++++++.+++++.......+.+...|..+...+.+.|+.++|.+.+++..+..+.  +..+.+.++.
T Consensus       113 --l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~--~~~~~~~l~~  188 (280)
T PF13429_consen  113 --LLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPD--DPDARNALAW  188 (280)
T ss_dssp             -------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT---HHHHHHHHH
T ss_pred             --hhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--CHHHHHHHHH
Confidence              777888899999999999999998544445567778899999999999999999999999998655  7888999999


Q ss_pred             HHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhc
Q 042593          181 TYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEEC  259 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~  259 (352)
                      .+...|+.+++.++++...+. +.|...+..+..+|...|+.++|...+++..+.                         
T Consensus       189 ~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~-------------------------  243 (280)
T PF13429_consen  189 LLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKL-------------------------  243 (280)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH-------------------------
T ss_pred             HHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccc-------------------------
Confidence            999999999998988887655 456677889999999999999999999998863                         


Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                       .+.|+.....+.+++...|+.++|.++.++.-.
T Consensus       244 -~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  244 -NPDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             -STT-HHHHHHHHHHHT-----------------
T ss_pred             -ccccccccccccccccccccccccccccccccc
Confidence             233788888999999999999999999877643

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.53  E-value=7.8e-12  Score=120.82  Aligned_cols=294  Identities=11%  Similarity=-0.049  Sum_probs=195.3

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLV  101 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~  101 (352)
                      ...+..+...+.+.|++++|+..++...+.. +.+.. +..+..++...|+.++|+..++++.+  |+...  .      
T Consensus        83 ~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~--~------  152 (765)
T PRK10049         83 DDYQRGLILTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQ--Y------  152 (765)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH--H------
Confidence            4445566666667777777777777776653 34445 66667777777777777777777654  32211  0      


Q ss_pred             hHHHHHHHHHhcCCH----------------------------------------------HHHHHHHHHhHhccCCCCC
Q 042593          102 KWTGIIDGYSRMNRS----------------------------------------------NEALALFRRMAACEYTEPS  135 (352)
Q Consensus       102 ~~~~li~~~~~~~~~----------------------------------------------~~a~~~~~~m~~~~~~~p~  135 (352)
                       +..+...+...++.                                              ++|++.++.+.+.....|+
T Consensus       153 -~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~  231 (765)
T PRK10049        153 -PTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPD  231 (765)
T ss_pred             -HHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCc
Confidence             22233333333333                                              4455555555332222333


Q ss_pred             hhh-HH----HHHHHHHhCCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC-----
Q 042593          136 EIT-IL----AVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN-----  204 (352)
Q Consensus       136 ~~t-~~----~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-----  204 (352)
                      ... +.    ..+.++...|+.++|...|+.+.+.+.. |.+...  .+..+|...|++++|+..|+++....|.     
T Consensus       232 ~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~--~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~  309 (765)
T PRK10049        232 ATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQR--WVASAYLKLHQPEKAQSILTELFYHPETIADLS  309 (765)
T ss_pred             cchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHH--HHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCC
Confidence            221 11    1134456778999999999998887643 312222  2567889999999999999987655442     


Q ss_pred             HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC-----------CCCcchh---h-----------hHhHHHHHHHHHHhc
Q 042593          205 LVSWTTIISGFAMHGMGKEAVENFERMQKVGL-----------KPNRSWR---I-----------GEEGLKFFDKMVEEC  259 (352)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----------~p~~~~~---~-----------~~~a~~~~~~m~~~~  259 (352)
                      ......+..++...|++++|...++++.+...           .|+....   .           .++|...++++... 
T Consensus       310 ~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~-  388 (765)
T PRK10049        310 DEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYN-  388 (765)
T ss_pred             hHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-
Confidence            24466677788899999999999999887531           1232111   1           88899999888764 


Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhHH
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAAL  332 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  332 (352)
                       .+-+...+..+...+...|+.++|++.+++.... +.+...+-.....+...|++++|..+.++.+..+|..-
T Consensus       389 -~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~  461 (765)
T PRK10049        389 -APGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDP  461 (765)
T ss_pred             -CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCH
Confidence             3446778888899999999999999999988877 55566777788888999999999999988887766553

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.52  E-value=8.9e-12  Score=111.38  Aligned_cols=272  Identities=10%  Similarity=-0.087  Sum_probs=207.5

Q ss_pred             cCCcchHHHHHHHHHHhCCCCchhh-HHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhc
Q 042593           37 LSYPNLGTQLHAVFSKVGFQSHVYV-NTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRM  113 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~~~~~~~~-~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~  113 (352)
                      .|+++.|.+......+.+  +++.. |-....+..+.|+++.|...++++.+  |+.....        .-.....+...
T Consensus        97 eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~--------~l~~a~l~l~~  166 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPV--------EITRVRIQLAR  166 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHH--------HHHHHHHHHHC
Confidence            599999998877665543  22333 43445555889999999999999876  4443211        11235678889


Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch-------hhHHHHHHHHHhhC
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI-------HVSNCLIDTYAKCG  186 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~li~~~~~~g  186 (352)
                      |+++.|...++++ .... +-+......+...+.+.|+++++..++..+.+.+..+ ..       .+|..++.......
T Consensus       167 g~~~~Al~~l~~~-~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~-~~~~~~l~~~a~~~l~~~~~~~~  243 (398)
T PRK10747        167 NENHAARHGVDKL-LEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGD-EEHRAMLEQQAWIGLMDQAMADQ  243 (398)
T ss_pred             CCHHHHHHHHHHH-HhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999 4333 2245678888999999999999999999999987653 22       23334444445556


Q ss_pred             ChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---------hHhHHHHHHHHH
Q 042593          187 CIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---------GEEGLKFFDKMV  256 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---------~~~a~~~~~~m~  256 (352)
                      +.+...++++.+.+. +.++.....+..++...|+.++|..++++..+..  |+.....         .+++....+...
T Consensus       244 ~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~--~~~~l~~l~~~l~~~~~~~al~~~e~~l  321 (398)
T PRK10747        244 GSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQ--YDERLVLLIPRLKTNNPEQLEKVLRQQI  321 (398)
T ss_pred             CHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCHHHHHHHhhccCCChHHHHHHHHHHH
Confidence            677888888888655 4578888999999999999999999999988843  3433211         677888888877


Q ss_pred             HhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          257 EECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       257 ~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      +.  .+-|......+...+.+.|++++|.+.|+......|+...+-.+...+...|+.++|.+++++.+
T Consensus       322 k~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        322 KQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             hh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            64  33356678889999999999999999999998778999999999999999999999998888765

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.50  E-value=2.3e-11  Score=103.18  Aligned_cols=284  Identities=11%  Similarity=0.003  Sum_probs=187.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC----CCCchhHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP----ERNLVTWNVIIT   98 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~~i~   98 (352)
                      +..+|.++|.++|+-...+.|.+++++-.+...+.+..+||.+|.+-.-..+    .++..+|.    .||..|      
T Consensus       206 T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~T------  275 (625)
T KOG4422|consen  206 TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFT------  275 (625)
T ss_pred             CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHh------
Confidence            6789999999999999999999999998887778999999999987654433    45555554    499999      


Q ss_pred             HHHhHHHHHHHHHhcCCHH----HHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhh-HHHHHHHHHhc----C---
Q 042593           99 GLVKWTGIIDGYSRMNRSN----EALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRN-CQLIHGYGEKR----G---  166 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~----~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~-a~~~~~~~~~~----~---  166 (352)
                          +|+++++.++.|+++    .|++++.+| +.-|+.|...+|..+|..+++.++..+ +..++.++...    .   
T Consensus       276 ----fNalL~c~akfg~F~~ar~aalqil~Em-KeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp  350 (625)
T KOG4422|consen  276 ----FNALLSCAAKFGKFEDARKAALQILGEM-KEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKP  350 (625)
T ss_pred             ----HHHHHHHHHHhcchHHHHHHHHHHHHHH-HHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccC
Confidence                888899999999765    467788889 889999999999999999888877644 34444444321    1   


Q ss_pred             CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhcc------------------------------------------C--C
Q 042593          167 FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSV------------------------------------------D--R  202 (352)
Q Consensus       167 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~------------------------------------------~--~  202 (352)
                      +.|.+...|...|..|.+..+.+-|.++-.-...                                          .  .
T Consensus       351 ~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~  430 (625)
T KOG4422|consen  351 ITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYF  430 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceec
Confidence            2233555666777777777777766665443322                                          1  3


Q ss_pred             CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc-----------------hhh--------hHhHHHHH-----
Q 042593          203 KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS-----------------WRI--------GEEGLKFF-----  252 (352)
Q Consensus       203 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-----------------~~~--------~~~a~~~~-----  252 (352)
                      |+..+-..++++....|.++-.-++|.+++..|-+.+..                 +-.        .+-|..++     
T Consensus       431 p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~  510 (625)
T KOG4422|consen  431 PHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYES  510 (625)
T ss_pred             CCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHh
Confidence            444445555566666666666666666655544211111                 110        11111111     


Q ss_pred             --HHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CCCchhhH---HHHHHHHhcccccCcccccccc
Q 042593          253 --DKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---ITNVVVWR---TGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       253 --~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~~---~li~~~~~~g~~~~a~~~~~~~  324 (352)
                        .++.+   ........+.+.-.+.+.|+.++|.+++..+.+.   .|-...-|   -++..-........|+....-+
T Consensus       511 ~~~R~r~---~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a  587 (625)
T KOG4422|consen  511 QPIRQRA---QDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLA  587 (625)
T ss_pred             hHHHHHh---ccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHH
Confidence              12222   2234445667777889999999999999877433   44445555   5555666667776666655544

>TIGR00540 hemY_coli hemY protein

Probab=99.45  E-value=7.9e-11  Score=105.83  Aligned_cols=285  Identities=10%  Similarity=-0.048  Sum_probs=200.9

Q ss_pred             cHHHHHHHHH--hcCCcchHHHHHHHHHHhCCCCchh-hHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           26 TYSFLIRTCV--TLSYPNLGTQLHAVFSKVGFQSHVY-VNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        26 ~~~~ll~~~~--~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      ....+..+..  ..|+++.|.+.+....+..  |++. .+-....++...|+.+.|.+.+++..+  |+....-      
T Consensus        84 ~~~~~~~glla~~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~------  155 (409)
T TIGR00540        84 AQKQTEEALLKLAEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILV------  155 (409)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHH------
Confidence            3444555544  5799999999998776654  5543 344556778889999999999999754  4432100      


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        --.....+...|+++.|...++++.+ .. +-+......+...+...|+++++...+..+.+.+..+ .......-..
T Consensus       156 --~~~~a~l~l~~~~~~~Al~~l~~l~~-~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~-~~~~~~l~~~  230 (409)
T TIGR00540       156 --EIARTRILLAQNELHAARHGVDKLLE-MA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFD-DEEFADLEQK  230 (409)
T ss_pred             --HHHHHHHHHHCCCHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCC-HHHHHHHHHH
Confidence              22235677889999999999999944 33 2244578899999999999999999999999997653 2222122222


Q ss_pred             HH---HhhCC----hHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc-----hhh---
Q 042593          181 TY---AKCGC----IFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS-----WRI---  244 (352)
Q Consensus       181 ~~---~~~g~----~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-----~~~---  244 (352)
                      ++   ...+.    .+...+.++..... +.+...+..+...+...|+.++|.+++++..+..  ||..     .+.   
T Consensus       231 a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~  308 (409)
T TIGR00540       231 AEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIP  308 (409)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhh
Confidence            22   22222    23334444443222 2478889999999999999999999999998854  3333     222   


Q ss_pred             ------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhc--CCCCCCCchhhHHHHHHHHhcccccC
Q 042593          245 ------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASG--IPSQITNVVVWRTGFLRLLINSYFFS  316 (352)
Q Consensus       245 ------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~--m~~~~~~~~~~~~li~~~~~~g~~~~  316 (352)
                            .+.+.+.+++..+...-.|+.....++...+.+.|++++|.+.|+.  .....|+...+..+...+...|+.++
T Consensus       309 ~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~  388 (409)
T TIGR00540       309 RLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAE  388 (409)
T ss_pred             hcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHH
Confidence                  4556666666665422222225666889999999999999999994  43336888889999999999999999


Q ss_pred             cccccccch
Q 042593          317 PITLNSQRL  325 (352)
Q Consensus       317 a~~~~~~~~  325 (352)
                      |.++.++.+
T Consensus       389 A~~~~~~~l  397 (409)
T TIGR00540       389 AAAMRQDSL  397 (409)
T ss_pred             HHHHHHHHH
Confidence            998888764

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=99.45  E-value=4.1e-11  Score=115.91  Aligned_cols=290  Identities=10%  Similarity=0.039  Sum_probs=216.1

Q ss_pred             CCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHH
Q 042593           21 LFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVII   97 (352)
Q Consensus        21 ~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i   97 (352)
                      ++++....-.+.+....|+.++|++++....... +.+...+..+..++.+.|++++|..++++..+  |+ ...     
T Consensus        12 ~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a-----   85 (765)
T PRK10049         12 ALSNNQIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDY-----   85 (765)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH-----
Confidence            3467778888999999999999999999987733 45666799999999999999999999999754  33 333     


Q ss_pred             HHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593           98 TGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                           +..+...+...|+.++|...+++.....  +.+.. +..+..++...|+.++|...++++.+....  +...+..
T Consensus        86 -----~~~la~~l~~~g~~~eA~~~l~~~l~~~--P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~--~~~~~~~  155 (765)
T PRK10049         86 -----QRGLILTLADAGQYDEALVKAKQLVSGA--PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ--TQQYPTE  155 (765)
T ss_pred             -----HHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHH
Confidence                 6677888999999999999999994432  22344 888888999999999999999999998655  6777777


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCCCH------hhHHHHHHHHH-----cCCCH---HHHHHHHHHHHhc-CCCCCcch
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRKNL------VSWTTIISGFA-----MHGMG---KEAVENFERMQKV-GLKPNRSW  242 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~~~------~~~~~li~~~~-----~~~~~---~~a~~~~~~m~~~-~~~p~~~~  242 (352)
                      +..++...|..++|++.++.... .|+.      .....++....     ..+++   ++|...++.+.+. ...|+...
T Consensus       156 la~~l~~~~~~e~Al~~l~~~~~-~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~  234 (765)
T PRK10049        156 YVQALRNNRLSAPALGAIDDANL-TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATA  234 (765)
T ss_pred             HHHHHHHCCChHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccch
Confidence            88899999999999999998765 4432      11222232222     12234   7788888888864 23333321


Q ss_pred             h------------h----hHhHHHHHHHHHHhcCC-CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCC-----chh
Q 042593          243 R------------I----GEEGLKFFDKMVEECEV-LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITN-----VVV  300 (352)
Q Consensus       243 ~------------~----~~~a~~~~~~m~~~~~~-~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~-----~~~  300 (352)
                      .            .    .++|...|+++.+. +. .|+. .-..+..+|...|++++|...|+++....|.     ...
T Consensus       235 ~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~-~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~  312 (765)
T PRK10049        235 DYQRARIDRLGALLARDRYKDVISEYQRLKAE-GQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEE  312 (765)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcc-CCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHH
Confidence            1            1    78899999998876 42 2332 1222577899999999999999987655222     234


Q ss_pred             hHHHHHHHHhcccccCcccccccchhhhh
Q 042593          301 WRTGFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       301 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                      ...+..++...|++++|++.+.+.....|
T Consensus       313 ~~~L~~a~~~~g~~~eA~~~l~~~~~~~P  341 (765)
T PRK10049        313 LADLFYSLLESENYPGALTVTAHTINNSP  341 (765)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHhhcCC
Confidence            66677788999999999999887765544

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

Probab=99.44  E-value=9.9e-12  Score=113.85  Aligned_cols=246  Identities=12%  Similarity=0.006  Sum_probs=168.8

Q ss_pred             hhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHh
Q 042593            3 VYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLF   82 (352)
Q Consensus         3 ~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~   82 (352)
                      ++-.|+.     .|+.|   |.+||..+|..||..|+.+.|- +|..|.-...+.+...++.++......++.+.+.   
T Consensus        12 fla~~e~-----~gi~P---nRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk---   79 (1088)
T KOG4318|consen   12 FLALHEI-----SGILP---NRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK---   79 (1088)
T ss_pred             HHHHHHH-----hcCCC---chhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC---
Confidence            4567777     89999   9999999999999999999999 9999999998889999999999999999988776   


Q ss_pred             ccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHH---HHHHHHHhH---hccCCCCChhhHHH--------------H
Q 042593           83 DELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNE---ALALFRRMA---ACEYTEPSEITILA--------------V  142 (352)
Q Consensus        83 ~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~---a~~~~~~m~---~~~~~~p~~~t~~~--------------l  142 (352)
                          +|...+          |+.|..+|...||+..   +.+.++...   ...|+.....-+-.              .
T Consensus        80 ----ep~aDt----------yt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~  145 (1088)
T KOG4318|consen   80 ----EPLADT----------YTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENA  145 (1088)
T ss_pred             ----CCchhH----------HHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHH
Confidence                677777          9999999999998765   222122110   11121111111111              1


Q ss_pred             HHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCC
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGM  220 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~  220 (352)
                      +.-....|-++.+.+++..+-.....  .  .+...++-+..  .....+++.+....-  .|+..+|.+++.+-...|+
T Consensus       146 illlv~eglwaqllkll~~~Pvsa~~--~--p~~vfLrqnv~--~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~  219 (1088)
T KOG4318|consen  146 ILLLVLEGLWAQLLKLLAKVPVSAWN--A--PFQVFLRQNVV--DNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGD  219 (1088)
T ss_pred             HHHHHHHHHHHHHHHHHhhCCccccc--c--hHHHHHHHhcc--CCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCc
Confidence            11122223333333333222111111  0  11111222211  233344444443322  6999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCcchhh--------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCCh
Q 042593          221 GKEAVENFERMQKVGLKPNRSWRI--------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRL  281 (352)
Q Consensus       221 ~~~a~~~~~~m~~~~~~p~~~~~~--------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  281 (352)
                      .+.|..++.+|++.|+..+.+.|+        ...+..++.-|... |+.|+..|+...+..+.+.|..
T Consensus       220 ~d~Ak~ll~emke~gfpir~HyFwpLl~g~~~~q~~e~vlrgmqe~-gv~p~seT~adyvip~l~N~~t  287 (1088)
T KOG4318|consen  220 VDGAKNLLYEMKEKGFPIRAHYFWPLLLGINAAQVFEFVLRGMQEK-GVQPGSETQADYVIPQLSNGQT  287 (1088)
T ss_pred             hhhHHHHHHHHHHcCCCcccccchhhhhcCccchHHHHHHHHHHHh-cCCCCcchhHHHHHhhhcchhh
Confidence            999999999999999999999887        56666677777777 9999999999888888885553

>PF13041 PPR_2: PPR repeat family

Probab=99.44  E-value=1.7e-13  Score=83.65  Aligned_cols=49  Identities=20%  Similarity=0.199  Sum_probs=48.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS   71 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~   71 (352)
                      |..+||++|++|++.|++++|.++|++|.+.|++||..||+.+|++||+
T Consensus         2 ~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    2 DVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             chHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999999999999999985

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.43  E-value=8.3e-11  Score=114.67  Aligned_cols=258  Identities=8%  Similarity=-0.051  Sum_probs=168.6

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      +...|..+..++.. ++.++|...+.......  |+......+...+...|++++|...|+++..  |+...        
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a--------  544 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNED--------  544 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHH--------
Confidence            34455555555555 77777887776666543  5544433444455678888888888877653  33333        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                        +..+...+.+.|+.++|...+++..+ ..  |+. ..+..+.....+.|++++|...+++..+..  | +...+..+.
T Consensus       545 --~~~la~all~~Gd~~eA~~~l~qAL~-l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P-~~~a~~~LA  616 (987)
T PRK09782        545 --LLAAANTAQAAGNGAARDRWLQQAEQ-RG--LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--P-SANAYVARA  616 (987)
T ss_pred             --HHHHHHHHHHCCCHHHHHHHHHHHHh-cC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--C-CHHHHHHHH
Confidence              45556677778888888888888733 22  332 233333344455688888888888877654  4 466777778


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHh
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEE  258 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~  258 (352)
                      .++.+.|+.++|...+++.....| +...++.+..++...|+.++|...+++..+.  .|+                   
T Consensus       617 ~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~-------------------  675 (987)
T PRK09782        617 TIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKG--LPD-------------------  675 (987)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCC-------------------
Confidence            888888888888888888766654 4666777777788888888888888887763  222                   


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                           +...+..+..++...|++++|+..+++.... +.+..+.-....-.....+++.|++-..++.
T Consensus       676 -----~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~  738 (987)
T PRK09782        676 -----DPALIRQLAYVNQRLDDMAATQHYARLVIDDIDNQALITPLTPEQNQQRFNFRRLHEEVGRRW  738 (987)
T ss_pred             -----CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHh
Confidence                 5566777777788888888888877777665 3233444444445556666666666555554

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.42  E-value=6.2e-11  Score=97.97  Aligned_cols=201  Identities=12%  Similarity=-0.026  Sum_probs=159.1

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW  103 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~  103 (352)
                      ...+..+...+...|++++|.+.++...+.. +.+...+..+...+...|++++|.+.+++..+.+......       +
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~-------~  102 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDV-------L  102 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHH-------H
Confidence            4567788888999999999999999988765 4567788889999999999999999999876522221111       7


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ..+...+...|++++|.+.+++.............+..+..++...|+.++|...+++..+....  +...+..+...+.
T Consensus       103 ~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~la~~~~  180 (234)
T TIGR02521       103 NNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ--RPESLLELAELYY  180 (234)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC--ChHHHHHHHHHHH
Confidence            77788889999999999999998443222223446777888889999999999999998876543  5677888999999


Q ss_pred             hhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          184 KCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..|++++|.+.+++.... +.+...+..+...+...|+.++|..+.+.+...
T Consensus       181 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       181 LRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            999999999999987655 345667777888888999999999988887653

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.

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.42  E-value=8.1e-11  Score=99.93  Aligned_cols=222  Identities=15%  Similarity=0.152  Sum_probs=151.3

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCCC----CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPER----NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY  131 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  131 (352)
                      +.+..+|.++|.+.|+....+.|.+++++-...    +..+          ||.+|.+-.-.    .-.+++.+| ....
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~a----------FN~lI~~~S~~----~~K~Lv~EM-isqk  268 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREA----------FNGLIGASSYS----VGKKLVAEM-ISQK  268 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHh----------hhhhhhHHHhh----ccHHHHHHH-HHhh
Confidence            446677777888888777777777777776542    3334          55555543322    225777888 6666


Q ss_pred             CCCChhhHHHHHHHHHhCCChhh----HHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH-HHHHHHHhcc----C-
Q 042593          132 TEPSEITILAVLPAIWKNGEVRN----CQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS-ASKLFEDTSV----D-  201 (352)
Q Consensus       132 ~~p~~~t~~~ll~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~----~-  201 (352)
                      ..||..|+|+++.+.++.|+++.    |.+++.+|++.|+.| ...+|..+|..+++-++..+ |..++.++..    + 
T Consensus       269 m~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVeP-sLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~  347 (625)
T KOG4422|consen  269 MTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEP-SLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKT  347 (625)
T ss_pred             cCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCc-chhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCc
Confidence            78888888888888888887655    457788888888888 88888888888888877654 3444444322    1 


Q ss_pred             ----CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC----CCCCc--chhh------------hHhHHHHHHHHHHh
Q 042593          202 ----RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG----LKPNR--SWRI------------GEEGLKFFDKMVEE  258 (352)
Q Consensus       202 ----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~--~~~~------------~~~a~~~~~~m~~~  258 (352)
                          .| |..-|...+..|.+..+.+-|.++-.-+....    +.|+.  ..|.            .+.....|+.|+..
T Consensus       348 fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~  427 (625)
T KOG4422|consen  348 FKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPS  427 (625)
T ss_pred             ccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence                22 45567777888887778777777765554321    22221  1111            66667777777776


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                       -+-|+..+...++++....|.++-.-+++.++...
T Consensus       428 -~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~  462 (625)
T KOG4422|consen  428 -AYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEY  462 (625)
T ss_pred             -eecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHh
Confidence             67788888888888888888888888888777544

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.40  E-value=9.5e-11  Score=114.29  Aligned_cols=230  Identities=11%  Similarity=-0.015  Sum_probs=183.3

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      +...|..+..++.. ++.++|...+.+...  |+...          ...+...+...|++++|...|+++ ...  .|+
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~Pd~~~----------~L~lA~al~~~Gr~eeAi~~~rka-~~~--~p~  541 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQPDAWQ----------HRAVAYQAYQVEDYATALAAWQKI-SLH--DMS  541 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhCCchHH----------HHHHHHHHHHCCCHHHHHHHHHHH-hcc--CCC
Confidence            56778888888877 888899997777654  54221          233344556899999999999998 433  345


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGF  215 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~  215 (352)
                      ...+..+..++.+.|+.++|...++...+....  ....+..+.....+.|++++|...+++.....|+...|..+..++
T Consensus       542 ~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~--~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l  619 (987)
T PRK09782        542 NEDLLAAANTAQAAGNGAARDRWLQQAEQRGLG--DNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIY  619 (987)
T ss_pred             cHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCc--cHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            555677778889999999999999999887533  444444444455566999999999999987788888999999999


Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-  294 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  294 (352)
                      .+.|+.++|...+++..+..  |                        -+...++.+..++...|+.++|...+++.... 
T Consensus       620 ~~lG~~deA~~~l~~AL~l~--P------------------------d~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~  673 (987)
T PRK09782        620 RQRHNVPAAVSDLRAALELE--P------------------------NNSNYQAALGYALWDSGDIAQSREMLERAHKGL  673 (987)
T ss_pred             HHCCCHHHHHHHHHHHHHhC--C------------------------CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            99999999999999988742  2                        25678888889999999999999999988777 


Q ss_pred             CCCchhhHHHHHHHHhcccccCcccccccchhhhh
Q 042593          295 ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       295 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                      +.+...+..+...+...|++++|+..+++.+...|
T Consensus       674 P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P  708 (987)
T PRK09782        674 PDDPALIRQLAYVNQRLDDMAATQHYARLVIDDID  708 (987)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            66778999999999999999999999998866444

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

Probab=99.39  E-value=1.7e-10  Score=94.55  Aligned_cols=271  Identities=13%  Similarity=0.044  Sum_probs=184.3

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHHHHHHHHHhHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVIITGLVKWT  104 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~~~~~  104 (352)
                      .|-.=++.+. ..+.+.|.++|-+|.+.. +-+..+--+|.+.|-+.|.+|.|+++.+.+.+ ||.. +.--..+   .-
T Consensus        38 ~Yv~GlNfLL-s~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT-~~qr~lA---l~  111 (389)
T COG2956          38 DYVKGLNFLL-SNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLT-FEQRLLA---LQ  111 (389)
T ss_pred             HHHhHHHHHh-hcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCc-hHHHHHH---HH
Confidence            4544454444 458899999999998854 44566777899999999999999999998765 6543 2322222   56


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc---hhhHHHHHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD---IHVSNCLIDT  181 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~li~~  181 (352)
                      .|..-|...|-+|.|.++|..+ .+.+ ..-....-.++..|-...+|++|.++-+++.+.+..+.+   .+.|--|...
T Consensus       112 qL~~Dym~aGl~DRAE~~f~~L-~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~  189 (389)
T COG2956         112 QLGRDYMAAGLLDRAEDIFNQL-VDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQ  189 (389)
T ss_pred             HHHHHHHHhhhhhHHHHHHHHH-hcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHH
Confidence            6778889999999999999999 4432 223446778999999999999999999999888766522   2344455556


Q ss_pred             HHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      +.-..+++.|..++.+.....|+ +..--.+-......|+++.|.+.++.+.+.+.                        
T Consensus       190 ~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~------------------------  245 (389)
T COG2956         190 ALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNP------------------------  245 (389)
T ss_pred             HhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhCh------------------------
Confidence            66678899999999887666554 44444455688899999999999999988632                        


Q ss_pred             CCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccchhhhh
Q 042593          261 VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                       .--+.+...|..+|...|+.++....+.++....++...-..+..--....-.+.|.....+.+...|
T Consensus       246 -~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~P  313 (389)
T COG2956         246 -EYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQLRRKP  313 (389)
T ss_pred             -HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHHHhhCC
Confidence             12234445566666666666666665555444333333444444433444444455555555554444

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.39  E-value=9.9e-10  Score=105.20  Aligned_cols=290  Identities=12%  Similarity=0.022  Sum_probs=200.0

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHH---------
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLV---------  101 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~---------  101 (352)
                      ...+...|+++.|.++++.+.+.. +-++..+..++..+...++.++|++.++++.+.++.....+..++.         
T Consensus       109 A~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~  187 (822)
T PRK14574        109 ARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYD  187 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHH
Confidence            456777799999999999988876 4456777778888888899999999988887633322222222222         


Q ss_pred             -----------------hHHHHHHHHHhcCC------------------------------------------------H
Q 042593          102 -----------------KWTGIIDGYSRMNR------------------------------------------------S  116 (352)
Q Consensus       102 -----------------~~~~li~~~~~~~~------------------------------------------------~  116 (352)
                                       .+..+..++.+.|-                                                .
T Consensus       188 AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~  267 (822)
T PRK14574        188 ALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIA  267 (822)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHH
Confidence                             11111122222221                                                2


Q ss_pred             HHHHHHHHHhHhccCCCCChh-----hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHH
Q 042593          117 NEALALFRRMAACEYTEPSEI-----TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       117 ~~a~~~~~~m~~~~~~~p~~~-----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      +.|+.-++.+....+..|...     ...-.+-++...|+..++.+.++.+...+... ...+-..+.++|...++.++|
T Consensus       268 d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~-P~y~~~a~adayl~~~~P~kA  346 (822)
T PRK14574        268 DKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKM-PDYARRWAASAYIDRRLPEKA  346 (822)
T ss_pred             HHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCC-CHHHHHHHHHHHHhcCCcHHH
Confidence            233333333322222223321     22244567778899999999999999888654 566778899999999999999


Q ss_pred             HHHHHHhccCC-------CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC-----------CCCcchhh---------
Q 042593          192 SKLFEDTSVDR-------KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGL-----------KPNRSWRI---------  244 (352)
Q Consensus       192 ~~~~~~~~~~~-------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----------~p~~~~~~---------  244 (352)
                      +.+++.+....       ++......|.-+|..++++++|..+++++.+...           .|+.....         
T Consensus       347 ~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~  426 (822)
T PRK14574        347 APILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSL  426 (822)
T ss_pred             HHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHH
Confidence            99999875432       2344457788899999999999999999987422           12221111         


Q ss_pred             -----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcc
Q 042593          245 -----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPI  318 (352)
Q Consensus       245 -----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~  318 (352)
                           ..+|++.++++...  -+-|......+.+.+...|++.+|++.++..... +.+..+.......+...|++.+|.
T Consensus       427 ~~~gdl~~Ae~~le~l~~~--aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~  504 (822)
T PRK14574        427 VALNDLPTAQKKLEDLSST--APANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQME  504 (822)
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHH
Confidence                 88999999998763  3447888889999999999999999999777666 556667777888888899999886


Q ss_pred             cccccc
Q 042593          319 TLNSQR  324 (352)
Q Consensus       319 ~~~~~~  324 (352)
                      .+.+.-
T Consensus       505 ~~~~~l  510 (822)
T PRK14574        505 LLTDDV  510 (822)
T ss_pred             HHHHHH
Confidence            666443

>PF13041 PPR_2: PPR repeat family

Probab=99.37  E-value=1.4e-12  Score=79.54  Aligned_cols=45  Identities=27%  Similarity=0.483  Sum_probs=35.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK  148 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~  148 (352)
                      ||.+|++|++.|++++|.++|++| ++.|+.||..||+.+|++|++
T Consensus         6 yn~li~~~~~~~~~~~a~~l~~~M-~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    6 YNTLISGYCKAGKFEEALKLFKEM-KKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHHcC
Confidence            777777788888888888888888 677778888888888877764

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.37  E-value=7.2e-10  Score=99.17  Aligned_cols=244  Identities=10%  Similarity=0.043  Sum_probs=181.4

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHH--HHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNT--ALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIID  108 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~--~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~  108 (352)
                      ..+..+.|+++.|.+.++.+.+.  .|+.....  .....+...|+++.|...+++..+.++.....       ...+..
T Consensus       125 A~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~a-------l~ll~~  195 (398)
T PRK10747        125 AEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEV-------LRLAEQ  195 (398)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHH-------HHHHHH
Confidence            44557899999999999999764  46654333  34678889999999999999987632222111       778889


Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCCCh------hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEPSE------ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      .|.+.|++++|.+++..+.+.....|..      .+|..++.......+.+...++++.+-+.- .. ++.....+..++
T Consensus       196 ~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~-~~-~~~~~~~~A~~l  273 (398)
T PRK10747        196 AYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKT-RH-QVALQVAMAEHL  273 (398)
T ss_pred             HHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHH-hC-CHHHHHHHHHHH
Confidence            9999999999999999994443332322      133444444445556666677777664432 22 778888999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------hHhHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------GEEGLK  250 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~  250 (352)
                      ...|+.++|.+++++..+..+|....  ++.+.+..++.+++.+..+...+.  .|+.....            +++|.+
T Consensus       274 ~~~g~~~~A~~~L~~~l~~~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~  349 (398)
T PRK10747        274 IECDDHDTAQQIILDGLKRQYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASL  349 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCCHHHH--HHHhhccCCChHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            99999999999999887766666322  344445669999999999998875  35544332            999999


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          251 FFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       251 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                      .|+...+.   .|+..++..+..++.+.|+.++|.+.+++-.
T Consensus       350 ~le~al~~---~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        350 AFRAALKQ---RPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHhc---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99998864   7999999999999999999999999998653

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

Probab=99.35  E-value=7.9e-10  Score=93.27  Aligned_cols=276  Identities=13%  Similarity=-0.046  Sum_probs=213.4

Q ss_pred             hcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCC--CchhHHHHHHHHHhHHHHHHHHHhc
Q 042593           36 TLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPER--NLVTWNVIITGLVKWTGIIDGYSRM  113 (352)
Q Consensus        36 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~~i~~~~~~~~li~~~~~~  113 (352)
                      ..|++..|++....-.+.+-.| ...|-.-..+....|+.+.+-.++.+..++  |... ..       +-.........
T Consensus        96 ~eG~~~qAEkl~~rnae~~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l-~v-------~ltrarlll~~  166 (400)
T COG3071          96 FEGDFQQAEKLLRRNAEHGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTL-AV-------ELTRARLLLNR  166 (400)
T ss_pred             hcCcHHHHHHHHHHhhhcCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchH-HH-------HHHHHHHHHhC
Confidence            3699999999988877777333 455666778888899999999999998764  3332 11       55666778889


Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch-------hhHHHHHHHHHhhC
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI-------HVSNCLIDTYAKCG  186 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~li~~~~~~g  186 (352)
                      |+.+.|..-+.++ ...+ +-+.........+|.+.|++.....++..+.+.|.-. +.       .+|+.+++=....+
T Consensus       167 ~d~~aA~~~v~~l-l~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~-~~e~~~le~~a~~glL~q~~~~~  243 (400)
T COG3071         167 RDYPAARENVDQL-LEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLS-DEEAARLEQQAWEGLLQQARDDN  243 (400)
T ss_pred             CCchhHHHHHHHH-HHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCC-hHHHHHHHHHHHHHHHHHHhccc
Confidence            9999999888888 3333 2345678889999999999999999999999998765 43       35566666655666


Q ss_pred             ChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-------hHhHHHHHHHHHHh
Q 042593          187 CIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-------GEEGLKFFDKMVEE  258 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-------~~~a~~~~~~m~~~  258 (352)
                      ..+.-...|+..... +.++..-.+++.-+.+.|+.++|.++..+-.+.+..|+-..+.       ...-.+..++-.+.
T Consensus       244 ~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~  323 (400)
T COG3071         244 GSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQ  323 (400)
T ss_pred             cchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHh
Confidence            666666677777655 4567777888899999999999999999999988888755544       33333344443333


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      ++..|  ..+..|...|.+.+.|.+|.+.|+...+..|+..+|+.+...+...|+.++|.+...+.+
T Consensus       324 h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         324 HPEDP--LLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREAL  388 (400)
T ss_pred             CCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            24444  788899999999999999999999777668999999999999999999999998888876

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

Probab=99.35  E-value=2.4e-11  Score=108.38  Aligned_cols=190  Identities=13%  Similarity=0.085  Sum_probs=119.5

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC------CCchhHHHHHHHHH-----------
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE------RNLVTWNVIITGLV-----------  101 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~------~~~~~~~~~i~~~~-----------  101 (352)
                      +.++|...|+.... .+.-+.....-+..+|-..+++++|+++|+.+.+      .+...|++.+=.+.           
T Consensus       334 ~~~~A~~~~~klp~-h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~  412 (638)
T KOG1126|consen  334 NCREALNLFEKLPS-HHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQD  412 (638)
T ss_pred             HHHHHHHHHHhhHH-hcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHH
Confidence            44667777777333 3344556677788888888888889888888864      34455444432221           


Q ss_pred             ----------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC
Q 042593          102 ----------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF  170 (352)
Q Consensus       102 ----------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  170 (352)
                                +|-++.++|.-.++.+.|++.|++..+   +.| ..++|+.+..-+.....+|.|...|+........  
T Consensus       413 Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ---ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~r--  487 (638)
T KOG1126|consen  413 LIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ---LDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPR--  487 (638)
T ss_pred             HHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc---cCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCch--
Confidence                      577777777777777777777777622   334 4556666666666677777777777665543221  


Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +-..|--+.-.|.|.++++.|+-.|+......| +....-.+...+-+.|+.++|++++++....
T Consensus       488 hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l  552 (638)
T KOG1126|consen  488 HYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHL  552 (638)
T ss_pred             hhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhc
Confidence            222333345556677777777777776655533 5555555566666777777777777776654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.33  E-value=4.3e-10  Score=92.87  Aligned_cols=201  Identities=13%  Similarity=0.063  Sum_probs=149.5

Q ss_pred             CchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh
Q 042593           57 SHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE  136 (352)
Q Consensus        57 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  136 (352)
                      .....+..+...+...|++++|.+.+++..+.++.....       +..+...+...|++++|.+.+++.....  +.+.
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~-------~~~la~~~~~~~~~~~A~~~~~~al~~~--~~~~   99 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLA-------YLALALYYQQLGELEKAEDSFRRALTLN--PNNG   99 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCH
Confidence            345677788888889999999999998876522221111       7777888888999999999998884322  2344


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      ..+..+...+...|++++|...++...+....+.....+..+..++...|++++|.+.+++.....| +...+..+...+
T Consensus       100 ~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~  179 (234)
T TIGR02521       100 DVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELY  179 (234)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHH
Confidence            5677778888889999999999998877543332455677788888899999999999988766544 466788888888


Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                      ...|++++|...+++..+.  .                        +.+...+..+...+...|+.++|..+.+.+.
T Consensus       180 ~~~~~~~~A~~~~~~~~~~--~------------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  230 (234)
T TIGR02521       180 YLRGQYKDARAYLERYQQT--Y------------------------NQTAESLWLGIRIARALGDVAAAQRYGAQLQ  230 (234)
T ss_pred             HHcCCHHHHHHHHHHHHHh--C------------------------CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            8999999999998887764  1                        1245556677788888888888888776654

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.32  E-value=6e-10  Score=106.67  Aligned_cols=284  Identities=10%  Similarity=-0.038  Sum_probs=182.5

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCch--hhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV--YVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWT  104 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~  104 (352)
                      |...+ ...+.|+++.|++.|++..+..  |+.  ..+ .++..+...|+.++|+..+++...|+...+..       .-
T Consensus        38 y~~ai-i~~r~Gd~~~Al~~L~qaL~~~--P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~-------ll  106 (822)
T PRK14574         38 YDSLI-IRARAGDTAPVLDYLQEESKAG--PLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRG-------LA  106 (822)
T ss_pred             HHHHH-HHHhCCCHHHHHHHHHHHHhhC--ccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHH-------HH
Confidence            43333 5668889999999998888765  442  233 77888888899999999999988765555322       23


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  184 (352)
                      .+...+...|++++|+++|+++.+...  -+...+..++..+...++.++|...++.+.+..  | +...+..++..+..
T Consensus       107 alA~ly~~~gdyd~Aiely~kaL~~dP--~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~d--p-~~~~~l~layL~~~  181 (822)
T PRK14574        107 SAARAYRNEKRWDQALALWQSSLKKDP--TNPDLISGMIMTQADAGRGGVVLKQATELAERD--P-TVQNYMTLSYLNRA  181 (822)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCC--CCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccC--c-chHHHHHHHHHHHh
Confidence            335577788999999999999854332  223455677788888899999998888887763  3 44445455555545


Q ss_pred             hCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHH--------------------------------
Q 042593          185 CGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERM--------------------------------  231 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m--------------------------------  231 (352)
                      .++..+|++.++++....| +...+..+..++.+.|-...|.++.++-                                
T Consensus       182 ~~~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~  261 (822)
T PRK14574        182 TDRNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSET  261 (822)
T ss_pred             cchHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccch
Confidence            6666668888888877655 4566666677777776655555544431                                


Q ss_pred             ----------------Hhc-CCCCCcchh-h---------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHc
Q 042593          232 ----------------QKV-GLKPNRSWR-I---------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERA  278 (352)
Q Consensus       232 ----------------~~~-~~~p~~~~~-~---------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~  278 (352)
                                      ... +-.|..... .               ..++.+.++.+... +.+.-..+-..+.++|...
T Consensus       262 ~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~-~~~~P~y~~~a~adayl~~  340 (822)
T PRK14574        262 ERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAE-GYKMPDYARRWAASAYIDR  340 (822)
T ss_pred             hhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhc-CCCCCHHHHHHHHHHHHhc
Confidence                            110 111211111 0               66666666666665 4443344556677777777


Q ss_pred             CChhHHHHHHhcCCCC-------CCCchhhHHHHHHHHhcccccCcccccccchhh
Q 042593          279 GRLEQAEEVASGIPSQ-------ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFF  327 (352)
Q Consensus       279 g~~~~A~~~~~~m~~~-------~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  327 (352)
                      +.+++|..+++.+...       +++......|.-+|...+++++|..+.......
T Consensus       341 ~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~  396 (822)
T PRK14574        341 RLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQ  396 (822)
T ss_pred             CCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Confidence            7777777777766432       112222355677777777777777777666543

>TIGR00540 hemY_coli hemY protein

Probab=99.29  E-value=2.5e-09  Score=96.16  Aligned_cols=247  Identities=11%  Similarity=-0.044  Sum_probs=174.4

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchh--hHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHh
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY--VNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVK  102 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~  102 (352)
                      -....+..+.|+.+.|.+.++...+..  |+..  ..-.....+...|+++.|...++.+.+  | +...          
T Consensus       122 llaA~aa~~~g~~~~A~~~l~~a~~~~--p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~----------  189 (409)
T TIGR00540       122 IKAAEAAQQRGDEARANQHLEEAAELA--GNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKEV----------  189 (409)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC--CcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHH----------
Confidence            334567778899999999999987654  4443  344457888899999999999999886  4 3333          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHH-HHHHHH---HhCCChhhHHHHHHHHHhcCCC--CCchhhHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITIL-AVLPAI---WKNGEVRNCQLIHGYGEKRGFN--AFDIHVSN  176 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~-~ll~~~---~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~  176 (352)
                      +..+...+...|++++|.+++..+ .+.++. +...+. .-..+.   ...+..+.+...+..+.+....  +.+...+.
T Consensus       190 l~ll~~~~~~~~d~~~a~~~l~~l-~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~  267 (409)
T TIGR00540       190 LKLAEEAYIRSGAWQALDDIIDNM-AKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKI  267 (409)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHH-HHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHH
Confidence            778889999999999999999999 544432 322221 111111   2222222233344444333221  12778888


Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccCCCCHhh---HHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc--hhh-------
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVDRKNLVS---WTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS--WRI-------  244 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--~~~-------  244 (352)
                      .+...+...|+.+.|.+++++..+..||...   ...........++.+.+.+.++...+.  .|+..  .+.       
T Consensus       268 ~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~ll~sLg~l~  345 (409)
T TIGR00540       268 ALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCINRALGQLL  345 (409)
T ss_pred             HHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHHHHHHHHHH
Confidence            9999999999999999999998877666542   122222334567888999999887764  45555  432       


Q ss_pred             -----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcC
Q 042593          245 -----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGI  291 (352)
Q Consensus       245 -----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  291 (352)
                           +++|.+.|++.... ...|+...+..+...+.+.|+.++|.+++++-
T Consensus       346 ~~~~~~~~A~~~le~a~a~-~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       346 MKHGEFIEAADAFKNVAAC-KEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHcccHHHHHHHHHHhHHh-hcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                 88999999964444 56799999999999999999999999999864

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.

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

Probab=99.27  E-value=2.7e-09  Score=98.54  Aligned_cols=298  Identities=15%  Similarity=0.099  Sum_probs=219.8

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWT  104 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~  104 (352)
                      ...-...+.+...|+.++|.+++.+.++.. +.+...|-.|...|-..|+.+++...+-..-.-++..+.-       |-
T Consensus       140 ~~ll~eAN~lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~-------W~  211 (895)
T KOG2076|consen  140 RQLLGEANNLFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYEL-------WK  211 (895)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHH-------HH
Confidence            333334444455699999999999999887 6688899999999999999999987665443322222211       88


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHH----HHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSN----CLID  180 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----~li~  180 (352)
                      .+..-..+.|+++.|.-.|.+..+..  +++...+---...|-+.|+...|...+.++.....+. +..-+.    ..++
T Consensus       212 ~ladls~~~~~i~qA~~cy~rAI~~~--p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~-d~er~~d~i~~~~~  288 (895)
T KOG2076|consen  212 RLADLSEQLGNINQARYCYSRAIQAN--PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPV-DIERIEDLIRRVAH  288 (895)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCch-hHHHHHHHHHHHHH
Confidence            89999999999999999999994433  2455555566677889999999999999998876533 443333    3456


Q ss_pred             HHHhhCChHHHHHHHHHhccC---CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-------------
Q 042593          181 TYAKCGCIFSASKLFEDTSVD---RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-------------  244 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-------------  244 (352)
                      .+...++.+.|.+.++...+.   ..+...+++++..|.+...++.|......+.....++|..-+.             
T Consensus       289 ~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~  368 (895)
T KOG2076|consen  289 YFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALC  368 (895)
T ss_pred             HHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccc
Confidence            677788889999999886653   3456778899999999999999999998888754455544331             


Q ss_pred             ------------------------hHhHHHHHHHHHHhcCCCC--ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CC
Q 042593          245 ------------------------GEEGLKFFDKMVEECEVLP--DIKHYGCLIDILERAGRLEQAEEVASGIPSQ--IT  296 (352)
Q Consensus       245 ------------------------~~~a~~~~~~m~~~~~~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~  296 (352)
                                              .+....+....... .+.|  +...|.-+..+|...|++.+|..+|..+...  -.
T Consensus       369 ~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~-n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~  447 (895)
T KOG2076|consen  369 EVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVED-NVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQ  447 (895)
T ss_pred             cCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHh-cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCcccc
Confidence                                    22333333333443 4333  4567788888999999999999999888777  34


Q ss_pred             CchhhHHHHHHHHhcccccCcccccccchhhhhhHHHH
Q 042593          297 NVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYA  334 (352)
Q Consensus       297 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  334 (352)
                      +...|-.+..+|...|.+++|++.+...+..-|..+-+
T Consensus       448 ~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~  485 (895)
T KOG2076|consen  448 NAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDA  485 (895)
T ss_pred             chhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhh
Confidence            56688888888999999999988888887766665444

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

Probab=99.27  E-value=5.3e-10  Score=95.90  Aligned_cols=252  Identities=12%  Similarity=0.079  Sum_probs=151.1

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCC------CchhHHHHHHHHHhHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPER------NLVTWNVIITGLVKWT  104 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------~~~~~~~~i~~~~~~~  104 (352)
                      ..++.+....+++..=.+.+...|++.+...-+-...+.-...+++.|+.+|+++.+.      |..+          |+
T Consensus       234 ~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdl----------yS  303 (559)
T KOG1155|consen  234 KKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDL----------YS  303 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHH----------Hh
Confidence            3555566677777777788888887766665555556666778899999999998763      3445          33


Q ss_pred             HHHHHHHhcCCHH-HHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          105 GIIDGYSRMNRSN-EALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       105 ~li~~~~~~~~~~-~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      .++-.-.....+. -|..++    .-+  +--..|+..+.+-|+-.++.++|...|++..+.+..  ....|+.+.+=|.
T Consensus       304 N~LYv~~~~skLs~LA~~v~----~id--KyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~--~~~aWTLmGHEyv  375 (559)
T KOG1155|consen  304 NVLYVKNDKSKLSYLAQNVS----NID--KYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPK--YLSAWTLMGHEYV  375 (559)
T ss_pred             HHHHHHhhhHHHHHHHHHHH----Hhc--cCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcc--hhHHHHHhhHHHH
Confidence            3332221111111 111111    111  122345556666666666666666666666665544  4556666666666


Q ss_pred             hhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCC
Q 042593          184 KCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVL  262 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~  262 (352)
                      ...+...|.+-++...+. +.|-..|-.|-++|.-.+.+.=|+-.|++..+  ++|                        
T Consensus       376 EmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kP------------------------  429 (559)
T KOG1155|consen  376 EMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKP------------------------  429 (559)
T ss_pred             HhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCC------------------------
Confidence            666666666666665544 34566666666666666666666666666554  222                        


Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      -|...|.+|.++|.+.++.++|.+.|.+.... ..+...+..|...|-+.++.++|.+.+..-+.
T Consensus       430 nDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  430 NDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             CchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            26667777777777777777777777665544 23445666666777777776666666655543

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

Probab=99.25  E-value=5e-10  Score=92.04  Aligned_cols=228  Identities=11%  Similarity=-0.010  Sum_probs=187.6

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~  105 (352)
                      +.+.+.|.+.|.+.+|.+.++...+..  |-+.||-.|-++|.+..+++.|+.+|.+-.+  |..+|+         ..-
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~--~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~---------l~g  295 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQF--PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTY---------LLG  295 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcC--CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhh---------hhh
Confidence            467888999999999999998887764  7778888899999999999999999998775  555553         445


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC  185 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  185 (352)
                      +.+.+-..++.++|.++|+...+...  .++.....+...|.-.++.+-|..+|+++.+.|+.  ++..|+.+.-+|.-.
T Consensus       296 ~ARi~eam~~~~~a~~lYk~vlk~~~--~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~--speLf~NigLCC~ya  371 (478)
T KOG1129|consen  296 QARIHEAMEQQEDALQLYKLVLKLHP--INVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ--SPELFCNIGLCCLYA  371 (478)
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHhcCC--ccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC--ChHHHhhHHHHHHhh
Confidence            66777788999999999999866543  35566777778888889999999999999999988  789999999999999


Q ss_pred             CChHHHHHHHHHhccC--CCC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCC
Q 042593          186 GCIFSASKLFEDTSVD--RKN--LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEV  261 (352)
Q Consensus       186 g~~~~a~~~~~~~~~~--~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~  261 (352)
                      +++|-++..|.+....  .|+  ...|..+-......|++..|.+.|+-....                          -
T Consensus       372 qQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~--------------------------d  425 (478)
T KOG1129|consen  372 QQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTS--------------------------D  425 (478)
T ss_pred             cchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhcc--------------------------C
Confidence            9999999999886544  343  466888888888999999999999887653                          2


Q ss_pred             CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCC
Q 042593          262 LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQIT  296 (352)
Q Consensus       262 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~  296 (352)
                      .-+...++.|.-.-.+.|++++|..+++......|
T Consensus       426 ~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~~P  460 (478)
T KOG1129|consen  426 AQHGEALNNLAVLAARSGDILGARSLLNAAKSVMP  460 (478)
T ss_pred             cchHHHHHhHHHHHhhcCchHHHHHHHHHhhhhCc
Confidence            23677899998888999999999999998776633

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

Probab=99.24  E-value=2.3e-10  Score=102.20  Aligned_cols=203  Identities=10%  Similarity=0.031  Sum_probs=168.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      .+.+|+.+.+.|.-.++.+.|++.|+...... +-..++|+.+.+-+.....+|+|...|+.....|+..||+       
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnA-------  491 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNA-------  491 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHH-------
Confidence            67899999999999999999999999888765 3378899999998999999999999999999999999998       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |.-+.-.|.+.++++.|+-.|++. ..-  .| +.+....+...+.+.|+.++|..++++.......  ++..--.....
T Consensus       492 wYGlG~vy~Kqek~e~Ae~~fqkA-~~I--NP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k--n~l~~~~~~~i  566 (638)
T KOG1126|consen  492 WYGLGTVYLKQEKLEFAEFHFQKA-VEI--NPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK--NPLCKYHRASI  566 (638)
T ss_pred             HHhhhhheeccchhhHHHHHHHhh-hcC--CccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC--CchhHHHHHHH
Confidence            888999999999999999999988 433  34 4456667777788899999999999998887655  55555566677


Q ss_pred             HHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKP  238 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p  238 (352)
                      +...+++++|+..+++++...|+ ...|..+...|.+.|+.+.|..-|.-+.+...++
T Consensus       567 l~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg  624 (638)
T KOG1126|consen  567 LFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKG  624 (638)
T ss_pred             HHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCcc
Confidence            88889999999999999877664 5667778889999999999998888888765444

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.23  E-value=2.9e-09  Score=95.68  Aligned_cols=243  Identities=16%  Similarity=0.118  Sum_probs=178.8

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHh-----CC-CCchh-hHHHHHHHHHhcCChhHHHHHhccCCC-------CCc
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKV-----GF-QSHVY-VNTALGDMYVSLGFLKDSSKLFDELPE-------RNL   90 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~~-~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~-------~~~   90 (352)
                      .+...+...|...|+++.|..++++..+.     |. .|... ..+.+...|...+++++|..+|+++..       ++.
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            44555889999999999999999988765     21 23443 355588899999999999999998863       333


Q ss_pred             hhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhH----hccCCC-CChh-hHHHHHHHHHhCCChhhHHHHHHHHHh
Q 042593           91 VTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMA----ACEYTE-PSEI-TILAVLPAIWKNGEVRNCQLIHGYGEK  164 (352)
Q Consensus        91 ~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~~~~~-p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~  164 (352)
                      ...-+.      ++.|...|.+.|++++|...+++..    +..+.. |... -++.+...+...+++++|..+++...+
T Consensus       280 ~~va~~------l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~  353 (508)
T KOG1840|consen  280 PAVAAT------LNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALK  353 (508)
T ss_pred             HHHHHH------HHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence            222221      8888899999999999988888752    122222 2332 477788889999999999999987754


Q ss_pred             c-----CCCC-CchhhHHHHHHHHHhhCChHHHHHHHHHhccC--------CC-CHhhHHHHHHHHHcCCCHHHHHHHHH
Q 042593          165 R-----GFNA-FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--------RK-NLVSWTTIISGFAMHGMGKEAVENFE  229 (352)
Q Consensus       165 ~-----~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--------~~-~~~~~~~li~~~~~~~~~~~a~~~~~  229 (352)
                      .     |... ....+++.|...|.+.|++++|++++++....        .+ .-..++.|...|.+.+++.+|.++|.
T Consensus       354 i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~  433 (508)
T KOG1840|consen  354 IYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFE  433 (508)
T ss_pred             HHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHH
Confidence            3     2111 13678999999999999999999999986543        12 23567888899999999999999999


Q ss_pred             HHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          230 RMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       230 ~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                      +-..-                 . ..... +.+-...+|..|...|.+.|++++|.++.+...
T Consensus       434 ~~~~i-----------------~-~~~g~-~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  434 EAKDI-----------------M-KLCGP-DHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHH-----------------H-HHhCC-CCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            86542                 1 11100 222235789999999999999999999877654

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

Probab=99.23  E-value=1.6e-08  Score=83.22  Aligned_cols=257  Identities=11%  Similarity=0.115  Sum_probs=186.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhC-CCC--chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVG-FQS--HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~   99 (352)
                      +..+--++.+.+.+.|.++.|+.+++.+.++. .+-  -....-.|..-|...|-+|.|+.+|..+.+.+...-++    
T Consensus        68 t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~A----  143 (389)
T COG2956          68 TFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGA----  143 (389)
T ss_pred             hhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHH----
Confidence            34444567788889999999999999988643 111  12345567788889999999999999998755554455    


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh----hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI----TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVS  175 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  175 (352)
                         .-.|+..|-...+|++|+++-+++.+ .+.++...    -|--+...+....+.+.|...++...+.+..  .+..-
T Consensus       144 ---lqqLl~IYQ~treW~KAId~A~~L~k-~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~--cvRAs  217 (389)
T COG2956         144 ---LQQLLNIYQATREWEKAIDVAERLVK-LGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKK--CVRAS  217 (389)
T ss_pred             ---HHHHHHHHHHhhHHHHHHHHHHHHHH-cCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCcc--ceehh
Confidence               67889999999999999999998844 33333322    3555666666678899999999998887655  45555


Q ss_pred             HHHHHHHHhhCChHHHHHHHHHhccCCCC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---------
Q 042593          176 NCLIDTYAKCGCIFSASKLFEDTSVDRKN--LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---------  244 (352)
Q Consensus       176 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---------  244 (352)
                      -.+.+.....|+++.|.+.++.+....|+  ..+...|..+|...|+.++....+.++.+....++..-..         
T Consensus       218 i~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G  297 (389)
T COG2956         218 IILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGADAELMLADLIELQEG  297 (389)
T ss_pred             hhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCccHHHHHHHHHHHhhC
Confidence            57888999999999999999999877775  4678899999999999999999999988864444432222         


Q ss_pred             hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHc---CChhHHHHHHhcCC
Q 042593          245 GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERA---GRLEQAEEVASGIP  292 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~---g~~~~A~~~~~~m~  292 (352)
                      .+.|..++.+-..+   +|+...+..+|..-..-   |...+-..+++.|.
T Consensus       298 ~~~Aq~~l~~Ql~r---~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mv  345 (389)
T COG2956         298 IDAAQAYLTRQLRR---KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMV  345 (389)
T ss_pred             hHHHHHHHHHHHhh---CCcHHHHHHHHHhhhccccccchhhhHHHHHHHH
Confidence            44555444443333   57777777777765532   23344444555543

>PRK12370 invasion protein regulator; Provisional

Probab=99.19  E-value=6.7e-09  Score=97.01  Aligned_cols=198  Identities=9%  Similarity=-0.070  Sum_probs=130.3

Q ss_pred             CcccHHHHHHHHHh-----cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh---------cCChhHHHHHhccCCCC
Q 042593           23 DSFTYSFLIRTCVT-----LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS---------LGFLKDSSKLFDELPER   88 (352)
Q Consensus        23 ~~~~~~~ll~~~~~-----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~---------~g~~~~a~~~~~~m~~~   88 (352)
                      +...|...+++-..     .++.++|...+++..+.. +-+...|..+..++..         .+++++|...+++..+-
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l  333 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL  333 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc
Confidence            44555566665432     233467788888777654 3345566666555442         23467888888877652


Q ss_pred             CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCC
Q 042593           89 NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGF  167 (352)
Q Consensus        89 ~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  167 (352)
                      ++....+       |..+...+...|++++|...|++..+.   .|+ ...+..+..++...|+.++|...+++..+...
T Consensus       334 dP~~~~a-------~~~lg~~~~~~g~~~~A~~~~~~Al~l---~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P  403 (553)
T PRK12370        334 DHNNPQA-------LGLLGLINTIHSEYIVGSLLFKQANLL---SPISADIKYYYGWNLFMAGQLEEALQTINECLKLDP  403 (553)
T ss_pred             CCCCHHH-------HHHHHHHHHHccCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            2221111       666667777888888888888888442   344 44677777888888888888888888887754


Q ss_pred             CCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          168 NAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       168 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .  +...+..++..+...|++++|...+++.... .| +...+..+..++...|+.++|...+.++..
T Consensus       404 ~--~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~  469 (553)
T PRK12370        404 T--RAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEIST  469 (553)
T ss_pred             C--ChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhh
Confidence            4  3333334444566678888888888876544 34 344566677778888888888888877654

>PRK12370 invasion protein regulator; Provisional

Probab=99.13  E-value=1.5e-08  Score=94.59  Aligned_cols=183  Identities=9%  Similarity=0.003  Sum_probs=139.5

Q ss_pred             CCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHH
Q 042593           38 SYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSN  117 (352)
Q Consensus        38 g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~  117 (352)
                      +++++|...++...+.. +-+...+..+..++...|++++|+..|++..+.++.....       |..+...+...|+++
T Consensus       318 ~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a-------~~~lg~~l~~~G~~~  389 (553)
T PRK12370        318 NAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADI-------KYYYGWNLFMAGQLE  389 (553)
T ss_pred             hHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHH-------HHHHHHHHHHCCCHH
Confidence            44788999999988876 5577888889999999999999999999987632222111       777888999999999


Q ss_pred             HHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHH
Q 042593          118 EALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFE  196 (352)
Q Consensus       118 ~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  196 (352)
                      +|...+++..+..   |+. ..+..++..+...|++++|...+++..+...+. ++..+..+..++...|+.++|...++
T Consensus       390 eAi~~~~~Al~l~---P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~-~~~~~~~la~~l~~~G~~~eA~~~~~  465 (553)
T PRK12370        390 EALQTINECLKLD---PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQD-NPILLSMQVMFLSLKGKHELARKLTK  465 (553)
T ss_pred             HHHHHHHHHHhcC---CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhcccc-CHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            9999999995533   432 233344555667899999999999987664332 56667788889999999999999999


Q ss_pred             HhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          197 DTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       197 ~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ++....|+ ....+.+...|+..|  ++|...++.+.+.
T Consensus       466 ~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~  502 (553)
T PRK12370        466 EISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLES  502 (553)
T ss_pred             HhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHH
Confidence            98666555 444566666778877  4888878776653

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

Probab=99.12  E-value=9.2e-08  Score=82.50  Aligned_cols=193  Identities=11%  Similarity=0.012  Sum_probs=142.1

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCC---chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQS---HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWT  104 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~  104 (352)
                      +....+.-...++++|+.+|++..+.. +-   |..+|+.++-.-..+.++.--....-.+.+-.+.|          +.
T Consensus       266 ~~~A~~~y~~rDfD~a~s~Feei~knD-PYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ET----------CC  334 (559)
T KOG1155|consen  266 TQIAAASYNQRDFDQAESVFEEIRKND-PYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPET----------CC  334 (559)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccc----------ee
Confidence            333344456889999999999999874 22   66788877765544444433222222333334445          56


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ++.+-|+-.++.++|...|++.++.   .|. ...|+.+..-|...++...|..-++..++....  |-..|-.|.++|.
T Consensus       335 iIaNYYSlr~eHEKAv~YFkRALkL---Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~--DyRAWYGLGQaYe  409 (559)
T KOG1155|consen  335 IIANYYSLRSEHEKAVMYFKRALKL---NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPR--DYRAWYGLGQAYE  409 (559)
T ss_pred             eehhHHHHHHhHHHHHHHHHHHHhc---CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCch--hHHHHhhhhHHHH
Confidence            6667788888899999999888542   233 457888888888889999999988888876544  7788888889998


Q ss_pred             hhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC
Q 042593          184 KCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGL  236 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  236 (352)
                      -.+...-|+-.|++...-.| |...|.+|-.+|.+.++.++|...|++....|-
T Consensus       410 im~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d  463 (559)
T KOG1155|consen  410 IMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD  463 (559)
T ss_pred             HhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc
Confidence            88888888888888765544 788899999999999999999999988887653

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.12  E-value=4.8e-09  Score=94.28  Aligned_cols=243  Identities=13%  Similarity=0.084  Sum_probs=177.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCCC-------CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhc--
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPER-------NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC--  129 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--  129 (352)
                      ..+...|...|...|+++.|+.+++...+.       +......+      .+.+...|...+++++|..+|+++..-  
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  272 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASM------LNILALVYRSLGKYDEAVNLYEEALTIRE  272 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHH------HHHHHHHHHHhccHHHHHHHHHHHHHHHH
Confidence            467777999999999999999999986531       22221222      556778899999999999999998321  


Q ss_pred             --cC-CCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhc-----CCCCCc-hhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          130 --EY-TEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKR-----GFNAFD-IHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       130 --~~-~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                        .| -.|.. .+++.|..+|.+.|++++|...++...+.     |..++. ...++.+...++..++++.|..+++...
T Consensus       273 ~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al  352 (508)
T KOG1840|consen  273 EVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKAL  352 (508)
T ss_pred             HhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence              22 23333 37888888999999999998887776532     222212 2355677888999999999999998743


Q ss_pred             cC--------CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHH
Q 042593          200 VD--------RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGC  270 (352)
Q Consensus       200 ~~--------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~  270 (352)
                      +.        .+ -..+++.|-..|...|++++|++++++.+...                 +..... ...-....++.
T Consensus       353 ~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~-----------------~~~~~~-~~~~~~~~l~~  414 (508)
T KOG1840|consen  353 KIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQIL-----------------RELLGK-KDYGVGKPLNQ  414 (508)
T ss_pred             HHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHH-----------------HhcccC-cChhhhHHHHH
Confidence            32        21 24779999999999999999999999976521                 111110 12223567888


Q ss_pred             HHHHHHHcCChhHHHHHHhcCCCC-------C-CCchhhHHHHHHHHhcccccCcccccccch
Q 042593          271 LIDILERAGRLEQAEEVASGIPSQ-------I-TNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       271 li~~~~~~g~~~~A~~~~~~m~~~-------~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      |...|.+.++.++|.++|.+....       . ....+|..|...|-..|++++|+++....+
T Consensus       415 la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  415 LAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            999999999999999998765432       2 334689999999999999999999877654

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

Probab=99.11  E-value=6.2e-09  Score=96.93  Aligned_cols=81  Identities=15%  Similarity=0.163  Sum_probs=63.5

Q ss_pred             hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCccccccc
Q 042593          245 GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQ  323 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~  323 (352)
                      .+.|+++|.+.++.  .+-|...-|-+.-.++..|++.+|..+|...++. ..+..+|-.+...|+.+|++..|++.+..
T Consensus       628 ~~KAlq~y~kvL~~--dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~  705 (1018)
T KOG2002|consen  628 QEKALQLYGKVLRN--DPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYEN  705 (1018)
T ss_pred             HHHHHHHHHHHHhc--CcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHH
Confidence            67778888877763  3446777788888888899999999999888766 44667888889999999999988888877


Q ss_pred             chhh
Q 042593          324 RLFF  327 (352)
Q Consensus       324 ~~~~  327 (352)
                      .+..
T Consensus       706 ~lkk  709 (1018)
T KOG2002|consen  706 CLKK  709 (1018)
T ss_pred             HHHH
Confidence            6543

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

Probab=99.08  E-value=1.5e-07  Score=84.53  Aligned_cols=295  Identities=12%  Similarity=0.043  Sum_probs=226.3

Q ss_pred             CCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCC--chhhHHHHHHHHHhcCChhHHHHHhccCCCC---C
Q 042593           15 HSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQS--HVYVNTALGDMYVSLGFLKDSSKLFDELPER---N   89 (352)
Q Consensus        15 ~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~   89 (352)
                      .|+.-   |...|-.=...|-+.|.+-.++.+....+..|+.-  -..||+.-...|.+.+.++-|..+|....+-   +
T Consensus       473 ngv~i---~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp~k  549 (913)
T KOG0495|consen  473 NGVEI---NRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFPCK  549 (913)
T ss_pred             cceee---cHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhccch
Confidence            55566   66667677777777777777777777777777643  2357777777788888888888888877652   2


Q ss_pred             chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC
Q 042593           90 LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus        90 ~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  169 (352)
                      ...          |......--..|..++...+|++....  .+-....|.......-..|++..|..++.+.-+.... 
T Consensus       550 ~sl----------Wlra~~~ek~hgt~Esl~Allqkav~~--~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-  616 (913)
T KOG0495|consen  550 KSL----------WLRAAMFEKSHGTRESLEALLQKAVEQ--CPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-  616 (913)
T ss_pred             hHH----------HHHHHHHHHhcCcHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-
Confidence            233          777766667778888888999888332  2234445666677777889999999999998887644 


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----  244 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----  244 (352)
                       +...|-.-+.....+.+++.|..+|.+.....|+...|..-+..---.++.++|.+++++-++.  -|+-.-+.     
T Consensus       617 -seeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQ  693 (913)
T KOG0495|consen  617 -SEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQ  693 (913)
T ss_pred             -cHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhH
Confidence             7889999999999999999999999999878899888888888778889999999999887764  34432222     


Q ss_pred             -------hHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhccccc
Q 042593          245 -------GEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFF  315 (352)
Q Consensus       245 -------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~  315 (352)
                             .+.|...|..=.   ...| ....|-.|.+.=-+.|.+-+|..++++..-+ +.|...|-..|..=.+.|+.+
T Consensus       694 i~e~~~~ie~aR~aY~~G~---k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~  770 (913)
T KOG0495|consen  694 IEEQMENIEMAREAYLQGT---KKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKE  770 (913)
T ss_pred             HHHHHHHHHHHHHHHHhcc---ccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHH
Confidence                   444444443322   2234 4557777888888999999999999998877 788899999999999999999


Q ss_pred             CcccccccchhhhhhH
Q 042593          316 SPITLNSQRLFFFPAA  331 (352)
Q Consensus       316 ~a~~~~~~~~~~~~~~  331 (352)
                      .|..++.++++.+|.+
T Consensus       771 ~a~~lmakALQecp~s  786 (913)
T KOG0495|consen  771 QAELLMAKALQECPSS  786 (913)
T ss_pred             HHHHHHHHHHHhCCcc
Confidence            9999999999999876

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

Probab=99.07  E-value=6.7e-08  Score=89.58  Aligned_cols=295  Identities=11%  Similarity=-0.002  Sum_probs=211.7

Q ss_pred             CCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHH
Q 042593           21 LFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGL  100 (352)
Q Consensus        21 ~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~  100 (352)
                      |++...|-+|...+-..|+.+.+...+-...-. .+.|...|..+.+...+.|+++.|.-.|.+..+.++..|-.     
T Consensus       170 p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL-~p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~p~n~~~-----  243 (895)
T KOG2076|consen  170 PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHL-NPKDYELWKRLADLSEQLGNINQARYCYSRAIQANPSNWEL-----  243 (895)
T ss_pred             ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhc-CCCChHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcchHH-----
Confidence            347788999999999999999887654333322 25577899999999999999999999999998754444333     


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh----hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI----TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSN  176 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  176 (352)
                        +---...|-+.|+...|.+-|.++....+ +.|..    +.-.+++.+...++.+.|.+.++.....+....+...++
T Consensus       244 --~~ers~L~~~~G~~~~Am~~f~~l~~~~p-~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~n  320 (895)
T KOG2076|consen  244 --IYERSSLYQKTGDLKRAMETFLQLLQLDP-PVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEASLEDLN  320 (895)
T ss_pred             --HHHHHHHHHHhChHHHHHHHHHHHHhhCC-chhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHH
Confidence              44455678899999999999999955433 22222    334556677778888888888887776433322677889


Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccC------------------------CCCHhhHH----HHHHHHHcCCCHHHHHHHH
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVD------------------------RKNLVSWT----TIISGFAMHGMGKEAVENF  228 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~------------------------~~~~~~~~----~li~~~~~~~~~~~a~~~~  228 (352)
                      .++..|.+...++.|......+...                        .|+...|+    .++-++...+..+....+.
T Consensus       321 i~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll  400 (895)
T KOG2076|consen  321 ILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALL  400 (895)
T ss_pred             HHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhcccccchHHHHH
Confidence            9999999999999998888776540                        11111121    1223344444455555555


Q ss_pred             HHHHhcCCCCCcchhh-------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-
Q 042593          229 ERMQKVGLKPNRSWRI-------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-  294 (352)
Q Consensus       229 ~~m~~~~~~p~~~~~~-------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  294 (352)
                      ....+..+.|....-.             +++|+.++..+... ...-+...|-.+..+|...|..++|.+.++..... 
T Consensus       401 ~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~-~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~  479 (895)
T KOG2076|consen  401 HFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNR-EGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILA  479 (895)
T ss_pred             HHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcC-ccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            5555655444433222             88899999888876 22234678889999999999999999999988777 


Q ss_pred             CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          295 ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       295 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      +-+.-.--+|-.-+...|+.++|.+...+..
T Consensus       480 p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  480 PDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             CCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            5566677777788889999999998888753

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

Probab=99.06  E-value=2.7e-08  Score=86.21  Aligned_cols=206  Identities=13%  Similarity=-0.032  Sum_probs=125.9

Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHH
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASK  193 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  193 (352)
                      |+.-.|..-|+.......-.++  .|--+..+|....+.++....|+.....+..  ++.+|..-...+.-.++++.|..
T Consensus       340 g~~~~a~~d~~~~I~l~~~~~~--lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~--n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  340 GDSLGAQEDFDAAIKLDPAFNS--LYIKRAAAYADENQSEKMWKDFNKAEDLDPE--NPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             CCchhhhhhHHHHHhcCcccch--HHHHHHHHHhhhhccHHHHHHHHHHHhcCCC--CCchhHhHHHHHHHHHHHHHHHH
Confidence            4555555555555222211111  1555556677777777777777776665544  56666666666666677777777


Q ss_pred             HHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHhHHHHHHHHHHh---
Q 042593          194 LFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEEGLKFFDKMVEE---  258 (352)
Q Consensus       194 ~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~a~~~~~~m~~~---  258 (352)
                      =|++.....| ++..|-.+.-+..+.+++++++..|++.++. ++.....++           ++.|.+.|+..++.   
T Consensus       416 DF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~  494 (606)
T KOG0547|consen  416 DFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPR  494 (606)
T ss_pred             HHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccc
Confidence            7776655544 4555666666666667777777777776654 222222222           66666666665543   


Q ss_pred             -cCCC--CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          259 -CEVL--PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       259 -~~~~--p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                       +++.  +.+.+--.++..-.+ +++..|.++++...+. +.....|.+|...-+..|+.++|+++|....
T Consensus       495 ~~~~~v~~~plV~Ka~l~~qwk-~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  495 EHLIIVNAAPLVHKALLVLQWK-EDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             cccccccchhhhhhhHhhhchh-hhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence             0111  112222233333333 8889999999888877 6667788888888899999999998888764

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

Probab=99.05  E-value=7e-09  Score=95.67  Aligned_cols=248  Identities=13%  Similarity=0.079  Sum_probs=166.1

Q ss_pred             HHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHH
Q 042593           45 QLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFR  124 (352)
Q Consensus        45 ~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~  124 (352)
                      .++..+...|+.||..||..+|.-||..|+++.|- +|.-|+-++..+-..+      ++.++.+...+++.+.+.    
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~v------f~~lv~sh~~And~Enpk----   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGV------FRGLVASHKEANDAENPK----   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchh------HHHHHhcccccccccCCC----
Confidence            56778889999999999999999999999999999 9998876443332222      888888888888776553    


Q ss_pred             HhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHH-------hcCCCCC-------------chhhHHHHHHHHHh
Q 042593          125 RMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGE-------KRGFNAF-------------DIHVSNCLIDTYAK  184 (352)
Q Consensus       125 ~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~-------~~~~~~~-------------~~~~~~~li~~~~~  184 (352)
                              .|...||..++.+|...||+..-..+-+.+.       ..|...+             ....-...+....-
T Consensus        80 --------ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~  151 (1088)
T KOG4318|consen   80 --------EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVL  151 (1088)
T ss_pred             --------CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHH
Confidence                    6888899999999999999765332222222       2232210             11111233444445


Q ss_pred             hCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHhHHHHHH
Q 042593          185 CGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEEGLKFFD  253 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~a~~~~~  253 (352)
                      .|-++.+++++..+.....+. ++..+++-+....  ....++.+..+...-.|+..++.           .+.|..++.
T Consensus       152 eglwaqllkll~~~Pvsa~~~-p~~vfLrqnv~~n--tpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~  228 (1088)
T KOG4318|consen  152 EGLWAQLLKLLAKVPVSAWNA-PFQVFLRQNVVDN--TPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLY  228 (1088)
T ss_pred             HHHHHHHHHHHhhCCcccccc-hHHHHHHHhccCC--chHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHH
Confidence            556666666666554331111 1111233332222  22333333332221147766666           899999999


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhhHHHHHHHHhcccccCcc
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVWRTGFLRLLINSYFFSPI  318 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~~~li~~~~~~g~~~~a~  318 (352)
                      .|++. |++.+..-|..|+-+   .|+...++.+++.|...  .|+..|+...+..+..+|+...+-
T Consensus       229 emke~-gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~~~~  291 (1088)
T KOG4318|consen  229 EMKEK-GFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTKYGE  291 (1088)
T ss_pred             HHHHc-CCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhhhcc
Confidence            99999 999998877777765   88888999999999887  899999999888888877644433

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

Probab=98.98  E-value=7.3e-07  Score=76.04  Aligned_cols=294  Identities=9%  Similarity=-0.034  Sum_probs=210.7

Q ss_pred             CcccHHHHHHHHHh--cCCcchHHHHHHHHHHh-CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVT--LSYPNLGTQLHAVFSKV-GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~--~g~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~   99 (352)
                      +-.+....+.+++.  .++-..+...+-.+... -++-|++....+.+++...|+.++|+..|++...-|+.+..++   
T Consensus       193 ~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~M---  269 (564)
T KOG1174|consen  193 HFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAM---  269 (564)
T ss_pred             CccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhH---
Confidence            55556666666654  44444455555444433 4566888999999999999999999999998776444432221   


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                       ..|..|   +.+.|+.+....+...+....  .-+...|..-.......++++.|..+-+...+.+..  +...+-.-.
T Consensus       270 -D~Ya~L---L~~eg~~e~~~~L~~~Lf~~~--~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r--~~~alilKG  341 (564)
T KOG1174|consen  270 -DLYAVL---LGQEGGCEQDSALMDYLFAKV--KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPR--NHEALILKG  341 (564)
T ss_pred             -HHHHHH---HHhccCHhhHHHHHHHHHhhh--hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcc--cchHHHhcc
Confidence             114444   456788887777777762211  122333444444555678888898888887766544  566666667


Q ss_pred             HHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-------------h
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-------------G  245 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-------------~  245 (352)
                      +++...|+.+.|.=.|+....-. -+...|.-|+++|...|++.+|.-+-+...+. +..+..+..             -
T Consensus       342 ~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~r  420 (564)
T KOG1174|consen  342 RLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMR  420 (564)
T ss_pred             HHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhH
Confidence            78889999999999999876555 58899999999999999999998877765442 122222222             6


Q ss_pred             HhHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          246 EEGLKFFDKMVEECEVLPD-IKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       246 ~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      +.|..++++-.   .+.|+ ....+.+...+...|+.+++..++++.....||....+.|...+.....+++|++.+.-+
T Consensus       421 EKAKkf~ek~L---~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~A  497 (564)
T KOG1174|consen  421 EKAKKFAEKSL---KINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKA  497 (564)
T ss_pred             HHHHHHHHhhh---ccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            77888888755   34554 346677888899999999999999987766899999999999999999999999988887


Q ss_pred             hhhhhhH
Q 042593          325 LFFFPAA  331 (352)
Q Consensus       325 ~~~~~~~  331 (352)
                      +..-|..
T Consensus       498 Lr~dP~~  504 (564)
T KOG1174|consen  498 LRQDPKS  504 (564)
T ss_pred             HhcCccc
Confidence            7655544

>PF12854 PPR_1: PPR repeat

Probab=98.98  E-value=6.7e-10  Score=60.99  Aligned_cols=34  Identities=29%  Similarity=0.443  Sum_probs=26.5

Q ss_pred             hCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           53 VGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        53 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      +|++||..|||+||++||+.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3677888888888888888888888888887774

>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=98.97  E-value=3.4e-08  Score=83.80  Aligned_cols=246  Identities=12%  Similarity=0.024  Sum_probs=131.9

Q ss_pred             HHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhc
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRM  113 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~  113 (352)
                      .--.|++..++.-.+ .....-+.+...-.-+.+++...|+.+.++.-...-..|....          ...+...+...
T Consensus        11 ~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl~ei~~~~~~~l~a----------v~~la~y~~~~   79 (290)
T PF04733_consen   11 QFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVLSEIKKSSSPELQA----------VRLLAEYLSSP   79 (290)
T ss_dssp             HHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHHHHS-TTSSCCCHH----------HHHHHHHHCTS
T ss_pred             HHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHHHHhccCCChhHHH----------HHHHHHHHhCc
Confidence            334566666654444 1111111223344456677777777776665555544455554          32222222222


Q ss_pred             CCHHHHHHHHHHhHhccCCC-CChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHH
Q 042593          114 NRSNEALALFRRMAACEYTE-PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSAS  192 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~-p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  192 (352)
                      ++-+.++.-+++. -..... .+..........+...|++++|.+++...      . +.......+.+|.+.++++.|.
T Consensus        80 ~~~e~~l~~l~~~-~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~-~lE~~al~Vqi~L~~~R~dlA~  151 (290)
T PF04733_consen   80 SDKESALEELKEL-LADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------G-SLELLALAVQILLKMNRPDLAE  151 (290)
T ss_dssp             TTHHCHHHHHHHC-CCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------T-CHHHHHHHHHHHHHTT-HHHHH
T ss_pred             cchHHHHHHHHHH-HHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------C-cccHHHHHHHHHHHcCCHHHHH
Confidence            3444444444443 222222 22222333334455667777777666532      2 5566667777788888888888


Q ss_pred             HHHHHhccCCCCHhhHH---HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHH
Q 042593          193 KLFEDTSVDRKNLVSWT---TIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYG  269 (352)
Q Consensus       193 ~~~~~~~~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~  269 (352)
                      +.++.|.+...|....+   +.+......+++++|..+|+++.+                          ...+++.+.+
T Consensus       152 k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~--------------------------~~~~t~~~ln  205 (290)
T PF04733_consen  152 KELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSD--------------------------KFGSTPKLLN  205 (290)
T ss_dssp             HHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHC--------------------------CS--SHHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHh--------------------------ccCCCHHHHH
Confidence            88887766555543322   222222223457777777777655                          4456777777


Q ss_pred             HHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccC-cccccccc
Q 042593          270 CLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFS-PITLNSQR  324 (352)
Q Consensus       270 ~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~  324 (352)
                      .+..+....|++++|++++.+.... +.+..+...++......|+..+ +.++..+.
T Consensus       206 g~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL  262 (290)
T PF04733_consen  206 GLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQL  262 (290)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            7778888888888888887776655 5566666667777777777643 33344443

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.

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

Probab=98.97  E-value=4.2e-07  Score=77.16  Aligned_cols=237  Identities=15%  Similarity=0.081  Sum_probs=173.6

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHH-
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLV-  101 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~-  101 (352)
                      +...+-+..+.....|+.+.|..-.+++.+.+ +.++........+|.+.|++....++..++.+.+..+-..+.+-=- 
T Consensus       152 ~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~  230 (400)
T COG3071         152 TLAVELTRARLLLNRRDYPAARENVDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQ  230 (400)
T ss_pred             hHHHHHHHHHHHHhCCCchhHHHHHHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHH
Confidence            44455555666667777777777777777766 5566777788888888888888888888887632211111000000 


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      +|+.+++-....+..+.-...++......  +-+...-.+++.-+.+.|+.++|.++.++..+.+..+ +    -...-.
T Consensus       231 a~~glL~q~~~~~~~~gL~~~W~~~pr~l--r~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~-~----L~~~~~  303 (400)
T COG3071         231 AWEGLLQQARDDNGSEGLKTWWKNQPRKL--RNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDP-R----LCRLIP  303 (400)
T ss_pred             HHHHHHHHHhccccchHHHHHHHhccHHh--hcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccCh-h----HHHHHh
Confidence            28888888888888888777888873332  3445566678888999999999999999999998876 4    222334


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      +.+-++.+.-++..+.-.+. +-++..+.+|-..|.+++.|.+|.+.|+...                           .
T Consensus       304 ~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl---------------------------~  356 (400)
T COG3071         304 RLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAAL---------------------------K  356 (400)
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHH---------------------------h
Confidence            45667777777777765544 3456788899999999999999999999665                           4


Q ss_pred             CCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          261 VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      ..|+..+|+-+.+++.+.|+..+|.++.++....
T Consensus       357 ~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         357 LRPSASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            5689999999999999999999999998876533

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

Probab=98.96  E-value=3.7e-07  Score=80.70  Aligned_cols=251  Identities=11%  Similarity=0.034  Sum_probs=186.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      ....+-.=|..+.+.|+..+-..+=..|++.- |..+.+|-++...|...|+.++|++.|.+...-|..--.+       
T Consensus       277 h~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpa-------  348 (611)
T KOG1173|consen  277 HLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPA-------  348 (611)
T ss_pred             CcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHH-------
Confidence            56667777777778888777666666676654 6677888888888888899999999998876533321111       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |-...++|+-.|..+.|+..|...-+.  .+-....+.-+..-|.+.++.+.|.+++.+....  .|.|+.+.+-+.-..
T Consensus       349 Wl~fghsfa~e~EhdQAmaaY~tAarl--~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai--~P~Dplv~~Elgvva  424 (611)
T KOG1173|consen  349 WLAFGHSFAGEGEHDQAMAAYFTAARL--MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALAI--APSDPLVLHELGVVA  424 (611)
T ss_pred             HHHHhHHhhhcchHHHHHHHHHHHHHh--ccCCcchHHHHHHHHHHhccHHHHHHHHHHHHhc--CCCcchhhhhhhhee
Confidence            788888888999999998888876221  1112223444555677888999999999887654  444788888887777


Q ss_pred             HhhCChHHHHHHHHHhccC-------CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVD-------RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDK  254 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~  254 (352)
                      -..+.+.+|...|+.....       .+ ...+++.|-++|.+.+++++|+..+++.+..                    
T Consensus       425 y~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l--------------------  484 (611)
T KOG1173|consen  425 YTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL--------------------  484 (611)
T ss_pred             ehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc--------------------
Confidence            7788899999888875422       12 4466888889999999999999999987763                    


Q ss_pred             HHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhc
Q 042593          255 MVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLIN  311 (352)
Q Consensus       255 m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~  311 (352)
                            .+-+..++.++.-.|...|+++.|.+.|.+.....|+..+-..++..++..
T Consensus       485 ------~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  485 ------SPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAIED  535 (611)
T ss_pred             ------CCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHHHh
Confidence                  234788899999999999999999999998876677777777777655544

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

Probab=98.95  E-value=7.8e-08  Score=82.78  Aligned_cols=266  Identities=10%  Similarity=0.001  Sum_probs=126.0

Q ss_pred             HHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh--cCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHH
Q 042593           32 RTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS--LGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDG  109 (352)
Q Consensus        32 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~--~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~  109 (352)
                      ..+.+.|+++.|.+++..+.+..-+.-...-+.|-..+.-  -.++.+|.+.-+....-|...-.+       ...--+.
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a-------~~nkgn~  499 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAA-------LTNKGNI  499 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHH-------hhcCCce
Confidence            4577888999988888877665433222222222222221  123444444443333211100000       0000111


Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChH
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIF  189 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  189 (352)
                      ....|++++|.+.|++.+. ....-....| .+--.+...|++++|...|-.+...-..  +..+.-.+.+.|-...+..
T Consensus       500 ~f~ngd~dka~~~ykeal~-ndasc~ealf-niglt~e~~~~ldeald~f~klh~il~n--n~evl~qianiye~led~a  575 (840)
T KOG2003|consen  500 AFANGDLDKAAEFYKEALN-NDASCTEALF-NIGLTAEALGNLDEALDCFLKLHAILLN--NAEVLVQIANIYELLEDPA  575 (840)
T ss_pred             eeecCcHHHHHHHHHHHHc-CchHHHHHHH-HhcccHHHhcCHHHHHHHHHHHHHHHHh--hHHHHHHHHHHHHHhhCHH
Confidence            1234555555555555411 1100001111 1122233445555555444433222111  4444444445555555555


Q ss_pred             HHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC-cchhh-----------hHhHHHHHHHHH
Q 042593          190 SASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN-RSWRI-----------GEEGLKFFDKMV  256 (352)
Q Consensus       190 ~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~-----------~~~a~~~~~~m~  256 (352)
                      .|.+++-+.... +.|+.....|...|-+.|+-..|++.+-+--+  .-|. ..+..           ++.++.+|++..
T Consensus       576 qaie~~~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyr--yfp~nie~iewl~ayyidtqf~ekai~y~ekaa  653 (840)
T KOG2003|consen  576 QAIELLMQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR--YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA  653 (840)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc--ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            555555444333 22444445555555555555555444332111  1111 11100           344444444332


Q ss_pred             HhcCCCCChhhHHHHHHHH-HHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhccc
Q 042593          257 EECEVLPDIKHYGCLIDIL-ERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSY  313 (352)
Q Consensus       257 ~~~~~~p~~~~~~~li~~~-~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~  313 (352)
                         -+.|++.-|..+|..| .+.|++++|.++++.+.++ +.|.....-|+.-+...|-
T Consensus       654 ---liqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  654 ---LIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             ---hcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence               4678999998887655 5789999999999999888 7777777777776655553

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

Probab=98.95  E-value=3.9e-08  Score=91.79  Aligned_cols=262  Identities=12%  Similarity=0.020  Sum_probs=162.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh---CCCCchh-------hHHHHHHHHHhcCChhHHHHHhccCCCCCchh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV---GFQSHVY-------VNTALGDMYVSLGFLKDSSKLFDELPERNLVT   92 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~-------~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~   92 (352)
                      -+...|.+...+...|++..|...|......   ...++..       -|| |..++-..++.+.|.+.|..+.+..+.-
T Consensus       451 p~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN-larl~E~l~~~~~A~e~Yk~Ilkehp~Y  529 (1018)
T KOG2002|consen  451 PPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN-LARLLEELHDTEVAEEMYKSILKEHPGY  529 (1018)
T ss_pred             CHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH-HHHHHHhhhhhhHHHHHHHHHHHHCchh
Confidence            5677777777777788888888777776654   1122221       232 3444445567777777777776522211


Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch
Q 042593           93 WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI  172 (352)
Q Consensus        93 ~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  172 (352)
                          |++   |-.+....-..+...+|...+++......-.|+  .++.+.+.+.+...+..|..-+....+.-...+|+
T Consensus       530 ----Id~---ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~--arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~  600 (1018)
T KOG2002|consen  530 ----IDA---YLRLGCMARDKNNLYEASLLLKDALNIDSSNPN--ARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDA  600 (1018)
T ss_pred             ----HHH---HHHhhHHHHhccCcHHHHHHHHHHHhcccCCcH--HHHHHHHHHHhhhhhcccccHHHHHHhhhccCCch
Confidence                111   333332333446777788888777444443343  44455556667777777777666555443222255


Q ss_pred             hhHHHHHHHHHh------------hCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Q 042593          173 HVSNCLIDTYAK------------CGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN  239 (352)
Q Consensus       173 ~~~~~li~~~~~------------~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~  239 (352)
                      ...-+|.+.|..            .+..++|+++|.+..+. +.|...-|-+.-.++..|++.+|..+|.++.+....-.
T Consensus       601 YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~  680 (1018)
T KOG2002|consen  601 YSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFE  680 (1018)
T ss_pred             hHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCC
Confidence            555555554442            34567788888877665 44777778787888888888888888888887654222


Q ss_pred             cchhh----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          240 RSWRI----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       240 ~~~~~----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      ..+.+          +..|.+.|+...+.+.-.-+....+.|.+++.++|++.+|.+.+......
T Consensus       681 dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  681 DVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             ceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            22222          77777777776666455556677777788888888888887776555544

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

Probab=98.94  E-value=5.2e-07  Score=71.14  Aligned_cols=195  Identities=13%  Similarity=-0.071  Sum_probs=150.0

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHh
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVK  102 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~  102 (352)
                      +.-.+.-.|.+.|+...|.+-+++..+.. +.+..++..+...|.+.|..+.|.+-|++..+  | +...          
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdV----------  105 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDV----------  105 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccch----------
Confidence            45556677888899999999999888877 55667888889999999999999999988664  3 3333          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      .|..-.-+|..|++++|...|++........--..||..+.-+..+.|+.+.|...+++..+....  ...+...+.+..
T Consensus       106 LNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~--~~~~~l~~a~~~  183 (250)
T COG3063         106 LNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ--FPPALLELARLH  183 (250)
T ss_pred             hhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC--CChHHHHHHHHH
Confidence            555555678888999999999988443333333458888888888899999999999988887654  566777888888


Q ss_pred             HhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+.|++-.|...++..... .++..+.-..|..-...|+.+.+-+.=..+.+
T Consensus       184 ~~~~~y~~Ar~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r  235 (250)
T COG3063         184 YKAGDYAPARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQR  235 (250)
T ss_pred             HhcccchHHHHHHHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            8899999999988887655 56666666677777788888888777666665

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

Probab=98.93  E-value=6e-08  Score=83.46  Aligned_cols=260  Identities=11%  Similarity=0.005  Sum_probs=181.7

Q ss_pred             HHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHH
Q 042593           67 DMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAI  146 (352)
Q Consensus        67 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~  146 (352)
                      .-+.+.|+++.|.++++-..+.|..+-++-..    --+.+.-+..-.++..|.+.-+......  .-+....+.--+..
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~----nl~~l~flqggk~~~~aqqyad~aln~d--ryn~~a~~nkgn~~  500 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAAN----NLCALRFLQGGKDFADAQQYADIALNID--RYNAAALTNKGNIA  500 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhh----hhHHHHHHhcccchhHHHHHHHHHhccc--ccCHHHhhcCCcee
Confidence            35679999999999999888766655433321    1122222223447777777666652222  22333344444455


Q ss_pred             HhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHH
Q 042593          147 WKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAV  225 (352)
Q Consensus       147 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~  225 (352)
                      ...|++++|...|++.....-.. ....||+ .-.+-..|++++|+++|-++... .-++...-.+...|-...+...|.
T Consensus       501 f~ngd~dka~~~ykeal~ndasc-~ealfni-glt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqai  578 (840)
T KOG2003|consen  501 FANGDLDKAAEFYKEALNNDASC-TEALFNI-GLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAI  578 (840)
T ss_pred             eecCcHHHHHHHHHHHHcCchHH-HHHHHHh-cccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHH
Confidence            67899999999999998775443 4444543 33567889999999999887433 456777777888888889999999


Q ss_pred             HHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          226 ENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       226 ~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      +++.+...  +.|+.....            ..+|++.+-.--+  -++-+..+...|...|....-+++|...|++..-
T Consensus       579 e~~~q~~s--lip~dp~ilskl~dlydqegdksqafq~~ydsyr--yfp~nie~iewl~ayyidtqf~ekai~y~ekaal  654 (840)
T KOG2003|consen  579 ELLMQANS--LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR--YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL  654 (840)
T ss_pred             HHHHHhcc--cCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc--ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            99877654  556655443            3333333322111  3445788989999999999999999999998764


Q ss_pred             CCCCchhhHHHHHHH-HhcccccCcccccccchhhhhhHHHHhhhh
Q 042593          294 QITNVVVWRTGFLRL-LINSYFFSPITLNSQRLFFFPAALYALTQI  338 (352)
Q Consensus       294 ~~~~~~~~~~li~~~-~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  338 (352)
                      ..|+..-|..+|..| -+.|++++|+.++++.-..||-.+-++..+
T Consensus       655 iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkfl  700 (840)
T KOG2003|consen  655 IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFL  700 (840)
T ss_pred             cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHH
Confidence            489999999998875 578999999999999988888777665443

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.91  E-value=6.9e-07  Score=76.70  Aligned_cols=194  Identities=13%  Similarity=-0.064  Sum_probs=132.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |..+...+.+.|+.++|...|++..+.   .| +...|+.+...+...|++++|...++...+....  +..++..+..+
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l---~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~--~~~a~~~lg~~  141 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALAL---RPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPT--YNYAYLNRGIA  141 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHH
Confidence            777778899999999999999998442   34 4568999999999999999999999999887544  67888889999


Q ss_pred             HHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc-chhh-------hHhHHHHHH
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR-SWRI-------GEEGLKFFD  253 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~-------~~~a~~~~~  253 (352)
                      +...|++++|.+.|+......|+-.........+...++.++|...+.+..... .|+. .+..       ...+ ..+.
T Consensus       142 l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~-~~~~~~~~~~~~~lg~~~~~-~~~~  219 (296)
T PRK11189        142 LYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL-DKEQWGWNIVEFYLGKISEE-TLME  219 (296)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC-CccccHHHHHHHHccCCCHH-HHHH
Confidence            999999999999999987666654322222223445678999999997755432 2221 1111       2112 2333


Q ss_pred             HHHHhcCCCC-----ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHH
Q 042593          254 KMVEECEVLP-----DIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRT  303 (352)
Q Consensus       254 ~m~~~~~~~p-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~  303 (352)
                      .+.+.....|     ....|..+...+.+.|+.++|...|++.... +++-+-+..
T Consensus       220 ~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~~~e~~~  275 (296)
T PRK11189        220 RLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNVYNFVEHRY  275 (296)
T ss_pred             HHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCchHHHHHH
Confidence            3332111111     2346677777777777777777777776655 344444444

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.90  E-value=4.3e-07  Score=78.00  Aligned_cols=191  Identities=11%  Similarity=-0.070  Sum_probs=131.4

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITGL  100 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~~  100 (352)
                      ...|......+.+.|+.++|...|+...+.. +.++..|+.+...+...|++++|...|+...+  |+. ..        
T Consensus        64 a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a--------  134 (296)
T PRK11189         64 AQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYA--------  134 (296)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHH--------
Confidence            3457777778888999999999999888865 45678899999999999999999999998865  432 33        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        |..+...+...|++++|.+.|++..+.   .|+..............++.++|...++...... .+ +...+ .  .
T Consensus       135 --~~~lg~~l~~~g~~~eA~~~~~~al~~---~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~-~~-~~~~~-~--~  204 (296)
T PRK11189        135 --YLNRGIALYYGGRYELAQDDLLAFYQD---DPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL-DK-EQWGW-N--I  204 (296)
T ss_pred             --HHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC-Cc-cccHH-H--H
Confidence              777778888899999999999988442   3443322222223445678899998886654332 22 22111 2  2


Q ss_pred             HHHhhCChHHHHHHHHHhcc---C-----CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          181 TYAKCGCIFSASKLFEDTSV---D-----RKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~---~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .....|+...+ +.+..+..   .     +.....|..+...+.+.|++++|...|++..+.
T Consensus       205 ~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        205 VEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             HHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            23335555443 24443332   1     123467888889999999999999999998874

>PF12854 PPR_1: PPR repeat

Probab=98.89  E-value=2.8e-09  Score=58.50  Aligned_cols=33  Identities=33%  Similarity=0.491  Sum_probs=31.9

Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                      |+.||..||+.||.+|++.|++++|.++|++|+
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            899999999999999999999999999999985

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

Probab=98.85  E-value=1.1e-06  Score=69.30  Aligned_cols=204  Identities=12%  Similarity=-0.012  Sum_probs=115.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHH
Q 042593           62 NTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITIL  140 (352)
Q Consensus        62 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~  140 (352)
                      ..-|.-.|...|+...|.+-+++..+.|+..+.+       |..+...|.+.|+.+.|.+-|++...   +.|+ ....|
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a-------~~~~A~~Yq~~Ge~~~A~e~YrkAls---l~p~~GdVLN  107 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLA-------HLVRAHYYQKLGENDLADESYRKALS---LAPNNGDVLN  107 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHH-------HHHHHHHHHHcCChhhHHHHHHHHHh---cCCCccchhh
Confidence            3445556666666666666666666544444444       66666666666666666666666533   2232 33555


Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG  219 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~  219 (352)
                      ..-..+|..|++++|...|++....---+.-..+|..+.-+..+.|+.+.|.+.|++-....| ...+.-.+.....+.|
T Consensus       108 NYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~  187 (250)
T COG3063         108 NYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAG  187 (250)
T ss_pred             hhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcc
Confidence            555556666666666666666655433332345566666666666666666666665544433 3444555555566666


Q ss_pred             CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCch
Q 042593          220 MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVV  299 (352)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~  299 (352)
                      ++-.|...++.....                          ..++..+.-..|+.-...||.+.+.+.=..+....|...
T Consensus       188 ~y~~Ar~~~~~~~~~--------------------------~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~s~  241 (250)
T COG3063         188 DYAPARLYLERYQQR--------------------------GGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPYSE  241 (250)
T ss_pred             cchHHHHHHHHHHhc--------------------------ccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcH
Confidence            666666666665553                          225555555666666667776666555444433334443


Q ss_pred             hh
Q 042593          300 VW  301 (352)
Q Consensus       300 ~~  301 (352)
                      -+
T Consensus       242 e~  243 (250)
T COG3063         242 EY  243 (250)
T ss_pred             HH
Confidence            33

>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=98.84  E-value=4.2e-07  Score=82.84  Aligned_cols=246  Identities=16%  Similarity=0.140  Sum_probs=133.7

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDG  109 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~  109 (352)
                      -...+...|++++|++.++.-... +.-...........+.+.|+.++|..++..+.+.|+..+.-       |..+..+
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Y-------y~~L~~~   81 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDY-------YRGLEEA   81 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHH-------HHHHHHH
Confidence            345667899999999999764433 34445667888899999999999999999998744433322       5555555


Q ss_pred             HHhc-----CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCCh-hhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          110 YSRM-----NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEV-RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       110 ~~~~-----~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ..-.     .+.+...++|+++ ...-  |.......+.-.+.....+ ..+..++..+...|+++    +|+.+-..|.
T Consensus        82 ~g~~~~~~~~~~~~~~~~y~~l-~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs----lF~~lk~Ly~  154 (517)
T PF12569_consen   82 LGLQLQLSDEDVEKLLELYDEL-AEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS----LFSNLKPLYK  154 (517)
T ss_pred             HhhhcccccccHHHHHHHHHHH-HHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch----HHHHHHHHHc
Confidence            5222     3577888888888 4332  3322222222112111111 22444455555555432    4555555555


Q ss_pred             hhCChHHHHHHHHHhccC----------------CCCH--hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-
Q 042593          184 KCGCIFSASKLFEDTSVD----------------RKNL--VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-  244 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~----------------~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-  244 (352)
                      ...+.+-..+++......                .|..  .++.-+.+.|...|++++|.++.++.++.  +|+..-+. 
T Consensus       155 d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~  232 (517)
T PF12569_consen  155 DPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYM  232 (517)
T ss_pred             ChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHH
Confidence            555555555555443211                2333  23344455666677777777777766653  22211110 


Q ss_pred             -----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          245 -----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       245 -----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                                 ..+|.+..+..... . .-|...-+..+..+.++|+.++|.+++....+.
T Consensus       233 ~KarilKh~G~~~~Aa~~~~~Ar~L-D-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~  291 (517)
T PF12569_consen  233 TKARILKHAGDLKEAAEAMDEAREL-D-LADRYINSKCAKYLLRAGRIEEAEKTASLFTRE  291 (517)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhC-C-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCC
Confidence                       33333333332221 1 124445555556666666666666666555443

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 [], [].

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

Probab=98.84  E-value=3.2e-06  Score=73.47  Aligned_cols=286  Identities=10%  Similarity=0.049  Sum_probs=186.9

Q ss_pred             CCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchh
Q 042593           15 HSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVT   92 (352)
Q Consensus        15 ~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~   92 (352)
                      ....|   +...|.+.++.=.+-..++.|..+|+..+-..  |++.+|-.....=-++|.+..|.++|+...+  .|...
T Consensus       168 ~~w~P---~eqaW~sfI~fElRykeieraR~IYerfV~~H--P~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~  242 (677)
T KOG1915|consen  168 MEWEP---DEQAWLSFIKFELRYKEIERARSIYERFVLVH--PKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEE  242 (677)
T ss_pred             HcCCC---cHHHHHHHHHHHHHhhHHHHHHHHHHHHheec--ccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHH
Confidence            34678   99999999999999999999999999887643  8888888777777788888888888776543  11111


Q ss_pred             HHHHHHHHH-----------------------------------------------------------------------
Q 042593           93 WNVIITGLV-----------------------------------------------------------------------  101 (352)
Q Consensus        93 ~~~~i~~~~-----------------------------------------------------------------------  101 (352)
                      -..+.-+++                                                                       
T Consensus       243 ~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~nY  322 (677)
T KOG1915|consen  243 AEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPYNY  322 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCCCc
Confidence            122222222                                                                       


Q ss_pred             -hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-------hHHHHHHHH---HhCCChhhHHHHHHHHHhcCCCCC
Q 042593          102 -KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-------TILAVLPAI---WKNGEVRNCQLIHGYGEKRGFNAF  170 (352)
Q Consensus       102 -~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-------t~~~ll~~~---~~~~~~~~a~~~~~~~~~~~~~~~  170 (352)
                       +|--.++.-...|+.+...++|++. ... ++|-..       .|.-+=-++   ....+.+.+.++++...+.  .|.
T Consensus       323 DsWfdylrL~e~~g~~~~Ire~yErA-Ian-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l--IPH  398 (677)
T KOG1915|consen  323 DSWFDYLRLEESVGDKDRIRETYERA-IAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL--IPH  398 (677)
T ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHHH-Hcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh--cCc
Confidence             4555555556667777777777776 322 333211       111111111   2456777777777777662  332


Q ss_pred             chhhHHHH----HHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh--
Q 042593          171 DIHVSNCL----IDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI--  244 (352)
Q Consensus       171 ~~~~~~~l----i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~--  244 (352)
                      ...||..+    ...-.++.++..|.+++.......|-..+|..-|..=.+.++++.+..++++.++-+.........  
T Consensus       399 kkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~kya  478 (677)
T KOG1915|consen  399 KKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSKYA  478 (677)
T ss_pred             ccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHH
Confidence            44444433    333346677888888887776667777778777777778888888888888887754322211111  


Q ss_pred             --------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHH
Q 042593          245 --------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL  309 (352)
Q Consensus       245 --------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~  309 (352)
                              .+.|..+|...+..+.+......|-+.|+.=...|.++.|..+++++....+...+|-++..--.
T Consensus       479 ElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~h~kvWisFA~fe~  551 (677)
T KOG1915|consen  479 ELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQHVKVWISFAKFEA  551 (677)
T ss_pred             HHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcccchHHHhHHHHhc
Confidence                    77778888877776444445566777777777888888888888888766566667777665433

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

Probab=98.83  E-value=5.5e-08  Score=80.30  Aligned_cols=225  Identities=11%  Similarity=0.038  Sum_probs=172.0

Q ss_pred             HHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhh-H
Q 042593           63 TALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEIT-I  139 (352)
Q Consensus        63 ~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t-~  139 (352)
                      +-+.++|.+.|.+.+|++.|+.-.+  |-+.|          |-.|-+.|.+..++..|+.+|.+-..   .-|-.+| .
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~~~dT----------fllLskvY~ridQP~~AL~~~~~gld---~fP~~VT~l  293 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDT----------FLLLSKVYQRIDQPERALLVIGEGLD---SFPFDVTYL  293 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCCchhH----------HHHHHHHHHHhccHHHHHHHHhhhhh---cCCchhhhh
Confidence            5677888888888888888887553  56666          77778888888888888888887733   2344444 4


Q ss_pred             HHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcC
Q 042593          140 LAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMH  218 (352)
Q Consensus       140 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~  218 (352)
                      .-+.+.+-..++.+++.++|+...+....  ++....++...|--.++.+.|++.++++.+- ..+...|+.+--+|.-.
T Consensus       294 ~g~ARi~eam~~~~~a~~lYk~vlk~~~~--nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~ya  371 (478)
T KOG1129|consen  294 LGQARIHEAMEQQEDALQLYKLVLKLHPI--NVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYA  371 (478)
T ss_pred             hhhHHHHHHHHhHHHHHHHHHHHHhcCCc--cceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhh
Confidence            45666777788888888888888776543  6677777777888888888888888887655 46778888888888888


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCC
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITN  297 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~  297 (352)
                      ++++-++.-|.+....--.|+                     .  -...|-.|.......||+..|.+.|+-.... ..+
T Consensus       372 qQ~D~~L~sf~RAlstat~~~---------------------~--aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h  428 (478)
T KOG1129|consen  372 QQIDLVLPSFQRALSTATQPG---------------------Q--AADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQH  428 (478)
T ss_pred             cchhhhHHHHHHHHhhccCcc---------------------h--hhhhhhccceeEEeccchHHHHHHHHHHhccCcch
Confidence            888888888888776432221                     1  2346777777788899999999999988777 667


Q ss_pred             chhhHHHHHHHHhcccccCcccccccch
Q 042593          298 VVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       298 ~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      ...+|.|.---.+.|+.+.|..+..-+-
T Consensus       429 ~ealnNLavL~~r~G~i~~Arsll~~A~  456 (478)
T KOG1129|consen  429 GEALNNLAVLAARSGDILGARSLLNAAK  456 (478)
T ss_pred             HHHHHhHHHHHhhcCchHHHHHHHHHhh
Confidence            7899999888899999999887776553

>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=98.83  E-value=6.1e-07  Score=76.19  Aligned_cols=215  Identities=14%  Similarity=0.067  Sum_probs=126.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCC-CchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQ-SHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLV  101 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~  101 (352)
                      .......+...+....+-+.+..-++.....+.. .+..........+...|++++|+++++.-  .+...         
T Consensus        65 ~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~--~~lE~---------  133 (290)
T PF04733_consen   65 ELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG--GSLEL---------  133 (290)
T ss_dssp             CCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT--TCHHH---------
T ss_pred             hHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc--CcccH---------
Confidence            5555544444443333333333333333222222 23333333334555678888888888765  34444         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                       ....+..+.+.++++.|.+.++.| ++..  .| .+...+..++..    ...+.+|..+|+++.+. ..+ ++.+.+.
T Consensus       134 -~al~Vqi~L~~~R~dlA~k~l~~~-~~~~--eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~-t~~~lng  206 (290)
T PF04733_consen  134 -LALAVQILLKMNRPDLAEKELKNM-QQID--ED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGS-TPKLLNG  206 (290)
T ss_dssp             -HHHHHHHHHHTT-HHHHHHHHHHH-HCCS--CC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S---SHHHHHH
T ss_pred             -HHHHHHHHHHcCCHHHHHHHHHHH-HhcC--Cc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCC-CHHHHHH
Confidence             556677788888888888888888 5432  23 344444444432    34688888888887654 334 7778888


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCH-HHHHHHHHHHHhcCCCCCcchhh-hHhHHHHHHH
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMG-KEAVENFERMQKVGLKPNRSWRI-GEEGLKFFDK  254 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~~~~~p~~~~~~-~~~a~~~~~~  254 (352)
                      +..++...|++++|.+++.+.... +.|..+...++.+....|+. +.+.+.+.+++..  .|+..... ..+....|++
T Consensus       207 ~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~--~p~h~~~~~~~~~~~~FD~  284 (290)
T PF04733_consen  207 LAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS--NPNHPLVKDLAEKEAEFDR  284 (290)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH--TTTSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh--CCCChHHHHHHHHHHHHHH
Confidence            888888888888888888886555 34566777777777777776 6677777777763  34433333 4445555555


Q ss_pred             HHH
Q 042593          255 MVE  257 (352)
Q Consensus       255 m~~  257 (352)
                      ...
T Consensus       285 ~~~  287 (290)
T PF04733_consen  285 AVA  287 (290)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

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.

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

Probab=98.77  E-value=6.9e-06  Score=74.19  Aligned_cols=274  Identities=12%  Similarity=0.022  Sum_probs=197.6

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKW  103 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~  103 (352)
                      .|-...+..-..|++..|+.++....+.. +.+...|-+-+..-.....++.|..+|.+...  ++...          |
T Consensus       586 lwlM~ake~w~agdv~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~llakar~~sgTeRv----------~  654 (913)
T KOG0495|consen  586 LWLMYAKEKWKAGDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLLAKARSISGTERV----------W  654 (913)
T ss_pred             HHHHHHHHHHhcCCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchh----------h
Confidence            34444445556788888888888887765 44677788888888888888889888888764  55555          4


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      .--++.---.++.++|.+++++..+.   -|+-. .|..+...+-+.++++.|...|..-.+.  -|..+..|-.|.+.=
T Consensus       655 mKs~~~er~ld~~eeA~rllEe~lk~---fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~--cP~~ipLWllLakle  729 (913)
T KOG0495|consen  655 MKSANLERYLDNVEEALRLLEEALKS---FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK--CPNSIPLWLLLAKLE  729 (913)
T ss_pred             HHHhHHHHHhhhHHHHHHHHHHHHHh---CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc--CCCCchHHHHHHHHH
Confidence            44444444567788888888877442   35543 6777777788888888888888765443  233678888888888


Q ss_pred             HhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---------hHhHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---------GEEGLKFF  252 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---------~~~a~~~~  252 (352)
                      -+.|.+-+|..+++.-... +.|...|-..|..=.+.|+.+.|..++.+.++.  -|++....         ...-....
T Consensus       730 Ek~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe--cp~sg~LWaEaI~le~~~~rkTks~  807 (913)
T KOG0495|consen  730 EKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQE--CPSSGLLWAEAIWLEPRPQRKTKSI  807 (913)
T ss_pred             HHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccchhHHHHHHhccCcccchHHH
Confidence            8999999999999987655 457888999999999999999999998887763  23333222         11111222


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccc
Q 042593          253 DKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITL  320 (352)
Q Consensus       253 ~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~  320 (352)
                      +.++   +..-|......+...+....+++.|.+.|.+..+. +.+.-+|.-+...++.+|.-++-.++
T Consensus       808 DALk---kce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev  873 (913)
T KOG0495|consen  808 DALK---KCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEV  873 (913)
T ss_pred             HHHH---hccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHH
Confidence            2232   23446677778888899999999999999988877 66778899999999999965544333

>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=98.76  E-value=2.6e-06  Score=77.71  Aligned_cols=250  Identities=9%  Similarity=-0.007  Sum_probs=156.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC-----ChhHHHHHhccCCC--C-------
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG-----FLKDSSKLFDELPE--R-------   88 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g-----~~~~a~~~~~~m~~--~-------   88 (352)
                      ...........+.+.|+.++|..+|..+++.+ |.|..-|..|..+..-..     +.+...++|+++.+  |       
T Consensus        37 k~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN-Pdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~r  115 (517)
T PF12569_consen   37 KLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-PDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRR  115 (517)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhH
Confidence            34556677788889999999999999999988 444455666666653332     46677788887753  1       


Q ss_pred             ------CchhHHHHHHHHH----------hHHHHHHHHHhcCCHHHHHHHHHHhHhc---cC----------CCCChh--
Q 042593           89 ------NLVTWNVIITGLV----------KWTGIIDGYSRMNRSNEALALFRRMAAC---EY----------TEPSEI--  137 (352)
Q Consensus        89 ------~~~~~~~~i~~~~----------~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~----------~~p~~~--  137 (352)
                            +...+...+..++          .|+.|-..|....+.+-..+++......   .+          -.|+..  
T Consensus       116 l~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw  195 (517)
T PF12569_consen  116 LPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLW  195 (517)
T ss_pred             hhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHH
Confidence                  1112222222222          4555555555555555555555554211   11          123332  


Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~  216 (352)
                      ++..+...|-..|++++|..++++..++.+.  .+..|..-.+.|-+.|++++|.+..+....- ..|-..-+..+..+.
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt--~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~L  273 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEHTPT--LVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLL  273 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC--cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHH
Confidence            3445556666778888888888777776433  5667777777777888888887777776544 345566666677777


Q ss_pred             cCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhH--HHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          217 MHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHY--GCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~--~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      +.|++++|.+++....+.+..|..                   .+.--+..|  .-...+|.+.|++..|.+-|..+.+.
T Consensus       274 Ra~~~e~A~~~~~~Ftr~~~~~~~-------------------~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~  334 (517)
T PF12569_consen  274 RAGRIEEAEKTASLFTREDVDPLS-------------------NLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLKH  334 (517)
T ss_pred             HCCCHHHHHHHHHhhcCCCCCccc-------------------CHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            788888887777777665432110                   000011122  34578899999999999999887764

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 [], [].

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

Probab=98.72  E-value=2.7e-06  Score=75.37  Aligned_cols=261  Identities=13%  Similarity=0.009  Sum_probs=192.3

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      .-++.....-.+-+-..+++.+..++++.+.+.|+..-+.       +-.-|.++...|+..+-..+=.++....  +-.
T Consensus       241 ~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~-------~~~~ia~l~el~~~n~Lf~lsh~LV~~y--P~~  311 (611)
T KOG1173|consen  241 AENLDLLAEKADRLYYGCRFKECLKITEELLEKDPFHLPC-------LPLHIACLYELGKSNKLFLLSHKLVDLY--PSK  311 (611)
T ss_pred             hhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcch-------HHHHHHHHHHhcccchHHHHHHHHHHhC--CCC
Confidence            3455555556666777889999999999988755443222       5555667888888877777766773322  234


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC--C-HhhHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK--N-LVSWTTII  212 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--~-~~~~~~li  212 (352)
                      ..+|-++..-|--.|+.++|.+.+.........  -...|-.....|+-.|..|.|...+....+--|  . +..|.  -
T Consensus       312 a~sW~aVg~YYl~i~k~seARry~SKat~lD~~--fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYl--g  387 (611)
T KOG1173|consen  312 ALSWFAVGCYYLMIGKYSEARRYFSKATTLDPT--FGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYL--G  387 (611)
T ss_pred             CcchhhHHHHHHHhcCcHHHHHHHHHHhhcCcc--ccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHH--H
Confidence            568999988888889999999999877655433  577888999999999999999888876543322  1 12222  2


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHhc-CCC----CChhhHHHHHHHH
Q 042593          213 SGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEEC-EVL----PDIKHYGCLIDIL  275 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~~-~~~----p~~~~~~~li~~~  275 (352)
                      --|.+.++.+.|.+.|.+...  +-|+.....            +.+|..+|+..+..- .+.    .-..+++.|..+|
T Consensus       388 mey~~t~n~kLAe~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~  465 (611)
T KOG1173|consen  388 MEYMRTNNLKLAEKFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAY  465 (611)
T ss_pred             HHHHHhccHHHHHHHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHH
Confidence            347788999999999988765  556554433            888888888776320 111    1334688999999


Q ss_pred             HHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          276 ERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       276 ~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      .++++.++|...++..... +.+..++.++.-.|...|+++.|+..+..++..-|.+
T Consensus       466 Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n  522 (611)
T KOG1173|consen  466 RKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDN  522 (611)
T ss_pred             HHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCcc
Confidence            9999999999999988777 7799999999999999999999999999987655544

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

Probab=98.70  E-value=1.6e-05  Score=70.33  Aligned_cols=287  Identities=7%  Similarity=-0.075  Sum_probs=173.6

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCC-CCchh-hHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGF-QSHVY-VNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITG   99 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~~~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~   99 (352)
                      ...|..+...+...|+.+.+...+....+... .++.. ........+...|++++|.+.+++..+  |+..  ..    
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~--~a----   79 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPRDL--LA----   79 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcH--HH----
Confidence            44566666667777888887766666554331 22321 222234455678999999999988764  3322  11    


Q ss_pred             HHhHHHHHHHHH----hcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593          100 LVKWTGIIDGYS----RMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus       100 ~~~~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                         ++. ...+.    ..+..+.+.+.+...   .+..|+. .....+...+...|++++|...+++..+....  +...
T Consensus        80 ---~~~-~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~--~~~~  150 (355)
T cd05804          80 ---LKL-HLGAFGLGDFSGMRDHVARVLPLW---APENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNPD--DAWA  150 (355)
T ss_pred             ---HHH-hHHHHHhcccccCchhHHHHHhcc---CcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC--CcHH
Confidence               221 11222    234455555544432   1223333 34445666788899999999999999887644  6778


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCC---CCH--hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC-CCCcchh----h
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDR---KNL--VSWTTIISGFAMHGMGKEAVENFERMQKVGL-KPNRSWR----I  244 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~---~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~----~  244 (352)
                      +..+..++...|++++|...+++.....   ++.  ..|..+...+...|++++|..++++...... .+.....    .
T Consensus       151 ~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  230 (355)
T cd05804         151 VHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAAS  230 (355)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHH
Confidence            8888999999999999999999876542   232  3455778889999999999999999864322 1111111    1


Q ss_pred             ---------hHhHHHHHHHHHHhc--CCC--CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CC---C-c---hhhHH
Q 042593          245 ---------GEEGLKFFDKMVEEC--EVL--PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-IT---N-V---VVWRT  303 (352)
Q Consensus       245 ---------~~~a~~~~~~m~~~~--~~~--p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~---~-~---~~~~~  303 (352)
                               ......-++.+....  ...  ...........++...|+.++|..+++.+... ..   . .   .+-..
T Consensus       231 ~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~  310 (355)
T cd05804         231 LLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLP  310 (355)
T ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHH
Confidence                     011111222222110  111  11122235677788999999999999887554 11   1 1   12222


Q ss_pred             HHH--HHHhcccccCcccccccch
Q 042593          304 GFL--RLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       304 li~--~~~~~g~~~~a~~~~~~~~  325 (352)
                      ++.  .+...|+.++|++.+.+.+
T Consensus       311 ~l~A~~~~~~g~~~~A~~~L~~al  334 (355)
T cd05804         311 LAEALYAFAEGNYATALELLGPVR  334 (355)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            333  4568999999999998876

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

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

Probab=98.70  E-value=6e-06  Score=71.85  Aligned_cols=270  Identities=12%  Similarity=0.040  Sum_probs=142.7

Q ss_pred             hcCCcchHHHHHHHHHHhCCCCch-hhHHHHHHHHHhcCChhHHHHHhccCC--CCCchhHHHHHHHHHhHHHHHHHHHh
Q 042593           36 TLSYPNLGTQLHAVFSKVGFQSHV-YVNTALGDMYVSLGFLKDSSKLFDELP--ERNLVTWNVIITGLVKWTGIIDGYSR  112 (352)
Q Consensus        36 ~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~m~--~~~~~~~~~~i~~~~~~~~li~~~~~  112 (352)
                      +...+..|..+++..+..=  |-+ ..|--.+..=-..|++..|.++|+.=.  +|+...          |++.|+-=.+
T Consensus       119 knk~vNhARNv~dRAvt~l--PRVdqlWyKY~ymEE~LgNi~gaRqiferW~~w~P~eqa----------W~sfI~fElR  186 (677)
T KOG1915|consen  119 KNKQVNHARNVWDRAVTIL--PRVDQLWYKYIYMEEMLGNIAGARQIFERWMEWEPDEQA----------WLSFIKFELR  186 (677)
T ss_pred             hhhhHhHHHHHHHHHHHhc--chHHHHHHHHHHHHHHhcccHHHHHHHHHHHcCCCcHHH----------HHHHHHHHHH
Confidence            4444444444444444321  211 222223333334466666666666532  367666          6667777777


Q ss_pred             cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhc-CCCCCchhhHHHHHHHHHhhCChHHH
Q 042593          113 MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKR-GFNAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      -+.++.|..+|++..-   +.|+..+|.-....=-+.|....+..+|+...+. |-...+...+.+....=.++..++.|
T Consensus       187 ykeieraR~IYerfV~---~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERa  263 (677)
T KOG1915|consen  187 YKEIERARSIYERFVL---VHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERA  263 (677)
T ss_pred             hhHHHHHHHHHHHHhe---ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777777777622   4577777777777777777777777777766543 11100122222222222223333333


Q ss_pred             HHHHHHhcc---------------------------------------------CCCCHhhHHHHHHHHHcCCCHHHHHH
Q 042593          192 SKLFEDTSV---------------------------------------------DRKNLVSWTTIISGFAMHGMGKEAVE  226 (352)
Q Consensus       192 ~~~~~~~~~---------------------------------------------~~~~~~~~~~li~~~~~~~~~~~a~~  226 (352)
                      .-+|.-..+                                             .+-|-.+|--.+..--..|+.+...+
T Consensus       264 r~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire  343 (677)
T KOG1915|consen  264 RFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRE  343 (677)
T ss_pred             HHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHH
Confidence            222221111                                             12244444445555555677777777


Q ss_pred             HHHHHHhcCCCCC-cchhh----------------------------------------------------------hHh
Q 042593          227 NFERMQKVGLKPN-RSWRI----------------------------------------------------------GEE  247 (352)
Q Consensus       227 ~~~~m~~~~~~p~-~~~~~----------------------------------------------------------~~~  247 (352)
                      +|++.... ++|- ..-+.                                                          +..
T Consensus       344 ~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~lIPHkkFtFaKiWlmyA~feIRq~~l~~  422 (677)
T KOG1915|consen  344 TYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIRQLNLTG  422 (677)
T ss_pred             HHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHcccHH
Confidence            77776654 3332 11111                                                          344


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      |.+++...+   |..|...+|...|..=.+.++++.+.+++++.... +.|-.+|.-...-=...|+.+.|..++.-+
T Consensus       423 ARkiLG~AI---G~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelA  497 (677)
T KOG1915|consen  423 ARKILGNAI---GKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELA  497 (677)
T ss_pred             HHHHHHHHh---ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            444444433   45566666666666666666666666666666555 445556666555555666666665555444

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

Probab=98.61  E-value=6.1e-06  Score=80.30  Aligned_cols=234  Identities=9%  Similarity=0.015  Sum_probs=158.4

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCC-C----CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-R----NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE  130 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~----~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  130 (352)
                      |.+...|...|......+++++|++++++... -    ...--|.       |.++++.-..-|.-+...++|++. .+.
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNi-------WiA~lNlEn~yG~eesl~kVFeRA-cqy 1526 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNI-------WIAYLNLENAYGTEESLKKVFERA-CQY 1526 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHH-------HHHHHhHHHhhCcHHHHHHHHHHH-HHh
Confidence            34455677777777788888888888887653 1    1112232       666666666667777888888888 322


Q ss_pred             CCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC---CHh
Q 042593          131 YTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK---NLV  206 (352)
Q Consensus       131 ~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~  206 (352)
                         -|. ..|..|...|.+.+..++|-++++.|.+.=- . ...+|...+..+.+.++-++|.+++.+..+.-|   .+.
T Consensus      1527 ---cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q-~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~ 1601 (1710)
T KOG1070|consen 1527 ---CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG-Q-TRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVE 1601 (1710)
T ss_pred             ---cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc-c-hhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHH
Confidence               233 3577888888888888888888888876532 2 677888888888888888888888877655433   344


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHH
Q 042593          207 SWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEE  286 (352)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~  286 (352)
                      .....+..-.+.|+.+++..+|+..+..                          .+--...|+.+|+.=.++|+.+.+..
T Consensus      1602 ~IskfAqLEFk~GDaeRGRtlfEgll~a--------------------------yPKRtDlW~VYid~eik~~~~~~vR~ 1655 (1710)
T KOG1070|consen 1602 FISKFAQLEFKYGDAERGRTLFEGLLSA--------------------------YPKRTDLWSVYIDMEIKHGDIKYVRD 1655 (1710)
T ss_pred             HHHHHHHHHhhcCCchhhHHHHHHHHhh--------------------------CccchhHHHHHHHHHHccCCHHHHHH
Confidence            4555556667778888888888877763                          23356689999999999999999999


Q ss_pred             HHhcCCCC---CCCc-hhhHHHHHHHHhcccccCcccccccchhhhh
Q 042593          287 VASGIPSQ---ITNV-VVWRTGFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       287 ~~~~m~~~---~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                      +|++....   +... ..|.-++..=-.+|+- ++++..+++-.++.
T Consensus      1656 lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde-~~vE~VKarA~EYv 1701 (1710)
T KOG1070|consen 1656 LFERVIELKLSIKKMKFFFKKWLEYEKSHGDE-KNVEYVKARAKEYV 1701 (1710)
T ss_pred             HHHHHHhcCCChhHhHHHHHHHHHHHHhcCch-hhHHHHHHHHHHHH
Confidence            99998776   2222 3445554444445554 44444444443443

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

Probab=98.60  E-value=1.7e-05  Score=76.19  Aligned_cols=250  Identities=12%  Similarity=0.011  Sum_probs=169.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      +...+..|+..+-..+++++|.++.+...+.. +-....|-.+...+...++.+++.-+  .                  
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv--~------------------   88 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL--N------------------   88 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh--h------------------
Confidence            45566677777777777777777777554433 22233333344455566665444433  1                  


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                         ++.......++.-+..+...| ...  .-+...+..+..+|-+.|+.+++..+++++.+....  ++.+.|.+...|
T Consensus        89 ---~l~~~~~~~~~~~ve~~~~~i-~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~--n~~aLNn~AY~~  160 (906)
T PRK14720         89 ---LIDSFSQNLKWAIVEHICDKI-LLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKADRD--NPEIVKKLATSY  160 (906)
T ss_pred             ---hhhhcccccchhHHHHHHHHH-Hhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcc--cHHHHHHHHHHH
Confidence               122222333343333344444 222  133457778889999999999999999999998743  899999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVL  262 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~  262 (352)
                      +.. ++++|.+.+.+.             +..+...+++.++.++|.++....  |+.    .+.-..+.+++...-+..
T Consensus       161 ae~-dL~KA~~m~~KA-------------V~~~i~~kq~~~~~e~W~k~~~~~--~~d----~d~f~~i~~ki~~~~~~~  220 (906)
T PRK14720        161 EEE-DKEKAITYLKKA-------------IYRFIKKKQYVGIEEIWSKLVHYN--SDD----FDFFLRIERKVLGHREFT  220 (906)
T ss_pred             HHh-hHHHHHHHHHHH-------------HHHHHhhhcchHHHHHHHHHHhcC--ccc----chHHHHHHHHHHhhhccc
Confidence            999 999999988876             444777889999999999998853  222    233455556666554555


Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      --..++.-+-..|-..++++++..+++.+.+. +.|.....-++..|.  +.+.. ...+.+.
T Consensus       221 ~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~--~kY~~-~~~~ee~  280 (906)
T PRK14720        221 RLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK--EKYKD-HSLLEDY  280 (906)
T ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH--HHccC-cchHHHH
Confidence            56677888889999999999999999999888 667788888888776  44443 4444444

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

Probab=98.57  E-value=9.4e-06  Score=70.93  Aligned_cols=213  Identities=12%  Similarity=0.052  Sum_probs=100.2

Q ss_pred             cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHhHHHHHHHHHhc
Q 042593           37 LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVKWTGIIDGYSRM  113 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~~~~li~~~~~~  113 (352)
                      .|+...|..-|+..+...-. +...|.-+..+|....+.++..+.|++...   .|+.+          |..-...+.-.
T Consensus       339 ~g~~~~a~~d~~~~I~l~~~-~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dv----------YyHRgQm~flL  407 (606)
T KOG0547|consen  339 KGDSLGAQEDFDAAIKLDPA-FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDV----------YYHRGQMRFLL  407 (606)
T ss_pred             cCCchhhhhhHHHHHhcCcc-cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCch----------hHhHHHHHHHH
Confidence            34444555555555444311 111144444445555555555555554433   12222          33333334444


Q ss_pred             CCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHH
Q 042593          114 NRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSAS  192 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  192 (352)
                      +++++|..=|++. ..  +.| +...|..+..+.-+.+.+++++..|++.++.=+.  -+.+|+.....+...++++.|.
T Consensus       408 ~q~e~A~aDF~Ka-i~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~--~~Evy~~fAeiLtDqqqFd~A~  482 (606)
T KOG0547|consen  408 QQYEEAIADFQKA-IS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPN--CPEVYNLFAEILTDQQQFDKAV  482 (606)
T ss_pred             HHHHHHHHHHHHH-hh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC--CchHHHHHHHHHhhHHhHHHHH
Confidence            4455555555544 11  112 2233444444444455555555555554443211  4445555555555555555555


Q ss_pred             HHHHHhccCCCC-------Hh--hHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCC
Q 042593          193 KLFEDTSVDRKN-------LV--SWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLP  263 (352)
Q Consensus       193 ~~~~~~~~~~~~-------~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p  263 (352)
                      +.|+....-.|+       ..  .--.++..- =.+++.                        +|..++.+..+   +.|
T Consensus       483 k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~------------------------~a~~Ll~KA~e---~Dp  534 (606)
T KOG0547|consen  483 KQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKEDIN------------------------QAENLLRKAIE---LDP  534 (606)
T ss_pred             HHHHHHHhhccccccccccchhhhhhhHhhhc-hhhhHH------------------------HHHHHHHHHHc---cCc
Confidence            555543332221       00  001111111 113444                        44444444432   223


Q ss_pred             -ChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          264 -DIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       264 -~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                       ....|..|...-...|++++|.++|++-..
T Consensus       535 kce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  535 KCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             hHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence             345788899999999999999999987653

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

Probab=98.56  E-value=2e-05  Score=69.73  Aligned_cols=65  Identities=18%  Similarity=0.077  Sum_probs=56.9

Q ss_pred             CCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           20 PLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        20 ~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      .|.|..+|+.||+-+... ..+++.+.++++... ++.++..|..-|..-.+..+++..+++|.+..
T Consensus        16 nP~di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCL   80 (656)
T KOG1914|consen   16 NPYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCL   80 (656)
T ss_pred             CCccHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            456999999999988877 999999999999875 36677889999999999999999999999865

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.56  E-value=5.9e-06  Score=68.58  Aligned_cols=182  Identities=11%  Similarity=-0.017  Sum_probs=122.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCch---hhHHHHHHHHHhcCChhHHHHHhccCCC--CCchh-HHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV---YVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVT-WNVI   96 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~~   96 (352)
                      ....+-.....+...|+++.|...++.+.... +.++   .++..+..++...|++++|...++++.+  |+... ... 
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a-  109 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA-  109 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH-
Confidence            56677778888899999999999999988754 2222   4677788999999999999999999865  32221 001 


Q ss_pred             HHHHHhHHHHHHHHHhc--------CCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCC
Q 042593           97 ITGLVKWTGIIDGYSRM--------NRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGF  167 (352)
Q Consensus        97 i~~~~~~~~li~~~~~~--------~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  167 (352)
                            +..+..++...        |+.++|.+.|+++...   .|+.. ....+... ..   ...      .      
T Consensus       110 ------~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~-~~---~~~------~------  164 (235)
T TIGR03302       110 ------YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRM-DY---LRN------R------  164 (235)
T ss_pred             ------HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHH-HH---HHH------H------
Confidence                  33333444433        7788999999998432   24432 22111111 00   000      0      


Q ss_pred             CCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          168 NAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       168 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                         .......+...|.+.|++++|...++......|+    ...+..+..++...|++++|...++.+...
T Consensus       165 ---~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       165 ---LAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             ---HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence               0111225566788999999999999887665443    467888889999999999999988887764

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.55  E-value=1.2e-05  Score=66.78  Aligned_cols=176  Identities=10%  Similarity=-0.038  Sum_probs=99.1

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      ....+-.+...+...|++++|...|+++.+  |+. ....+       +..+..++.+.|++++|...++++.+...-.|
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a-------~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~  104 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQA-------QLDLAYAYYKSGDYAEAIAAADRFIRLHPNHP  104 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHH-------HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCC
Confidence            345566666777777888888888877654  322 11111       56667777778888888888888744332222


Q ss_pred             Ch-hhHHHHHHHHHhC--------CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          135 SE-ITILAVLPAIWKN--------GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       135 ~~-~t~~~ll~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .. .++..+..++...        |+.++|...++.+.+....  +...+..+.....    .....            .
T Consensus       105 ~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~--~~~~~~a~~~~~~----~~~~~------------~  166 (235)
T TIGR03302       105 DADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN--SEYAPDAKKRMDY----LRNRL------------A  166 (235)
T ss_pred             chHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC--ChhHHHHHHHHHH----HHHHH------------H
Confidence            21 1344444444433        5566677777766655333  2222222211100    00000            0


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC-CCCc--chhh----------hHhHHHHHHHHHHh
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVGL-KPNR--SWRI----------GEEGLKFFDKMVEE  258 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~--~~~~----------~~~a~~~~~~m~~~  258 (352)
                      .....+...+.+.|++++|...+++..+... .|..  ..+.          .++|..+++.+..+
T Consensus       167 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       167 GKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            0112455678899999999999999887532 1211  1111          78888888887765

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).

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

Probab=98.49  E-value=0.00023  Score=63.02  Aligned_cols=250  Identities=10%  Similarity=-0.033  Sum_probs=151.0

Q ss_pred             HHHHhcCCcchHHHHHHHHHHhCCCCchhhHHH---HHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHH
Q 042593           32 RTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTA---LGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIID  108 (352)
Q Consensus        32 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~---li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~  108 (352)
                      ..+...|++++|.++++...+.. +.+...+..   +.......+..+.+.+.++.....+...+..       ...+..
T Consensus        51 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~-------~~~~a~  122 (355)
T cd05804          51 LSAWIAGDLPKALALLEQLLDDY-PRDLLALKLHLGAFGLGDFSGMRDHVARVLPLWAPENPDYWYL-------LGMLAF  122 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHhHHHHHhcccccCchhHHHHHhccCcCCCCcHHH-------HHHHHH
Confidence            34557899999999999988764 445545442   2222223456666777666533222222111       445556


Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc--hhhHHHHHHHHHhhC
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD--IHVSNCLIDTYAKCG  186 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~g  186 (352)
                      .+...|++++|...+++.....  +.+...+..+..++...|++++|...++........+++  ...|..+...+...|
T Consensus       123 ~~~~~G~~~~A~~~~~~al~~~--p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G  200 (355)
T cd05804         123 GLEEAGQYDRAEEAARRALELN--PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERG  200 (355)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCC
Confidence            7889999999999999994422  234557788888999999999999999988876432212  245567888999999


Q ss_pred             ChHHHHHHHHHhccCCC---CHhhH-H--HHHHHHHcCCCHHHHHHHHHHHHhcC-CC-CCc-chhh-------------
Q 042593          187 CIFSASKLFEDTSVDRK---NLVSW-T--TIISGFAMHGMGKEAVENFERMQKVG-LK-PNR-SWRI-------------  244 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~~~---~~~~~-~--~li~~~~~~~~~~~a~~~~~~m~~~~-~~-p~~-~~~~-------------  244 (352)
                      +.++|.+++++.....|   ..... +  .++.-+...|....+.+. +.+.... .. |+. ..+.             
T Consensus       201 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  279 (355)
T cd05804         201 DYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRW-EDLADYAAWHFPDHGLAFNDLHAALALAGAGD  279 (355)
T ss_pred             CHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHH-HHHHHHHHhhcCcccchHHHHHHHHHHhcCCC
Confidence            99999999999754433   12111 2  223333444433333222 2221110 00 111 0111             


Q ss_pred             hHhHHHHHHHHHHhcCCCC--------ChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          245 GEEGLKFFDKMVEECEVLP--------DIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p--------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      .+.+...++.+... ...+        ....--...-++...|+.++|.+.+.....
T Consensus       280 ~~~a~~~L~~l~~~-~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~  335 (355)
T cd05804         280 KDALDKLLAALKGR-ASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRD  335 (355)
T ss_pred             HHHHHHHHHHHHHH-HhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            77788888887664 2110        112222333445689999999998876543

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.48  E-value=7.5e-05  Score=61.48  Aligned_cols=264  Identities=12%  Similarity=0.080  Sum_probs=176.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      ...-+.+++..+.+..+++.|.+++..-.+.. +.+....+.|..+|-...++..|...++++-+  |...-|..     
T Consensus         9 ~EGeftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrl-----   82 (459)
T KOG4340|consen    9 PEGEFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRL-----   82 (459)
T ss_pred             CCCchHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHH-----
Confidence            34457888888899999999999998877765 44777888999999999999999999999875  54444322     


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHH--HhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAI--WKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                        |.  ...+-+++.+..|+++...| .+.   |+...-..-+.+.  -..+++..+..++++.-..|    +..+.+..
T Consensus        83 --Y~--AQSLY~A~i~ADALrV~~~~-~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en----~Ad~~in~  150 (459)
T KOG4340|consen   83 --YQ--AQSLYKACIYADALRVAFLL-LDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN----EADGQINL  150 (459)
T ss_pred             --HH--HHHHHHhcccHHHHHHHHHh-cCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC----ccchhccc
Confidence              21  24566788899999999998 432   3332222223333  35688889998888765433    44455555


Q ss_pred             HHHHHhhCChHHHHHHHHHhccC-C-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh--hHh---HHHH
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVD-R-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI--GEE---GLKF  251 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~-~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~--~~~---a~~~  251 (352)
                      ....-+.|+++.|.+-|+...+. . .....||..+. ..+.|+++.|.+...+++++|++.......  .-+   +..+
T Consensus       151 gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsv  229 (459)
T KOG4340|consen  151 GCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSV  229 (459)
T ss_pred             hheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcc
Confidence            56667999999999999987655 2 34456776554 556789999999999999998764433222  000   0000


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CCCchhhHHHHHH
Q 042593          252 FDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---ITNVVVWRTGFLR  307 (352)
Q Consensus       252 ~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~~~li~~  307 (352)
                      =+... . ...--...+|.-...+.+.|+.+.|.+.+-+|..+   ..|++|...+...
T Consensus       230 gNt~~-l-h~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~  286 (459)
T KOG4340|consen  230 GNTLV-L-HQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALM  286 (459)
T ss_pred             cchHH-H-HHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHh
Confidence            00000 0 00001223454555667899999999999999877   5667766665443

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

Probab=98.48  E-value=4.3e-05  Score=74.72  Aligned_cols=205  Identities=16%  Similarity=0.101  Sum_probs=167.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh-CCCC---chhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV-GFQS---HVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i   97 (352)
                      ++..|-.-|....+.++.+.|+++.+..... ++.-   -...|.++++.-...|.-+...++|++..+ -|+.+     
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~----- 1531 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDAYT----- 1531 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHH-----
Confidence            5667888888999999999999999988753 2221   234688888888888988899999999865 33322     


Q ss_pred             HHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593           98 TGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                          .|..|...|.+....++|.++++.|.++.+  -....|...+..+.+..+-+.|..++.+..+.-...........
T Consensus      1532 ----V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~Isk 1605 (1710)
T KOG1070|consen 1532 ----VHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISK 1605 (1710)
T ss_pred             ----HHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHH
Confidence                289999999999999999999999977666  45568999999999999999999999998876444224555566


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKP  238 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p  238 (352)
                      .+..--+.|+.+++..+|+......| -...|+..|+.=.++|+.+.+..+|++....++.|
T Consensus      1606 fAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1606 FAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            66677789999999999999876654 67899999999999999999999999999987765

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.46  E-value=3.4e-07  Score=50.83  Aligned_cols=35  Identities=34%  Similarity=0.632  Sum_probs=32.2

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999998873

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.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.45  E-value=0.00024  Score=59.98  Aligned_cols=78  Identities=14%  Similarity=0.067  Sum_probs=54.4

Q ss_pred             hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHH-HHHHHhcccccCcccccc
Q 042593          245 GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTG-FLRLLINSYFFSPITLNS  322 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~l-i~~~~~~g~~~~a~~~~~  322 (352)
                      +++++.++..+..- -..-|...+ .+..+++..|+..+|+++|-.+... ..|..+|.++ ..+|.+.+.++.|+.++-
T Consensus       375 FddVl~YlnSi~sY-F~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~l  452 (557)
T KOG3785|consen  375 FDDVLTYLNSIESY-FTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMML  452 (557)
T ss_pred             HHHHHHHHHHHHHH-hcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHH
Confidence            44444444444432 222333333 4788999999999999999888766 4577788775 557899999999998876


Q ss_pred             cc
Q 042593          323 QR  324 (352)
Q Consensus       323 ~~  324 (352)
                      .+
T Consensus       453 k~  454 (557)
T KOG3785|consen  453 KT  454 (557)
T ss_pred             hc
Confidence            55

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

Probab=98.45  E-value=7.9e-05  Score=60.25  Aligned_cols=160  Identities=12%  Similarity=0.001  Sum_probs=130.3

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      |... ..+-..+.-.|+-+....+......   .|...          .+..++...+.|++..|...+.+. ... -++
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~l----------l~~~gk~~~~~g~~~~A~~~~rkA-~~l-~p~  132 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAYPKDREL----------LAAQGKNQIRNGNFGEAVSVLRKA-ARL-APT  132 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccCcccHHH----------HHHHHHHHHHhcchHHHHHHHHHH-hcc-CCC
Confidence            3444 5566777778888888877777543   23333          556888899999999999999999 433 357


Q ss_pred             ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHH
Q 042593          135 SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIIS  213 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~  213 (352)
                      |..+|+.+.-+|-+.|+.++|..-|.+..+....  ++...|.+.-.|.-.|+.+.|..++.......+ |...-..+..
T Consensus       133 d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~--~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl  210 (257)
T COG5010         133 DWEAWNLLGAALDQLGRFDEARRAYRQALELAPN--EPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLAL  210 (257)
T ss_pred             ChhhhhHHHHHHHHccChhHHHHHHHHHHHhccC--CchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHH
Confidence            8889999999999999999999999999887655  788899999999999999999999998766644 8888899999


Q ss_pred             HHHcCCCHHHHHHHHHHHH
Q 042593          214 GFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~  232 (352)
                      .....|++++|.++...-.
T Consensus       211 ~~~~~g~~~~A~~i~~~e~  229 (257)
T COG5010         211 VVGLQGDFREAEDIAVQEL  229 (257)
T ss_pred             HHhhcCChHHHHhhccccc
Confidence            9999999999998876543

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

Probab=98.44  E-value=2.6e-05  Score=71.45  Aligned_cols=207  Identities=12%  Similarity=0.038  Sum_probs=123.6

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      --..=..+...+...|-..+|..+++..         +.|.-+|.+|+..|+-++|..+..+-.+  ||+..        
T Consensus       397 ~Wq~q~~laell~slGitksAl~I~Erl---------emw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~l--------  459 (777)
T KOG1128|consen  397 IWQLQRLLAELLLSLGITKSALVIFERL---------EMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRL--------  459 (777)
T ss_pred             cchHHHHHHHHHHHcchHHHHHHHHHhH---------HHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchh--------
Confidence            3334455566677778888888887754         3455577888888888888777665443  55565        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        |..+.+......-+++|.++.+.....        .-..+..-..+.++++++.+.++.-.+.+.-  ...+|-.+-.
T Consensus       460 --yc~LGDv~~d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~npl--q~~~wf~~G~  527 (777)
T KOG1128|consen  460 --YCLLGDVLHDPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPL--QLGTWFGLGC  527 (777)
T ss_pred             --HHHhhhhccChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCcc--chhHHHhccH
Confidence              555555555555566666666655111        0011111122356667777666665554432  4566666666


Q ss_pred             HHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh----------hHhHH
Q 042593          181 TYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI----------GEEGL  249 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~----------~~~a~  249 (352)
                      +..+.++++.|.+.|.....-.| +...||++-.+|.+.|+-.+|...+++..+.+-.+-...-+          +++|+
T Consensus       528 ~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~  607 (777)
T KOG1128|consen  528 AALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAI  607 (777)
T ss_pred             HHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHH
Confidence            66677777777777776655544 35667777777777777777777777766654333322222          55555


Q ss_pred             HHHHHHHHh
Q 042593          250 KFFDKMVEE  258 (352)
Q Consensus       250 ~~~~~m~~~  258 (352)
                      +.+.++...
T Consensus       608 ~A~~rll~~  616 (777)
T KOG1128|consen  608 KAYHRLLDL  616 (777)
T ss_pred             HHHHHHHHh
Confidence            555555543

>PLN02789 farnesyltranstransferase

Probab=98.43  E-value=0.00012  Score=63.10  Aligned_cols=195  Identities=11%  Similarity=0.024  Sum_probs=135.4

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC-ChhHHHHHhccCCCCCchhHHHHHHHHHhHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG-FLKDSSKLFDELPERNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~  105 (352)
                      +..+-..+...++.++|+.+.+.+++.. +-+..+|+..-.++...| ++++++..++++.+.++..+.+       |+.
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqa-------W~~  111 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQI-------WHH  111 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHH-------hHH
Confidence            4445555666788999999999998765 334456766666666777 5799999999887655544444       665


Q ss_pred             HHHHHHhcCC--HHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          106 IIDGYSRMNR--SNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       106 li~~~~~~~~--~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      .-..+.+.|+  .++++.+++++....  +-|..+|+...-++.+.|+++++.+.++++.+.++.  +...|+....++.
T Consensus       112 R~~~l~~l~~~~~~~el~~~~kal~~d--pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~--N~sAW~~R~~vl~  187 (320)
T PLN02789        112 RRWLAEKLGPDAANKELEFTRKILSLD--AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR--NNSAWNQRYFVIT  187 (320)
T ss_pred             HHHHHHHcCchhhHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC--chhHHHHHHHHHH
Confidence            5444555555  367888888884322  235668888888888999999999999999998766  7788887776666


Q ss_pred             hh---CCh----HHHHHHHHHhccC-CCCHhhHHHHHHHHHcC----CCHHHHHHHHHHHHh
Q 042593          184 KC---GCI----FSASKLFEDTSVD-RKNLVSWTTIISGFAMH----GMGKEAVENFERMQK  233 (352)
Q Consensus       184 ~~---g~~----~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~  233 (352)
                      +.   |+.    +++.+...+.... +-|...|+-+...+...    ++..+|.+.+.+..+
T Consensus       188 ~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        188 RSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             hccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            55   222    4566666554444 45778888877777763    334567777766554

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.42  E-value=4.5e-07  Score=50.00  Aligned_cols=33  Identities=24%  Similarity=0.508  Sum_probs=31.0

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVGLKP  238 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p  238 (352)
                      .+|++++.+|++.|+++.|.++|++|++.|++|
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            689999999999999999999999999998887

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

Probab=98.41  E-value=0.00013  Score=58.53  Aligned_cols=163  Identities=10%  Similarity=-0.055  Sum_probs=120.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      --.-+..|...|+++.+..-.+.+ ..    |. .       .+...++.+++...++...+.+..  +...|..+...|
T Consensus        19 ~~~~~~~Y~~~g~~~~v~~~~~~~-~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~~P~--~~~~w~~Lg~~~   83 (198)
T PRK10370         19 VFLCVGSYLLSPKWQAVRAEYQRL-AD----PL-H-------QFASQQTPEAQLQALQDKIRANPQ--NSEQWALLGEYY   83 (198)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHHH-hC----cc-c-------cccCchhHHHHHHHHHHHHHHCCC--CHHHHHHHHHHH
Confidence            344456788899988875554333 11    11 0       122356677777777777776544  889999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH-HcCCC--HHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF-AMHGM--GKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEE  258 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~-~~~~~--~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~  258 (352)
                      ...|++++|...|+......| +...+..+..++ ...|+  .++|..++++..+..                       
T Consensus        84 ~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-----------------------  140 (198)
T PRK10370         84 LWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-----------------------  140 (198)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-----------------------
Confidence            999999999999999876655 678888888764 67777  599999999988742                       


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHH
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLR  307 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~  307 (352)
                         +-+...+..+...+.+.|++++|...++++... +|+..-+. +|.+
T Consensus       141 ---P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~~~~r~~-~i~~  186 (198)
T PRK10370        141 ---ANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSPRVNRTQ-LVES  186 (198)
T ss_pred             ---CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCccHHH-HHHH
Confidence               226678888999999999999999999999877 66665443 3344

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

Probab=98.39  E-value=9.3e-05  Score=63.62  Aligned_cols=204  Identities=14%  Similarity=0.033  Sum_probs=145.7

Q ss_pred             CCChhhHHHHHHHHH--hCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhh-HH
Q 042593          133 EPSEITILAVLPAIW--KNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVS-WT  209 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~  209 (352)
                      .|+..+....+.+++  ..++...+...+-.+.....-+.+.+....+..++...|+.+.|...|+......|+..+ ..
T Consensus       191 ~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD  270 (564)
T KOG1174|consen  191 PDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMD  270 (564)
T ss_pred             CCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHH
Confidence            344445555666554  455556666666555555545548999999999999999999999999998666664322 22


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcC
Q 042593          210 TIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAG  279 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g  279 (352)
                      .-.-.+.+.|+.+....+...+....-..-..++.          ...|+.+-++-++.  -+-+...|-.-...+...|
T Consensus       271 ~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~--~~r~~~alilKG~lL~~~~  348 (564)
T KOG1174|consen  271 LYAVLLGQEGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDS--EPRNHEALILKGRLLIALE  348 (564)
T ss_pred             HHHHHHHhccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhcc--CcccchHHHhccHHHHhcc
Confidence            22233567888888888888876643222222332          66777777776643  1123444544466788999


Q ss_pred             ChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhHHHHhhhh
Q 042593          280 RLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQI  338 (352)
Q Consensus       280 ~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  338 (352)
                      +.++|.-.|+..+.. +-+...|.-|+.+|+..|.+++|.-...+.+..+|.+...+.-+
T Consensus       349 R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~~sA~~LtL~  408 (564)
T KOG1174|consen  349 RHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQNSARSLTLF  408 (564)
T ss_pred             chHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhhcchhhhhhh
Confidence            999999999999887 67889999999999999999999999999999998886665443

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

Probab=98.39  E-value=0.0002  Score=65.01  Aligned_cols=296  Identities=12%  Similarity=0.066  Sum_probs=167.4

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chh------HHHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVT------WNVI   96 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~------~~~~   96 (352)
                      |.....-.+...|+-++|.+......+.. ..+...|..+.-.+-...++++|++.|.....  || ...      -.+-
T Consensus        43 slAmkGL~L~~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslLQ~Q  121 (700)
T KOG1156|consen   43 SLAMKGLTLNCLGKKEEAYELVRLGLRND-LKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLLQIQ  121 (700)
T ss_pred             hHHhccchhhcccchHHHHHHHHHHhccC-cccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHH
Confidence            33333334455566666666555554433 23445555555555555666666666665432  11 111      1111


Q ss_pred             HHHHH------------------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHH------HHHHhCCCh
Q 042593           97 ITGLV------------------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVL------PAIWKNGEV  152 (352)
Q Consensus        97 i~~~~------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll------~~~~~~~~~  152 (352)
                      ++-+.                  .|..+.-++.-.|+...|..+.++..+...-.|+...|....      ....+.|..
T Consensus       122 mRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~  201 (700)
T KOG1156|consen  122 MRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSL  201 (700)
T ss_pred             HHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccH
Confidence            11111                  477888888888999999999999855554456665554332      234566777


Q ss_pred             hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHH-cCCCHHHHH-HHHHH
Q 042593          153 RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFA-MHGMGKEAV-ENFER  230 (352)
Q Consensus       153 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~-~~~~~~~a~-~~~~~  230 (352)
                      +.|.+.+..-...-+.  ....-..-...+.+.+++++|..++..+....||-.-|+.....+. +-.+.-++. .+|..
T Consensus       202 q~ale~L~~~e~~i~D--kla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~  279 (700)
T KOG1156|consen  202 QKALEHLLDNEKQIVD--KLAFEETKADLLMKLGQLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAI  279 (700)
T ss_pred             HHHHHHHHhhhhHHHH--HHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            7777766654443221  2333345567788999999999999998877887766665554333 232222332 44444


Q ss_pred             HHh----------------------------------cCCCCCcch---hh--hHhHHHHHHHHHHhc--CC--------
Q 042593          231 MQK----------------------------------VGLKPNRSW---RI--GEEGLKFFDKMVEEC--EV--------  261 (352)
Q Consensus       231 m~~----------------------------------~~~~p~~~~---~~--~~~a~~~~~~m~~~~--~~--------  261 (352)
                      ..+                                  .|+.+--..   +.  .. -..+++++...+  ++        
T Consensus       280 ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~-k~~~le~Lvt~y~~~L~~~~~f~~  358 (700)
T KOG1156|consen  280 LSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPE-KVAFLEKLVTSYQHSLSGTGMFNF  358 (700)
T ss_pred             HhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCchhhhhHHHHhchh-HhHHHHHHHHHHHhhcccccCCCc
Confidence            332                                  222211111   11  11 111222222110  11        


Q ss_pred             -------CCChhhH--HHHHHHHHHcCChhHHHHHHhcCCCCCCCc-hhhHHHHHHHHhcccccCcccccccch
Q 042593          262 -------LPDIKHY--GCLIDILERAGRLEQAEEVASGIPSQITNV-VVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       262 -------~p~~~~~--~~li~~~~~~g~~~~A~~~~~~m~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                             +|+...|  -.++..+-+.|+++.|+..++....+.|+. ..|-.-.+-+...|+.++|...+.+..
T Consensus       359 ~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~  432 (700)
T KOG1156|consen  359 LDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQ  432 (700)
T ss_pred             ccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence                   3444433  467888889999999999999988873333 344444566788889998888877763

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

Probab=98.36  E-value=1.8e-05  Score=72.42  Aligned_cols=250  Identities=14%  Similarity=0.133  Sum_probs=168.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh---------------------CCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV---------------------GFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~---------------------~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      .......+++...+.++.....+-+.+|...                     +++|--..-..+...+.+.|-...|..+
T Consensus       341 ~i~~salllr~~~E~~~~RtveR~~~q~q~lv~~iq~~e~~v~nRlsy~ya~~lpp~Wq~q~~laell~slGitksAl~I  420 (777)
T KOG1128|consen  341 SIQASALLLRFLLESTRSRTVERALSQMQFLVKAIQMKEYSVLNRLSYIYAPHLPPIWQLQRLLAELLLSLGITKSALVI  420 (777)
T ss_pred             eeehHHHHHHHHHHhcCccchhhHHHHHHHHHHHHhhccHhHHhcccccccCCCCCcchHHHHHHHHHHHcchHHHHHHH
Confidence            3455666777777777766665555554321                     1233333445677788889999999999


Q ss_pred             hccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHH
Q 042593           82 FDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGY  161 (352)
Q Consensus        82 ~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  161 (352)
                      |+++.     .          |.-+|.+|+..|+..+|..+..+- -+  .+||...|..+........-+++|.++.+.
T Consensus       421 ~Erle-----m----------w~~vi~CY~~lg~~~kaeei~~q~-le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~  482 (777)
T KOG1128|consen  421 FERLE-----M----------WDPVILCYLLLGQHGKAEEINRQE-LE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNY  482 (777)
T ss_pred             HHhHH-----H----------HHHHHHHHHHhcccchHHHHHHHH-hc--CCCcchhHHHhhhhccChHHHHHHHHHhhh
Confidence            99863     3          888888999999999998887776 32  468888888888777777777777777765


Q ss_pred             HHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          162 GEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       162 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                      ....        .-..+.....+.++++++.+.|+.-... +--..+|-..-.+..+.++++.|.+.|..-..  ..|| 
T Consensus       483 ~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvt--L~Pd-  551 (777)
T KOG1128|consen  483 ISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVT--LEPD-  551 (777)
T ss_pred             hhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhh--cCCC-
Confidence            4322        1222222333478999999999864433 44678888888888899999999999998776  2343 


Q ss_pred             chhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCccc
Q 042593          241 SWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPIT  319 (352)
Q Consensus       241 ~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~  319 (352)
                                             +...||.+-.+|.+.|+-.+|...+.+..+- ..+...|...+......|.+++|++
T Consensus       552 -----------------------~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~  608 (777)
T KOG1128|consen  552 -----------------------NAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIK  608 (777)
T ss_pred             -----------------------chhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHH
Confidence                                   3456666666666666666666666655444 4455556555555666666666666


Q ss_pred             ccccc
Q 042593          320 LNSQR  324 (352)
Q Consensus       320 ~~~~~  324 (352)
                      ...+.
T Consensus       609 A~~rl  613 (777)
T KOG1128|consen  609 AYHRL  613 (777)
T ss_pred             HHHHH
Confidence            55554

>PLN02789 farnesyltranstransferase

Probab=98.36  E-value=0.00018  Score=62.12  Aligned_cols=213  Identities=9%  Similarity=-0.072  Sum_probs=142.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcC-CHHHHHHHHHHhHhccCCCCChhhHH
Q 042593           62 NTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMN-RSNEALALFRRMAACEYTEPSEITIL  140 (352)
Q Consensus        62 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~p~~~t~~  140 (352)
                      ++.+-..+...++.++|+.+.+++.+.++..+++       |+..-..+...| ++++++..++++.+ .. +-+..+|+
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~lnP~~yta-------W~~R~~iL~~L~~~l~eeL~~~~~~i~-~n-pknyqaW~  110 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLNPGNYTV-------WHFRRLCLEALDADLEEELDFAEDVAE-DN-PKNYQIWH  110 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHH-------HHHHHHHHHHcchhHHHHHHHHHHHHH-HC-CcchHHhH
Confidence            3344445556678889999999888766655555       776666666677 68999999999844 22 12333566


Q ss_pred             HHHHHHHhCCCh--hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHc
Q 042593          141 AVLPAIWKNGEV--RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAM  217 (352)
Q Consensus       141 ~ll~~~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~  217 (352)
                      .-...+.+.|+.  +++..+++.+.+....  +.++|+....++.+.|+++++++.++++.+. ..|...|+.....+.+
T Consensus       111 ~R~~~l~~l~~~~~~~el~~~~kal~~dpk--Ny~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~  188 (320)
T PLN02789        111 HRRWLAEKLGPDAANKELEFTRKILSLDAK--NYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITR  188 (320)
T ss_pred             HHHHHHHHcCchhhHHHHHHHHHHHHhCcc--cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHh
Confidence            555555566653  6678888888877654  8999999999999999999999999998766 4567777776655544


Q ss_pred             CC---CH----HHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHc----CChhHHHH
Q 042593          218 HG---MG----KEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERA----GRLEQAEE  286 (352)
Q Consensus       218 ~~---~~----~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~----g~~~~A~~  286 (352)
                      .+   ..    ++..+...+++..                          .+-|...|+-+...+...    ++..+|.+
T Consensus       189 ~~~l~~~~~~~e~el~y~~~aI~~--------------------------~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~  242 (320)
T PLN02789        189 SPLLGGLEAMRDSELKYTIDAILA--------------------------NPRNESPWRYLRGLFKDDKEALVSDPEVSS  242 (320)
T ss_pred             ccccccccccHHHHHHHHHHHHHh--------------------------CCCCcCHHHHHHHHHhcCCcccccchhHHH
Confidence            32   11    2334444343331                          123667777777777663    34456777


Q ss_pred             HHhcCCCC-CCCchhhHHHHHHHHhc
Q 042593          287 VASGIPSQ-ITNVVVWRTGFLRLLIN  311 (352)
Q Consensus       287 ~~~~m~~~-~~~~~~~~~li~~~~~~  311 (352)
                      .+.+.... +.+......|+..|...
T Consensus       243 ~~~~~~~~~~~s~~al~~l~d~~~~~  268 (320)
T PLN02789        243 VCLEVLSKDSNHVFALSDLLDLLCEG  268 (320)
T ss_pred             HHHHhhcccCCcHHHHHHHHHHHHhh
Confidence            77776554 45666777788877753

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

Probab=98.35  E-value=1e-05  Score=72.06  Aligned_cols=184  Identities=14%  Similarity=0.075  Sum_probs=149.5

Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHH
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEA  224 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a  224 (352)
                      +.+.|++.+|.-.|+..++..+.  +...|..|.......++-..|+..+++..+..| |....-.|.-.|...|.-..|
T Consensus       295 lm~nG~L~~A~LafEAAVkqdP~--haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQDPQ--HAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhChH--HHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHH
Confidence            45789999999999999888655  889999999999999999999999998877655 688888999999999999999


Q ss_pred             HHHHHHHHhcCCC--------CCcc-----hhh----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHH
Q 042593          225 VENFERMQKVGLK--------PNRS-----WRI----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEV  287 (352)
Q Consensus       225 ~~~~~~m~~~~~~--------p~~~-----~~~----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~  287 (352)
                      .+.++..+....+        ++..     .+.    .....++|-.+....+..+|+.+...|.-.|--.|++++|...
T Consensus       373 l~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDc  452 (579)
T KOG1125|consen  373 LKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDC  452 (579)
T ss_pred             HHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHH
Confidence            9999998654311        1111     111    5555566655555446668888889999999999999999999


Q ss_pred             HhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          288 ASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       288 ~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      |+..... +.|...||.|...++...+.++|++.+.+++.-.|.-
T Consensus       453 f~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~y  497 (579)
T KOG1125|consen  453 FEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGY  497 (579)
T ss_pred             HHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCe
Confidence            9988877 7788899999999999999999999999998766643

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

Probab=98.33  E-value=7.6e-05  Score=60.35  Aligned_cols=159  Identities=10%  Similarity=0.066  Sum_probs=126.6

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li  107 (352)
                      ...-+.+.-.|+-+....+....... .+.|....+.++....+.|++..|...|.+...+++.-|..       |+.+-
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~-------~~~lg  141 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEA-------WNLLG  141 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhh-------hhHHH
Confidence            45556666777777777666554332 24566677779999999999999999999988744444433       99999


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      -+|.+.|+.+.|..-|.+..+..+-  +...++.+...+.-.|+.+.|..++......+..  +..+-..+.......|+
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L~~~--~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a--d~~v~~NLAl~~~~~g~  217 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALELAPN--EPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA--DSRVRQNLALVVGLQGD  217 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHhccC--CchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC--chHHHHHHHHHHhhcCC
Confidence            9999999999999999998664432  3457788888899999999999999999887655  78888899999999999


Q ss_pred             hHHHHHHHHHh
Q 042593          188 IFSASKLFEDT  198 (352)
Q Consensus       188 ~~~a~~~~~~~  198 (352)
                      ++.|.++...-
T Consensus       218 ~~~A~~i~~~e  228 (257)
T COG5010         218 FREAEDIAVQE  228 (257)
T ss_pred             hHHHHhhcccc
Confidence            99999987654

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

Probab=98.32  E-value=0.00031  Score=63.79  Aligned_cols=285  Identities=14%  Similarity=0.106  Sum_probs=177.5

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHh-CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKV-GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      -.-+..+.+.|++..-...|+..... .+......|...+......+-++-+..+++...+-++..          -+--
T Consensus       106 l~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~~P~~----------~eey  175 (835)
T KOG2047|consen  106 LDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKVAPEA----------REEY  175 (835)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhcCHHH----------HHHH
Confidence            33344444556666666666655432 223334567777777777788888888888877766655          5566


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccC-----CCCChhhHHHHHHHHHhCCChh---hHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEY-----TEPSEITILAVLPAIWKNGEVR---NCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~-----~~p~~~t~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                      |..++..+++++|-+.+.....+..     .+-+...|..+.+-.++.-+.-   .+..+++.+...=... -...|.+|
T Consensus       176 ie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq-~g~Lw~SL  254 (835)
T KOG2047|consen  176 IEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQ-LGFLWCSL  254 (835)
T ss_pred             HHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHH-HHHHHHHH
Confidence            7778899999999999888732211     1223345666655555543332   2344444443332222 35688999


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcC----------------C------CHHHHHHHHHHHHhcCC
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMH----------------G------MGKEAVENFERMQKVGL  236 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~----------------~------~~~~a~~~~~~m~~~~~  236 (352)
                      .+.|.++|.+++|.++|++......++.-|+.+.++|+.-                +      +++-.+.-|+.+.+.+.
T Consensus       255 AdYYIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~  334 (835)
T KOG2047|consen  255 ADYYIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRP  334 (835)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccc
Confidence            9999999999999999998765555555555555555421                1      22233334444333221


Q ss_pred             -CCCcchhh-------------------hHhHHHHHHHHHHhcCCCCC------hhhHHHHHHHHHHcCChhHHHHHHhc
Q 042593          237 -KPNRSWRI-------------------GEEGLKFFDKMVEECEVLPD------IKHYGCLIDILERAGRLEQAEEVASG  290 (352)
Q Consensus       237 -~p~~~~~~-------------------~~~a~~~~~~m~~~~~~~p~------~~~~~~li~~~~~~g~~~~A~~~~~~  290 (352)
                       -.|+....                   ..+-...+.+.++  .+.|.      ...|..+.+.|-+.|+++.|..+|++
T Consensus       335 ~~lNsVlLRQn~~nV~eW~kRV~l~e~~~~~~i~tyteAv~--~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifek  412 (835)
T KOG2047|consen  335 LLLNSVLLRQNPHNVEEWHKRVKLYEGNAAEQINTYTEAVK--TVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEK  412 (835)
T ss_pred             hHHHHHHHhcCCccHHHHHhhhhhhcCChHHHHHHHHHHHH--ccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHH
Confidence             11111111                   4444555666555  34442      34688899999999999999999999


Q ss_pred             CCCC-CCC----chhhHHHHHHHHhcccccCcccccccch
Q 042593          291 IPSQ-ITN----VVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       291 m~~~-~~~----~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      .... -+.    ..+|......=+++.+++.|+++++.+.
T Consensus       413 a~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~  452 (835)
T KOG2047|consen  413 ATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRAT  452 (835)
T ss_pred             hhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhh
Confidence            8776 222    2456666666678999999999888774

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.32  E-value=3.9e-05  Score=58.23  Aligned_cols=94  Identities=14%  Similarity=0.048  Sum_probs=78.5

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHc
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAM  217 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~  217 (352)
                      +.....++...|++++|...++........  +...+..+..++.+.|++++|...|+...... .+...+..+..++..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~--~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~  104 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQPW--SWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKM  104 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH
Confidence            555677788899999999999988876543  78888899999999999999999999877664 467888888888999


Q ss_pred             CCCHHHHHHHHHHHHhc
Q 042593          218 HGMGKEAVENFERMQKV  234 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~~  234 (352)
                      .|+.++|...|+...+.
T Consensus       105 ~g~~~eAi~~~~~Al~~  121 (144)
T PRK15359        105 MGEPGLAREAFQTAIKM  121 (144)
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            99999999999998764

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.31  E-value=9.3e-07  Score=48.68  Aligned_cols=33  Identities=27%  Similarity=0.518  Sum_probs=31.1

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCC
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQS   57 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~   57 (352)
                      .+|+.++.+|++.|+++.|.++|+.|.+.|++|
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            589999999999999999999999999999887

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.30  E-value=1.2e-06  Score=48.58  Aligned_cols=33  Identities=36%  Similarity=0.591  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE  136 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  136 (352)
                      ||.+|++|++.|++++|.++|++| ...|+.||.
T Consensus         3 ~n~li~~~~~~~~~~~a~~~~~~M-~~~g~~p~~   35 (35)
T TIGR00756         3 YNTLIDGLCKAGRVEEALELFKEM-LERGIEPDV   35 (35)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHH-HHcCCCCCC
Confidence            899999999999999999999999 778888873

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.

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

Probab=98.30  E-value=5.5e-05  Score=67.54  Aligned_cols=192  Identities=13%  Similarity=0.069  Sum_probs=136.7

Q ss_pred             HHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHH
Q 042593           32 RTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYS  111 (352)
Q Consensus        32 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~  111 (352)
                      ..+.+.|++.+|.-.|+..+... |-+...|-.|.......++-..|+..+.+..+-|+..-.+       .-.|.-.|.
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~Nlea-------LmaLAVSyt  364 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEA-------LMALAVSYT  364 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHH-------HHHHHHHHh
Confidence            45668899999999999999877 5678999999999999999999999999887744433222       455666788


Q ss_pred             hcCCHHHHHHHHHHhHhccC-----CC--CChhhHHHHHHHHHhCCChhhHHHHHHHH-HhcCCCCCchhhHHHHHHHHH
Q 042593          112 RMNRSNEALALFRRMAACEY-----TE--PSEITILAVLPAIWKNGEVRNCQLIHGYG-EKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~~~-----~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ..|.-..|+..++...+...     ..  ++...-..  ..+..........++|-++ .+.+... ++.+...|.-.|-
T Consensus       365 Neg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~-DpdvQ~~LGVLy~  441 (579)
T KOG1125|consen  365 NEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKI-DPDVQSGLGVLYN  441 (579)
T ss_pred             hhhhHHHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCC-ChhHHhhhHHHHh
Confidence            88888888888877633220     00  01110000  1222223334444444444 3444335 7788888888899


Q ss_pred             hhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          184 KCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      -.|++++|.+.|+......| |..+||.|-..++...+.++|+..|++.++.
T Consensus       442 ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL  493 (579)
T KOG1125|consen  442 LSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQL  493 (579)
T ss_pred             cchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc
Confidence            99999999999998877765 6788999999999999999999999998874

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.27  E-value=0.00013  Score=69.31  Aligned_cols=144  Identities=7%  Similarity=0.011  Sum_probs=115.3

Q ss_pred             CCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCC
Q 042593           55 FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYT  132 (352)
Q Consensus        55 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  132 (352)
                      .+.++..+-.|.....+.|+.++|+.+++...+  ||...  +       ...+...+.+.+++++|+..+++...   .
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~--a-------~~~~a~~L~~~~~~eeA~~~~~~~l~---~  149 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSE--A-------FILMLRGVKRQQGIEAGRAEIELYFS---G  149 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHH--H-------HHHHHHHHHHhccHHHHHHHHHHHhh---c
Confidence            455678888899999999999999999999876  65433  1       66777889999999999999999844   3


Q ss_pred             CCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHH
Q 042593          133 EPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTT  210 (352)
Q Consensus       133 ~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~  210 (352)
                      .|+. .....+..++.+.|++++|..+|+++...+..  +..++..+..++.+.|+.++|...|+...+. .+.+..|+.
T Consensus       150 ~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~--~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~  227 (694)
T PRK15179        150 GSSSAREILLEAKSWDEIGQSEQADACFERLSRQHPE--FENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTR  227 (694)
T ss_pred             CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCCC--cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHH
Confidence            4554 46777888889999999999999999985433  6888999999999999999999999987654 555555554


Q ss_pred             HH
Q 042593          211 II  212 (352)
Q Consensus       211 li  212 (352)
                      .+
T Consensus       228 ~~  229 (694)
T PRK15179        228 RL  229 (694)
T ss_pred             HH
Confidence            43

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

Probab=98.27  E-value=0.00013  Score=58.49  Aligned_cols=118  Identities=8%  Similarity=0.025  Sum_probs=78.8

Q ss_pred             cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH-HhhCC--hH
Q 042593          113 MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY-AKCGC--IF  189 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~-~~~g~--~~  189 (352)
                      .++.+++...+++..+..  +.|...|..+...+...|+.++|...++...+....  +...+..+..++ ...|+  .+
T Consensus        52 ~~~~~~~i~~l~~~L~~~--P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~--~~~~~~~lA~aL~~~~g~~~~~  127 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGE--NAELYAALATVLYYQAGQHMTP  127 (198)
T ss_pred             chhHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHhcCCCCcH
Confidence            445555655555552322  244556777777777777777777777777776543  666676666653 56566  47


Q ss_pred             HHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          190 SASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       190 ~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +|.+++++..+..| +...+..+...+.+.|++++|...|+++.+.
T Consensus       128 ~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        128 QTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            77777777766544 5667777777777778888888888777764

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

Probab=98.27  E-value=0.00013  Score=69.35  Aligned_cols=197  Identities=14%  Similarity=0.055  Sum_probs=131.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+.+.++-.+.|...+|.+-|-+.       -|...|.-+++.+.+.|.+++-.+++....+..-.| ..  =+.||-+|
T Consensus      1107 WsqlakAQL~~~~v~dAieSyika-------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~-~i--d~eLi~Ay 1176 (1666)
T KOG0985|consen 1107 WSQLAKAQLQGGLVKDAIESYIKA-------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREP-YI--DSELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHhcCchHHHHHHHHhc-------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCc-cc--hHHHHHHH
Confidence            888999999999999988877666       466689999999999999999999998888776655 43  45889999


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-hHhHHHHHHHHHHhcCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-GEEGLKFFDKMVEECEV  261 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-~~~a~~~~~~m~~~~~~  261 (352)
                      ++.+++.+.++++.     .||......+-+-|...|.++.|.-+|...-.-.  .-..|.. ..+-....+...    -
T Consensus      1177 Akt~rl~elE~fi~-----gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a--~La~TLV~LgeyQ~AVD~aR----K 1245 (1666)
T KOG0985|consen 1177 AKTNRLTELEEFIA-----GPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFA--KLASTLVYLGEYQGAVDAAR----K 1245 (1666)
T ss_pred             HHhchHHHHHHHhc-----CCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHH--HHHHHHHHHHHHHHHHHHhh----h
Confidence            99999888776553     7787777778888888888888877776543210  0000000 000000111111    1


Q ss_pred             CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          262 LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       262 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      .-+..||-.+-.+|...+.+..|.     |...  .....-..-++.-|-..|.+++-+.+++-.+
T Consensus      1246 Ans~ktWK~VcfaCvd~~EFrlAQ-----iCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1246 ANSTKTWKEVCFACVDKEEFRLAQ-----ICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             ccchhHHHHHHHHHhchhhhhHHH-----hcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            235567776666666666655443     3332  1123334567888888888888888776653

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.25  E-value=0.00032  Score=66.77  Aligned_cols=126  Identities=13%  Similarity=0.082  Sum_probs=99.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      +-.|.....+.|.+++|..+++....   ..||.. ....+..++.+.+++++|....++.......  +......+..+
T Consensus        89 ~~~La~i~~~~g~~~ea~~~l~~~~~---~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~--~~~~~~~~a~~  163 (694)
T PRK15179         89 QVLVARALEAAHRSDEGLAVWRGIHQ---RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSS--SAREILLEAKS  163 (694)
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHh---hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCC--CHHHHHHHHHH
Confidence            66777788888888888888888733   456654 6777788888888888888888888877654  67777788888


Q ss_pred             HHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +.+.|++++|..+|++.....|+ ..++..+-.++-..|+.++|...|+...+
T Consensus       164 l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        164 WDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             HHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            88888888888888887765554 67788888888888888888888888776

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

Probab=98.24  E-value=0.00025  Score=57.52  Aligned_cols=55  Identities=13%  Similarity=-0.035  Sum_probs=27.4

Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccc
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYF  314 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~  314 (352)
                      +..|+..+.+-...++...|++++|+.++++...+ ..++.+...++..-...|..
T Consensus       202 k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~Nliv~a~~~Gkd  257 (299)
T KOG3081|consen  202 KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLANLIVLALHLGKD  257 (299)
T ss_pred             ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCC
Confidence            34455555555555555555555555555555544 33344444444444444444

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.22  E-value=0.00037  Score=58.68  Aligned_cols=284  Identities=12%  Similarity=0.011  Sum_probs=177.7

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~  105 (352)
                      --+.+.+...|++..|+.-|...++-. +.+-.++-.-...|...|+-..|+.=+....+  ||-..-         --.
T Consensus        42 lElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelKpDF~~A---------RiQ  111 (504)
T KOG0624|consen   42 LELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGKSKAALQDLSRVLELKPDFMAA---------RIQ  111 (504)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcCCccchhhHHHHHhcCccHHHH---------HHH
Confidence            344555666667777766666665533 11222333334456666766666665555543  443211         111


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCC-----------CCChh--hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYT-----------EPSEI--TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI  172 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~-----------~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  172 (352)
                      -...+.+.|+++.|..=|+..++...-           .+...  .....+..+.-.|+...|......+.+..+.  +.
T Consensus       112 Rg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~W--da  189 (504)
T KOG0624|consen  112 RGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPW--DA  189 (504)
T ss_pred             hchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcc--hh
Confidence            123567889999999988888432210           01111  1223445556678888898888888876544  88


Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-------
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-------  244 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-------  244 (352)
                      ..|..-..+|...|++..|+.=++...+. ..++.++-.+-..+...|+.+.++...++-++  +.||....-       
T Consensus       190 ~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpdHK~Cf~~YKklk  267 (504)
T KOG0624|consen  190 SLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPDHKLCFPFYKKLK  267 (504)
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcchhhHHHHHHHHH
Confidence            88888899999999999988877766544 45667777777778888888888888877766  456654433       


Q ss_pred             -----------------hHhHHHHHHHHHHhcCCC---CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHH
Q 042593          245 -----------------GEEGLKFFDKMVEECEVL---PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRT  303 (352)
Q Consensus       245 -----------------~~~a~~~~~~m~~~~~~~---p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~  303 (352)
                                       +.++.+-.++..+. ...   .....+..+-.++...|++.+|.+...+.... +.|+.++.-
T Consensus       268 Kv~K~les~e~~ie~~~~t~cle~ge~vlk~-ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~d  346 (504)
T KOG0624|consen  268 KVVKSLESAEQAIEEKHWTECLEAGEKVLKN-EPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVLCD  346 (504)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhc-CCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcCchHHHHHHH
Confidence                             33333333333332 111   11234445566777888899998888877766 445777777


Q ss_pred             HHHHHHhcccccCcccccccchh
Q 042593          304 GFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       304 li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      =..+|+-...+++|+.-+..+..
T Consensus       347 RAeA~l~dE~YD~AI~dye~A~e  369 (504)
T KOG0624|consen  347 RAEAYLGDEMYDDAIHDYEKALE  369 (504)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHh
Confidence            77888888888888876665543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.20  E-value=3.7e-05  Score=58.34  Aligned_cols=103  Identities=9%  Similarity=-0.203  Sum_probs=85.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +..+...+...|++++|...|+......  +.+...+..+..++.+.|++++|...++...+....  +...+..+..++
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~--~~~a~~~lg~~l  102 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ--PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDAS--HPEPVYQTGVCL  102 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC--CcHHHHHHHHHH
Confidence            4456677889999999999999984422  235668999999999999999999999999987544  889999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCC-HhhHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKN-LVSWT  209 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~-~~~~~  209 (352)
                      .+.|+.++|...|+......|+ ...|.
T Consensus       103 ~~~g~~~eAi~~~~~Al~~~p~~~~~~~  130 (144)
T PRK15359        103 KMMGEPGLAREAFQTAIKMSYADASWSE  130 (144)
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCChHHHH
Confidence            9999999999999998776665 44443

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

Probab=98.17  E-value=0.0015  Score=53.16  Aligned_cols=170  Identities=13%  Similarity=0.043  Sum_probs=95.2

Q ss_pred             HHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 042593           46 LHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRR  125 (352)
Q Consensus        46 ~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~  125 (352)
                      +.+++.......+......-...|++.|++++|++.......-+...            .=+..+.+..+.+-|.+.+++
T Consensus        95 l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~~lE~~A------------l~VqI~lk~~r~d~A~~~lk~  162 (299)
T KOG3081|consen   95 LYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGENLEAAA------------LNVQILLKMHRFDLAEKELKK  162 (299)
T ss_pred             HHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccchHHHHH------------HHHHHHHHHHHHHHHHHHHHH
Confidence            34444444434443434444456667777777777776633222222            222334556667777777777


Q ss_pred             hHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          126 MAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       126 m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                      | .+.   -+..|.+.+..++.+    .+.+.+|.-+|++|.+. ..| +.-+.+-...++...|++++|..++++....
T Consensus       163 m-q~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~-T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  163 M-QQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPP-TPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             H-Hcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCC-ChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            7 321   234456555555543    34567777777777653 223 6666666677777777777777777776555


Q ss_pred             -CCCHhhHHHHHHHHHcCCCH-HHHHHHHHHHHh
Q 042593          202 -RKNLVSWTTIISGFAMHGMG-KEAVENFERMQK  233 (352)
Q Consensus       202 -~~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~  233 (352)
                       ..++.+...+|.+-...|.. +-..+...+++.
T Consensus       237 d~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  237 DAKDPETLANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             cCCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence             34555655555554455544 334455555554

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

Probab=98.15  E-value=3.2e-06  Score=45.34  Aligned_cols=31  Identities=35%  Similarity=0.697  Sum_probs=25.9

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVGL  236 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  236 (352)
                      .+||+++++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            3788888888888888888888888888764

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.

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

Probab=98.15  E-value=0.00015  Score=55.12  Aligned_cols=127  Identities=10%  Similarity=0.081  Sum_probs=96.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc--hhhHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD--IHVSNCLI  179 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~li  179 (352)
                      |..++..+ ..++...+...++.+....+-.| .......+...+...|++++|...|+........+ .  ......|.
T Consensus        15 y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~-~l~~~a~l~LA   92 (145)
T PF09976_consen   15 YEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDP-ELKPLARLRLA   92 (145)
T ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCH-HHHHHHHHHHH
Confidence            66667766 48999999999999944322111 12344556678889999999999999999877433 3  23445678


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERM  231 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (352)
                      ..+...|++++|+..++...........+...-..|.+.|+.++|...|+..
T Consensus        93 ~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   93 RILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            8899999999999999886544556667778888999999999999999863

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

Probab=98.14  E-value=0.0032  Score=56.86  Aligned_cols=194  Identities=12%  Similarity=0.011  Sum_probs=122.9

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      .-+=++-+...|++++|.+....+...+ +-+...+..=+-+....+++++|+++.+.-..-  .+++..      +--=
T Consensus        15 l~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~------~fEK   85 (652)
T KOG2376|consen   15 LLTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSF------FFEK   85 (652)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchh------hHHH
Confidence            3344566777888899999888888766 445566666677788889999999776654321  121110      1111


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC---------------
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF---------------  170 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------  170 (352)
                      ..+.-+.+..++|+..++-.      .++ ..+...-...+.+.|++++|..+|+.+.+.+....               
T Consensus        86 AYc~Yrlnk~Dealk~~~~~------~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l  159 (652)
T KOG2376|consen   86 AYCEYRLNKLDEALKTLKGL------DRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAAL  159 (652)
T ss_pred             HHHHHHcccHHHHHHHHhcc------cccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhh
Confidence            22344678888888887744      233 33566666677888999999999988866533310               


Q ss_pred             -----------chhhHHHH---HHHHHhhCChHHHHHHHHHhcc--------CCCC-------Hhh-HHHHHHHHHcCCC
Q 042593          171 -----------DIHVSNCL---IDTYAKCGCIFSASKLFEDTSV--------DRKN-------LVS-WTTIISGFAMHGM  220 (352)
Q Consensus       171 -----------~~~~~~~l---i~~~~~~g~~~~a~~~~~~~~~--------~~~~-------~~~-~~~li~~~~~~~~  220 (352)
                                 ...+|..+   ...+...|++..|+++++...+        ...+       +.+ ---|.-.+-..|+
T Consensus       160 ~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gq  239 (652)
T KOG2376|consen  160 QVQLLQSVPEVPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQ  239 (652)
T ss_pred             hHHHHHhccCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcc
Confidence                       11233333   2345578999999999987621        1111       111 1123445678899


Q ss_pred             HHHHHHHHHHHHhcC
Q 042593          221 GKEAVENFERMQKVG  235 (352)
Q Consensus       221 ~~~a~~~~~~m~~~~  235 (352)
                      .++|..++...++..
T Consensus       240 t~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  240 TAEASSIYVDIIKRN  254 (652)
T ss_pred             hHHHHHHHHHHHHhc
Confidence            999999999988764

>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=98.13  E-value=8.5e-05  Score=65.48  Aligned_cols=123  Identities=11%  Similarity=0.055  Sum_probs=94.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      -..|++.+...++++.|..+|+++ ....  |+  ....+++.+...++-.+|.+++++..+....  +........+.+
T Consensus       172 v~~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  172 VDTLLKYLSLTQRYDEAIELLEKL-RERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQ--DSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHH-HhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence            445566677778888999999988 4332  44  4445777777778888888888888765433  667777777888


Q ss_pred             HhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      .+.++.+.|+++.++.....|+ ..+|..|..+|...|++++|+-.++.+-
T Consensus       245 l~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            8889999999999888776664 5688899999999999999988888764

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

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.12  E-value=0.0016  Score=60.49  Aligned_cols=175  Identities=10%  Similarity=-0.016  Sum_probs=113.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCC--chhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERN--LVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--~~~~~~~i~~~  100 (352)
                      |...|..+.-++.+.|+++.+-+.|++....- --..+.|..+...|.-.|.-..|..+.++-..+.  +.....++.+.
T Consensus       322 d~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmas  400 (799)
T KOG4162|consen  322 DAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMAS  400 (799)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHH
Confidence            88889999999999999999999998876533 2345678888888888888888888888765422  21122222221


Q ss_pred             H---------------------------------hHHHHHHHHHhc-----------CCHHHHHHHHHHhHhccCCCCCh
Q 042593          101 V---------------------------------KWTGIIDGYSRM-----------NRSNEALALFRRMAACEYTEPSE  136 (352)
Q Consensus       101 ~---------------------------------~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~~~~p~~  136 (352)
                      .                                 .|-.+.-+|...           ....++++.+++..+..+-.|+.
T Consensus       401 klc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~  480 (799)
T KOG4162|consen  401 KLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLV  480 (799)
T ss_pred             HHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchH
Confidence            1                                 111121122111           11345666666664445555555


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                      .-|.++-  |+..++++.|.+..++..+.+... +...|..|.-.+...+++.+|+.+.+.....
T Consensus       481 if~lalq--~A~~R~l~sAl~~~~eaL~l~~~~-~~~~whLLALvlSa~kr~~~Al~vvd~al~E  542 (799)
T KOG4162|consen  481 IFYLALQ--YAEQRQLTSALDYAREALALNRGD-SAKAWHLLALVLSAQKRLKEALDVVDAALEE  542 (799)
T ss_pred             HHHHHHH--HHHHHhHHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            4444443  455667888888888888875555 7888888888888888888888887765433

>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=98.10  E-value=9.9e-05  Score=65.07  Aligned_cols=96  Identities=11%  Similarity=0.020  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHc
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAM  217 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~  217 (352)
                      ...++..+...++++.|..+++++.+..  |   .+...+++.+...++-.+|.+++++.....| +..........|.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--p---ev~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--P---EVAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--C---cHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence            4455555556666677777777666553  2   2333456666666666666666666554433 55555555566666


Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          218 HGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      .++.+.|..+.+++.+  ..|+..
T Consensus       247 k~~~~lAL~iAk~av~--lsP~~f  268 (395)
T PF09295_consen  247 KKKYELALEIAKKAVE--LSPSEF  268 (395)
T ss_pred             cCCHHHHHHHHHHHHH--hCchhH
Confidence            6677777777766665  345544

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

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

Probab=98.10  E-value=0.0015  Score=57.71  Aligned_cols=118  Identities=14%  Similarity=0.088  Sum_probs=59.0

Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCCh
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCI  188 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  188 (352)
                      +...|++++|+..++.+.+.   .||. .-.......+.+.++.++|.+.++.+......  .....-.+.++|.+.|+.
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~---~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~--~~~l~~~~a~all~~g~~  390 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAA---QPDNPYYLELAGDILLEANKAKEAIERLKKALALDPN--SPLLQLNLAQALLKGGKP  390 (484)
T ss_pred             HHHhcccchHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHhcCCh
Confidence            33455555555555555221   2332 23334444455555555555555555544322  234444555555555555


Q ss_pred             HHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          189 FSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       189 ~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      .+|.+.++..... +-|+..|..|.++|...|+..++..-..+..
T Consensus       391 ~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~  435 (484)
T COG4783         391 QEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEGY  435 (484)
T ss_pred             HHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHHH
Confidence            5555555554433 2345555555555555555555555554443

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

Probab=98.07  E-value=0.00011  Score=55.17  Aligned_cols=94  Identities=7%  Similarity=-0.025  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~  216 (352)
                      ....+...+...|+.++|...++.+.+.+..  +...+..+..++.+.|++++|...++...... .+...+..+...+.
T Consensus        19 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~--~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~   96 (135)
T TIGR02552        19 QIYALAYNLYQQGRYDEALKLFQLLAAYDPY--NSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLL   96 (135)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHhCCC--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHH
Confidence            4455555566666666666666666655432  55666666666666666666666666654443 34555555666666


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 042593          217 MHGMGKEAVENFERMQK  233 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (352)
                      ..|++++|...|++..+
T Consensus        97 ~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        97 ALGEPESALKALDLAIE  113 (135)
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            66666666666666554

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

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.06  E-value=0.00075  Score=57.12  Aligned_cols=60  Identities=10%  Similarity=0.109  Sum_probs=37.6

Q ss_pred             cHHHHHH-HHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           26 TYSFLIR-TCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        26 ~~~~ll~-~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      ..+..|. .+-+.|++++|+..+..+.... .++...+-.|..++--.|.+.+|..+-.+..
T Consensus        58 ~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~  118 (557)
T KOG3785|consen   58 SLQLWIAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQYIEAKSIAEKAP  118 (557)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHHHHHHHHHhhCC
Confidence            3444443 4447899999999988877654 4555555555555555566666666655554

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.03  E-value=0.00085  Score=59.72  Aligned_cols=98  Identities=12%  Similarity=0.080  Sum_probs=52.0

Q ss_pred             HHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHH-------HH
Q 042593          142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTI-------IS  213 (352)
Q Consensus       142 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~l-------i~  213 (352)
                      +.++.-+..+++.+.+-+.......  . +..-++..-.+|...|++..+...-+....... ...-|+.+       -.
T Consensus       230 lgnaaykkk~f~~a~q~y~~a~el~--~-~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~  306 (539)
T KOG0548|consen  230 LGNAAYKKKDFETAIQHYAKALELA--T-DITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGN  306 (539)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHhHh--h-hhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhh
Confidence            3444444445555555555554444  2 455555666666666666555554444322211 11223332       23


Q ss_pred             HHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          214 GFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      +|.+.++++.|...|.+......+|+..+
T Consensus       307 a~~k~~~~~~ai~~~~kaLte~Rt~~~ls  335 (539)
T KOG0548|consen  307 AYTKREDYEGAIKYYQKALTEHRTPDLLS  335 (539)
T ss_pred             hhhhHHhHHHHHHHHHHHhhhhcCHHHHH
Confidence            45566788888888888776655655443

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

Probab=98.03  E-value=0.0015  Score=57.63  Aligned_cols=206  Identities=10%  Similarity=-0.001  Sum_probs=134.5

Q ss_pred             HHHHHHhCCCCc--hhhHHHHHHHHHhc--------------CChhHHHHHhccCCCC---CchhHHHHHHHHHhHHHHH
Q 042593           47 HAVFSKVGFQSH--VYVNTALGDMYVSL--------------GFLKDSSKLFDELPER---NLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        47 ~~~m~~~~~~~~--~~~~~~li~~~~~~--------------g~~~~a~~~~~~m~~~---~~~~~~~~i~~~~~~~~li  107 (352)
                      +..+.+.|..|.  +.+|..+-+.+...              .++.+++..-+.++.+   |...+..       +...+
T Consensus       209 i~~L~raGydp~gM~~ff~rl~~~~~~~~~~p~yl~THPlp~~RIa~lr~ra~q~p~~~~~d~~~~~~-------~~~r~  281 (484)
T COG4783         209 ITTLVRAGYDPQGMPEFFERLADQLRYGGQPPEYLLTHPLPEERIADLRNRAEQSPPYNKLDSPDFQL-------ARARI  281 (484)
T ss_pred             HHHHHHcCCCchhHHHHHHHHHHHHhcCCCCChHHhcCCCchhHHHHHHHHHHhCCCCCCCCCccHHH-------HHHHH
Confidence            445555665554  34555555544222              2455566666666641   2222111       45555


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      .+......-..+..++.+- .+.  .-...-|..-+ .....|+.+.|+..++.+.+....  |+..+....+.+.+.++
T Consensus       282 ~~~~~~~~~~~~~~~~~~~-~~~--~~~aa~YG~A~-~~~~~~~~d~A~~~l~~L~~~~P~--N~~~~~~~~~i~~~~nk  355 (484)
T COG4783         282 RAKYEALPNQQAADLLAKR-SKR--GGLAAQYGRAL-QTYLAGQYDEALKLLQPLIAAQPD--NPYYLELAGDILLEANK  355 (484)
T ss_pred             HHHhccccccchHHHHHHH-hCc--cchHHHHHHHH-HHHHhcccchHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCC
Confidence            5444433333333333333 221  11122333333 345778999999999998877443  78888888999999999


Q ss_pred             hHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChh
Q 042593          188 IFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIK  266 (352)
Q Consensus       188 ~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~  266 (352)
                      .++|.+.++.+....|+ ....-.+..+|.+.|+.++|..++++...                          ..+-|+.
T Consensus       356 ~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~--------------------------~~p~dp~  409 (484)
T COG4783         356 AKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLF--------------------------NDPEDPN  409 (484)
T ss_pred             hHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhh--------------------------cCCCCch
Confidence            99999999999887787 56667778899999999999999998776                          3344777


Q ss_pred             hHHHHHHHHHHcCChhHHHHHHhcC
Q 042593          267 HYGCLIDILERAGRLEQAEEVASGI  291 (352)
Q Consensus       267 ~~~~li~~~~~~g~~~~A~~~~~~m  291 (352)
                      .|..|..+|...|+..+|.....+.
T Consensus       410 ~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         410 GWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             HHHHHHHHHHHhCchHHHHHHHHHH
Confidence            8888888888888887777665554

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

Probab=98.02  E-value=0.0038  Score=57.07  Aligned_cols=118  Identities=10%  Similarity=0.142  Sum_probs=85.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC----------CCchh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE----------RNLVT   92 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----------~~~~~   92 (352)
                      ....|...++.....+-++.+..+++.-.+..    +..-+--|..+++.+++++|.+.+.....          .+...
T Consensus       137 H~rIW~lyl~Fv~~~~lPets~rvyrRYLk~~----P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~ql  212 (835)
T KOG2047|consen  137 HDRIWDLYLKFVESHGLPETSIRVYRRYLKVA----PEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQL  212 (835)
T ss_pred             hccchHHHHHHHHhCCChHHHHHHHHHHHhcC----HHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhH
Confidence            56677778888888888888899888876543    44466678899999999999999888763          12333


Q ss_pred             HHHHHHHHH----------------------------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHH
Q 042593           93 WNVIITGLV----------------------------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLP  144 (352)
Q Consensus        93 ~~~~i~~~~----------------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~  144 (352)
                      |.-+-+-.+                            -|++|.+-|.+.|.+++|-++|++... .  ..+..-|+.+.+
T Consensus       213 w~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~-~--v~tvrDFt~ifd  289 (835)
T KOG2047|consen  213 WLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ-T--VMTVRDFTQIFD  289 (835)
T ss_pred             HHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH-h--heehhhHHHHHH
Confidence            443333333                            689999999999999999999998723 2  234445666666


Q ss_pred             HHH
Q 042593          145 AIW  147 (352)
Q Consensus       145 ~~~  147 (352)
                      +|+
T Consensus       290 ~Ya  292 (835)
T KOG2047|consen  290 AYA  292 (835)
T ss_pred             HHH
Confidence            664

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.01  E-value=0.00077  Score=54.41  Aligned_cols=189  Identities=14%  Similarity=0.045  Sum_probs=128.1

Q ss_pred             cCCHHHHHHHHHHhHhc--cC-CCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCCh
Q 042593          113 MNRSNEALALFRRMAAC--EY-TEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCI  188 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~--~~-~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  188 (352)
                      ..+.++.++++.++...  .| ..++.. .|..++-+....|+.+.|...++++...-..  +..+-..-.-.+-..|.+
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~--S~RV~~lkam~lEa~~~~  102 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPG--SKRVGKLKAMLLEATGNY  102 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCC--ChhHHHHHHHHHHHhhch
Confidence            44677788887777322  22 445554 4667777777888888888888888766422  333333333345567888


Q ss_pred             HHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhh
Q 042593          189 FSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKH  267 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~  267 (352)
                      ++|.++++.+....| |..++-.-+...-..|+--+|++-+.+..+                          .+.-|...
T Consensus       103 ~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~--------------------------~F~~D~EA  156 (289)
T KOG3060|consen  103 KEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLD--------------------------KFMNDQEA  156 (289)
T ss_pred             hhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH--------------------------HhcCcHHH
Confidence            889999988876655 566666666666667777777777777666                          55668899


Q ss_pred             HHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcc---cccCcccccccchhhhh
Q 042593          268 YGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINS---YFFSPITLNSQRLFFFP  329 (352)
Q Consensus       268 ~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~  329 (352)
                      |.-+-..|...|+++.|.-.++++.-. |.+..-+..+...+...|   +.+.|.+++.+.+..=|
T Consensus       157 W~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~  222 (289)
T KOG3060|consen  157 WHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNP  222 (289)
T ss_pred             HHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhCh
Confidence            999999999999999999998888766 455555556665544433   34455666666655444

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

Probab=98.01  E-value=8.5e-05  Score=55.69  Aligned_cols=92  Identities=7%  Similarity=-0.060  Sum_probs=44.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      ...+...+...|++++|.+.++.....+ +.+...+..+..++.+.|++++|...++...+.++.....       +..+
T Consensus        20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~-------~~~l   91 (135)
T TIGR02552        20 IYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRP-------YFHA   91 (135)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHH-------HHHH
Confidence            3344444445555555555555554443 3344555555555555555555555555543321111111       4444


Q ss_pred             HHHHHhcCCHHHHHHHHHHh
Q 042593          107 IDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m  126 (352)
                      ...+...|++++|...|++.
T Consensus        92 a~~~~~~g~~~~A~~~~~~a  111 (135)
T TIGR02552        92 AECLLALGEPESALKALDLA  111 (135)
T ss_pred             HHHHHHcCCHHHHHHHHHHH
Confidence            44555555555555555554

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

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.99  E-value=0.00062  Score=62.92  Aligned_cols=185  Identities=13%  Similarity=0.113  Sum_probs=109.3

Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCCh
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCI  188 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  188 (352)
                      +...+.+|.+|+.+++.+ +...  .-.--|..+..-|+..|+++-|+++|-+          ...++-.|..|.+.|++
T Consensus       741 aai~akew~kai~ildni-qdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e----------~~~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNI-QDQK--TASGYYGEIADHYANKGDFEIAEELFTE----------ADLFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHh-hhhc--cccccchHHHHHhccchhHHHHHHHHHh----------cchhHHHHHHHhccccH
Confidence            344556777777777776 4332  1223466777778888888888877753          23355667888888888


Q ss_pred             HHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------hHhHHHHHHHHHHhcCCC
Q 042593          189 FSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------GEEGLKFFDKMVEECEVL  262 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------~~~a~~~~~~m~~~~~~~  262 (352)
                      ++|.++-.+..........|-+-..-+-.+|++.+|+++|-.+..    |+...-.      .+..+++.++--    -.
T Consensus       808 ~da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~----p~~aiqmydk~~~~ddmirlv~k~h----~d  879 (1636)
T KOG3616|consen  808 EDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGE----PDKAIQMYDKHGLDDDMIRLVEKHH----GD  879 (1636)
T ss_pred             HHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEEccC----chHHHHHHHhhCcchHHHHHHHHhC----hh
Confidence            888888877754445566676666667777777777776643322    2211111      222222222211    11


Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCccccc
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLN  321 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  321 (352)
                      .-..|--.+..-|-..|+...|+.-|-+..+       |.+-++.|-.++.+++|-++.
T Consensus       880 ~l~dt~~~f~~e~e~~g~lkaae~~flea~d-------~kaavnmyk~s~lw~dayria  931 (1636)
T KOG3616|consen  880 HLHDTHKHFAKELEAEGDLKAAEEHFLEAGD-------FKAAVNMYKASELWEDAYRIA  931 (1636)
T ss_pred             hhhHHHHHHHHHHHhccChhHHHHHHHhhhh-------HHHHHHHhhhhhhHHHHHHHH
Confidence            1123445566777778888888877766654       444455555555555554443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.97  E-value=0.0018  Score=64.99  Aligned_cols=295  Identities=8%  Similarity=-0.060  Sum_probs=180.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCC------CCc--hhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGF------QSH--VYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVI   96 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~------~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~   96 (352)
                      .......+...|+++++..+++.....--      .+.  ......+...+...|++++|...+++..+  +....+...
T Consensus       412 ~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  491 (903)
T PRK04841        412 VLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRI  491 (903)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHH
Confidence            33444555678899999998887754310      111  12223344556678999999998887543  221111110


Q ss_pred             HHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC-C-CCC--hhhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCC
Q 042593           97 ITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY-T-EPS--EITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFN  168 (352)
Q Consensus        97 i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~-~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~  168 (352)
                       .   ..+.+...+...|++++|...+.+...... . .+.  ..++..+...+...|++++|...+++....    +..
T Consensus       492 -~---a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~  567 (903)
T PRK04841        492 -V---ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLE  567 (903)
T ss_pred             -H---HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence             0   156667778889999999999988732211 0 111  234556667788899999999988876543    221


Q ss_pred             --CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC----CC--CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          169 --AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD----RK--NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       169 --~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                        +.....+..+...+...|++++|...+++....    .+  ....+..+...+...|+.++|...+.+.....-....
T Consensus       568 ~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~  647 (903)
T PRK04841        568 QLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRY  647 (903)
T ss_pred             cccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccc
Confidence              101233445566777889999999998875432    22  2344555667788999999999999887553111110


Q ss_pred             ch-hh----------------hHhHHHHHHHHHHhcCCCCC---hhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CC-
Q 042593          241 SW-RI----------------GEEGLKFFDKMVEECEVLPD---IKHYGCLIDILERAGRLEQAEEVASGIPSQ---IT-  296 (352)
Q Consensus       241 ~~-~~----------------~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~-  296 (352)
                      .. ..                .+.+..++...... .....   ...+..+..++...|+.++|...+++....   .. 
T Consensus       648 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~-~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~  726 (903)
T PRK04841        648 HSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKP-EFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRL  726 (903)
T ss_pred             cHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCC-CCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCc
Confidence            00 00                33333333332211 11111   111346777888999999999988876543   11 


Q ss_pred             ---CchhhHHHHHHHHhcccccCcccccccchh
Q 042593          297 ---NVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       297 ---~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                         ...+...+..++...|+.++|...+.+.+.
T Consensus       727 ~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~  759 (903)
T PRK04841        727 MSDLNRNLILLNQLYWQQGRKSEAQRVLLEALK  759 (903)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               123566667778899999999888888754

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

Probab=97.90  E-value=0.00042  Score=52.71  Aligned_cols=128  Identities=11%  Similarity=0.087  Sum_probs=78.8

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHhccCCCCCchh-HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh--
Q 042593           60 YVNTALGDMYVSLGFLKDSSKLFDELPERNLVT-WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE--  136 (352)
Q Consensus        60 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~--  136 (352)
                      ..|..++..+ ..++...+...++.+.+....+ |..+.     .-.+...+...|++++|...|+.. ......|+.  
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A-----~l~lA~~~~~~g~~~~A~~~l~~~-~~~~~d~~l~~   85 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALA-----ALQLAKAAYEQGDYDEAKAALEKA-LANAPDPELKP   85 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHH-----HHHHHHHHHHCCCHHHHHHHHHHH-HhhCCCHHHHH
Confidence            3455555555 3677777777777766522222 33322     344556777778888888888887 433322322  


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      .....+...+...|++++|...++.......   ....+....++|.+.|+.++|...|+.
T Consensus        86 ~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~---~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   86 LARLRLARILLQQGQYDEALATLQQIPDEAF---KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHhccCcch---HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            2344556667778888888888766433222   445666777888888888888887765

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

Probab=97.90  E-value=1.3e-05  Score=42.91  Aligned_cols=30  Identities=17%  Similarity=0.214  Sum_probs=21.4

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCC
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGF   55 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~   55 (352)
                      +|++++++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            677777777777777777777777776653

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.

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

Probab=97.89  E-value=0.00016  Score=50.71  Aligned_cols=81  Identities=15%  Similarity=0.031  Sum_probs=64.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCC-CCChhhHHHHHHHHHhCC--------ChhhHHHHHHHHHhcCCCCCchh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYT-EPSEITILAVLPAIWKNG--------EVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                      -...|..+...+++.....+|+.+ ++.|+ .|+..+|+.++.+.+++.        ++-....+|+.|...++.| +..
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqsl-kRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP-~~e  105 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSL-KRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKP-NDE  105 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHH-HhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCC-cHH
Confidence            344555566669999999999999 88888 899999999999988764        2445678888888888888 888


Q ss_pred             hHHHHHHHHHhh
Q 042593          174 VSNCLIDTYAKC  185 (352)
Q Consensus       174 ~~~~li~~~~~~  185 (352)
                      +|+.++..+.+.
T Consensus       106 tYnivl~~Llkg  117 (120)
T PF08579_consen  106 TYNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHHh
Confidence            888888877653

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

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

Probab=97.86  E-value=0.00019  Score=63.68  Aligned_cols=123  Identities=8%  Similarity=-0.008  Sum_probs=100.6

Q ss_pred             hCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCch---hHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHh
Q 042593           53 VGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLV---TWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAA  128 (352)
Q Consensus        53 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~---~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  128 (352)
                      .+.+-+......+++.+....+++.+..++-+... |+..   .++        ..++++.|...|..++++.+++.= .
T Consensus        60 ~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t--------~ha~vR~~l~~~~~~~~l~~L~n~-~  130 (429)
T PF10037_consen   60 RKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPST--------HHALVRQCLELGAEDELLELLKNR-L  130 (429)
T ss_pred             cCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCcc--------HHHHHHHHHhcCCHHHHHHHHhCh-h
Confidence            34466777888889999888999999988888764 2221   111        668999999999999999999998 8


Q ss_pred             ccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh
Q 042593          129 CEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC  185 (352)
Q Consensus       129 ~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  185 (352)
                      ..|+-||.+|++.++..+.+.|++..|.++..+|...+... +..++..-+.+|.+.
T Consensus       131 ~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~-~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  131 QYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFD-NPSTQALALYSCYKY  186 (429)
T ss_pred             hcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccC-CchHHHHHHHHHHHh
Confidence            89999999999999999999999999999999998887766 777777666666665

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 [].

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.85  E-value=0.002  Score=53.31  Aligned_cols=253  Identities=9%  Similarity=-0.021  Sum_probs=128.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHH-HHHHHHhcCChhHHHHHhccCCC-CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTA-LGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~-li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~  100 (352)
                      +......+...|-+..++..|-+.++++...-  |...-|.. -...+-+.+.+.+|+++...|.. ++...-..-+.+ 
T Consensus        43 ~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqa-  119 (459)
T KOG4340|consen   43 SRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRLYQAQSLYKACIYADALRVAFLLLDNPALHSRVLQLQA-  119 (459)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHH-
Confidence            55667777788888889999999999887654  43333321 12344466778888888777765 222211111111 


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                             ...-+.+|+..+..++++. ...   -+..+.+.......+.|+++.|.+-|+...+-+--. ....||..+ 
T Consensus       120 -------AIkYse~Dl~g~rsLveQl-p~e---n~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyq-pllAYniAL-  186 (459)
T KOG4340|consen  120 -------AIKYSEGDLPGSRSLVEQL-PSE---NEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQ-PLLAYNLAL-  186 (459)
T ss_pred             -------HHhcccccCcchHHHHHhc-cCC---CccchhccchheeeccccHHHHHHHHHHHHhhcCCC-chhHHHHHH-
Confidence                   1112345555555555555 111   122222233333345555555555555554433222 334444333 


Q ss_pred             HHHhhCChHHHHHHHHHhccC---------------CCCH---------------hhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          181 TYAKCGCIFSASKLFEDTSVD---------------RKNL---------------VSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~---------------~~~~---------------~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      +.-+.|+.+.|++...++...               .||+               ..+|.-...+.+.|+++.|.+.+-.
T Consensus       187 aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtD  266 (459)
T KOG4340|consen  187 AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTD  266 (459)
T ss_pred             HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhc
Confidence            233344555555555443321               1111               1122223334556666666666655


Q ss_pred             HHhc-CCCCCcchhh----------hHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          231 MQKV-GLKPNRSWRI----------GEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       231 m~~~-~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      |--+ .-..|..|..          +....+-++-+.   ++.| ...||..++-.|||..-++.|-.++-+-...
T Consensus       267 mPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqFLL---~~nPfP~ETFANlLllyCKNeyf~lAADvLAEn~~l  339 (459)
T KOG4340|consen  267 MPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQFLL---QQNPFPPETFANLLLLYCKNEYFDLAADVLAENAHL  339 (459)
T ss_pred             CCCcccccCCchhhhHHHHhcccCCccccHHHHHHHH---hcCCCChHHHHHHHHHHhhhHHHhHHHHHHhhCcch
Confidence            5321 2233344433          112222222222   2233 4578888999999999999999888775554

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

Probab=97.82  E-value=0.019  Score=55.40  Aligned_cols=47  Identities=15%  Similarity=0.227  Sum_probs=25.0

Q ss_pred             hhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhccccc
Q 042593          265 IKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFF  315 (352)
Q Consensus       265 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~  315 (352)
                      +..|..|...+...|+++.|...-++..    +..+|...-.+|...+.+.
T Consensus      1220 vSN~a~La~TLV~LgeyQ~AVD~aRKAn----s~ktWK~VcfaCvd~~EFr 1266 (1666)
T KOG0985|consen 1220 VSNFAKLASTLVYLGEYQGAVDAARKAN----STKTWKEVCFACVDKEEFR 1266 (1666)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhhcc----chhHHHHHHHHHhchhhhh
Confidence            3345555555555555555555554443    4455665555555554443

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

Probab=97.81  E-value=0.0014  Score=61.50  Aligned_cols=259  Identities=13%  Similarity=0.062  Sum_probs=139.2

Q ss_pred             hcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCC
Q 042593           36 TLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNR  115 (352)
Q Consensus        36 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~  115 (352)
                      +.|.+++|+.+|++.++..         .|=..|...|.+++|.++-+.=..  +..-+       ||..-..-+-..+|
T Consensus       812 eLgMlEeA~~lYr~ckR~D---------LlNKlyQs~g~w~eA~eiAE~~DR--iHLr~-------Tyy~yA~~Lear~D  873 (1416)
T KOG3617|consen  812 ELGMLEEALILYRQCKRYD---------LLNKLYQSQGMWSEAFEIAETKDR--IHLRN-------TYYNYAKYLEARRD  873 (1416)
T ss_pred             HHhhHHHHHHHHHHHHHHH---------HHHHHHHhcccHHHHHHHHhhccc--eehhh-------hHHHHHHHHHhhcc
Confidence            3445555555555444322         233445555666666555443211  11111       15555555666777


Q ss_pred             HHHHHHHHHHh----------HhccC--------CCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593          116 SNEALALFRRM----------AACEY--------TEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus       116 ~~~a~~~~~~m----------~~~~~--------~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                      .+.|++.|++.          ++...        ...|...|.-....+-..|+++.|..+|...+          -|-+
T Consensus       874 i~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~----------D~fs  943 (1416)
T KOG3617|consen  874 IEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAK----------DYFS  943 (1416)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhh----------hhhh
Confidence            88888777754          11110        01233334444444555677777777766432          2445


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc----------CCCCCcchhh---
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKV----------GLKPNRSWRI---  244 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----------~~~p~~~~~~---  244 (352)
                      +++..|-.|+.++|-++-++-    -|......|.+-|-..|++.+|...|.+....          +++....+..   
T Consensus       944 ~VrI~C~qGk~~kAa~iA~es----gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d~L~nlal~s 1019 (1416)
T KOG3617|consen  944 MVRIKCIQGKTDKAARIAEES----GDKAACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKDRLANLALMS 1019 (1416)
T ss_pred             heeeEeeccCchHHHHHHHhc----ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhhc
Confidence            666666777777777766543    35555666777788888888888888775431          1110000000   


Q ss_pred             ----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHh---------cCCCC---CCCchhhHHHHHHH
Q 042593          245 ----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVAS---------GIPSQ---ITNVVVWRTGFLRL  308 (352)
Q Consensus       245 ----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~---------~m~~~---~~~~~~~~~li~~~  308 (352)
                          .-.|-++|++.    |.     -+..-+..|-++|-+.+|.++--         -+.+.   ..|+...+.-..-+
T Consensus      1020 ~~~d~v~aArYyEe~----g~-----~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF 1090 (1416)
T KOG3617|consen 1020 GGSDLVSAARYYEEL----GG-----YAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFF 1090 (1416)
T ss_pred             CchhHHHHHHHHHHc----ch-----hhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence                22333333332    11     12334556778888888876522         11111   45667777777778


Q ss_pred             HhcccccCcccccccchhhhhhHHHHhh
Q 042593          309 LINSYFFSPITLNSQRLFFFPAALYALT  336 (352)
Q Consensus       309 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~  336 (352)
                      ..+.++++|..+..... .|..++..|.
T Consensus      1091 ~~~~qyekAV~lL~~ar-~~~~AlqlC~ 1117 (1416)
T KOG3617|consen 1091 ENNQQYEKAVNLLCLAR-EFSGALQLCK 1117 (1416)
T ss_pred             HhHHHHHHHHHHHHHHH-HHHHHHHHHh
Confidence            88899998888776654 2333444443

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

Probab=97.80  E-value=0.019  Score=52.13  Aligned_cols=114  Identities=11%  Similarity=-0.014  Sum_probs=72.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHH--------HHHhcCCCCCcchhh----------------hHhHHHHHHHHHHhcCCC
Q 042593          207 SWTTIISGFAMHGMGKEAVENFE--------RMQKVGLKPNRSWRI----------------GEEGLKFFDKMVEECEVL  262 (352)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~--------~m~~~~~~p~~~~~~----------------~~~a~~~~~~m~~~~~~~  262 (352)
                      .--.+++.....|+++.|.+++.        .+.+.+-.|-.....                .++|...|..-... . .
T Consensus       378 v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~-s-~  455 (652)
T KOG2376|consen  378 VLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTG-S-I  455 (652)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhccc-c-h
Confidence            34455666778889999988888        566655566554444                45555555443221 1 1


Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCccccccc
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQ  323 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~  323 (352)
                      --..++......-.+.|+-++|..+++++... +++..+...++.+|+.. +.++|..+.+.
T Consensus       456 ~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~-d~eka~~l~k~  516 (652)
T KOG2376|consen  456 ALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL-DPEKAESLSKK  516 (652)
T ss_pred             HHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc-CHHHHHHHhhc
Confidence            11223444445556779999999999988876 77888888888887765 34555544443

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

Probab=97.80  E-value=0.00055  Score=63.99  Aligned_cols=181  Identities=10%  Similarity=0.100  Sum_probs=108.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh-C-------C-CCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV-G-------F-QSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTW   93 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~-------~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~   93 (352)
                      +...|..+.+-|.+.++++-|.-.+-.|... |       . .|+ .+=..+.-.....|.+++|+.+|.+.+.      
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR------  828 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKR------  828 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHH------
Confidence            4557888888888888888887777666531 1       1 222 2222333344577889999999888764      


Q ss_pred             HHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC-----
Q 042593           94 NVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN-----  168 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-----  168 (352)
                               |..|=+.|...|.|++|.++-+.- .+  + .=..||.....-+...+|++.|.+.|+........     
T Consensus       829 ---------~DLlNKlyQs~g~w~eA~eiAE~~-DR--i-HLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL  895 (1416)
T KOG3617|consen  829 ---------YDLLNKLYQSQGMWSEAFEIAETK-DR--I-HLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRML  895 (1416)
T ss_pred             ---------HHHHHHHHHhcccHHHHHHHHhhc-cc--e-ehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHH
Confidence                     555557788899999998886544 21  1 12346777777777788888888777653221100     


Q ss_pred             ---C----------CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          169 ---A----------FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       169 ---~----------~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                         |          .+...|.=....+-..|+.+.|+.++...+       -|-+++...|-.|+.++|-.+-++
T Consensus       896 ~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~-------D~fs~VrI~C~qGk~~kAa~iA~e  963 (1416)
T KOG3617|consen  896 KEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAK-------DYFSMVRIKCIQGKTDKAARIAEE  963 (1416)
T ss_pred             HhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhh-------hhhhheeeEeeccCchHHHHHHHh
Confidence               0          022223223333334555666666555442       355555566666666666665554

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.80  E-value=0.0081  Score=48.72  Aligned_cols=134  Identities=10%  Similarity=0.046  Sum_probs=98.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |..+.-+....|+.+-|...++++ ...-  |.+. .--.-..-+-..|++++|.++++.+.+.+..  +..++..-+-+
T Consensus        55 ~EqV~IAAld~~~~~lAq~C~~~L-~~~f--p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~ddpt--~~v~~KRKlAi  129 (289)
T KOG3060|consen   55 YEQVFIAALDTGRDDLAQKCINQL-RDRF--PGSKRVGKLKAMLLEATGNYKEAIEYYESLLEDDPT--DTVIRKRKLAI  129 (289)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHH-HHhC--CCChhHHHHHHHHHHHhhchhhHHHHHHHHhccCcc--hhHHHHHHHHH
Confidence            777777888889999999999998 4332  4332 2111112244568899999999999887633  77777777777


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchh
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWR  243 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~  243 (352)
                      .-..|+--+|++-+.+..+. ..|...|.-+...|...|++++|.-.++++.-  +.|-...+
T Consensus       130 lka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll--~~P~n~l~  190 (289)
T KOG3060|consen  130 LKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLL--IQPFNPLY  190 (289)
T ss_pred             HHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH--cCCCcHHH
Confidence            77788877888877776555 56889999999999999999999999999886  34444333

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.77  E-value=0.00064  Score=49.45  Aligned_cols=95  Identities=13%  Similarity=0.035  Sum_probs=44.5

Q ss_pred             HHHHHHHHhCCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHH
Q 042593          140 LAVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISG  214 (352)
Q Consensus       140 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~  214 (352)
                      ......+.+.|++++|...++.+.+.... +.....+..+..++.+.|+++.|.+.|+.+....|+    ...+..+..+
T Consensus         6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~   85 (119)
T TIGR02795         6 YDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMS   85 (119)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHH
Confidence            33444444555555555555555443211 001233444555555555555555555554433222    2334444455


Q ss_pred             HHcCCCHHHHHHHHHHHHhc
Q 042593          215 FAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +.+.|+.++|...++++.+.
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        86 LQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHhCChHHHHHHHHHHHHH
Confidence            55555555555555555543

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

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

Probab=97.77  E-value=0.00066  Score=57.78  Aligned_cols=128  Identities=17%  Similarity=0.116  Sum_probs=98.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHH-HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPA-IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |-.+++..-+.+..+.|..+|.+..+......  ..|...... +...++.+.|..+|+...+.- .. +...|...++.
T Consensus         4 ~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~--~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f-~~-~~~~~~~Y~~~   79 (280)
T PF05843_consen    4 WIQYMRFMRRTEGIEAARKVFKRARKDKRCTY--HVYVAYALMEYYCNKDPKRARKIFERGLKKF-PS-DPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-T--HHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH-TT--HHHHHHHHHH
T ss_pred             HHHHHHHHHHhCChHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CC-CHHHHHHHHHH
Confidence            88889999999999999999999943222333  344443333 333567777999999998873 33 88899999999


Q ss_pred             HHhhCChHHHHHHHHHhccCCCCH----hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKNL----VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +.+.|+.+.|..+|+.....-+..    ..|...+..=.+.|+.+.+..+.+++.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999987764444    48999999999999999999999998874

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

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

Probab=97.76  E-value=0.012  Score=50.24  Aligned_cols=209  Identities=12%  Similarity=0.037  Sum_probs=118.3

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCC---C--chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQ---S--HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITG   99 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~---~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~   99 (352)
                      ..|......|-..|++++|.+.|.........   +  -...|.....+|-+. ++++|.+.                  
T Consensus        36 ~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~------------------   96 (282)
T PF14938_consen   36 DLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIEC------------------   96 (282)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHH------------------
T ss_pred             HHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHH------------------
Confidence            34556666666666666666666655432111   1  011222222222222 44444333                  


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC-CChhhHHHHHHHHHhc----CCCCCchhh
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN-GEVRNCQLIHGYGEKR----GFNAFDIHV  174 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~----~~~~~~~~~  174 (352)
                         |...+..|...|++..|-..+.++                ...|... |+++.|...|++..+.    +-...-..+
T Consensus        97 ---~~~A~~~y~~~G~~~~aA~~~~~l----------------A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~  157 (282)
T PF14938_consen   97 ---YEKAIEIYREAGRFSQAAKCLKEL----------------AEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAEC  157 (282)
T ss_dssp             ---HHHHHHHHHHCT-HHHHHHHHHHH----------------HHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             ---HHHHHHHHHhcCcHHHHHHHHHHH----------------HHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHH
Confidence               555556677777777776666665                3445555 7888888888877643    321112456


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCC-------CCHh-hHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhH
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDR-------KNLV-SWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGE  246 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~-------~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  246 (352)
                      +..+...+.+.|++++|.++|+++....       .++. .|-..+-++...|+...|...+++.....  |        
T Consensus       158 ~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~--~--------  227 (282)
T PF14938_consen  158 LLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQD--P--------  227 (282)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTS--T--------
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--C--------
Confidence            7788899999999999999999875431       1222 23334456777899999999999987642  1        


Q ss_pred             hHHHHHHHHHHhcCCCC--ChhhHHHHHHHHHH--cCChhHHHHHHhcCCCC
Q 042593          247 EGLKFFDKMVEECEVLP--DIKHYGCLIDILER--AGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       247 ~a~~~~~~m~~~~~~~p--~~~~~~~li~~~~~--~g~~~~A~~~~~~m~~~  294 (352)
                                   ++..  .......||.++-.  ...+++|..-|+.+...
T Consensus       228 -------------~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~l  266 (282)
T PF14938_consen  228 -------------SFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRL  266 (282)
T ss_dssp             -------------TSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS--
T ss_pred             -------------CCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCcc
Confidence                         2222  23455666776653  34566777777777654

>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=97.76  E-value=0.0005  Score=47.17  Aligned_cols=89  Identities=16%  Similarity=0.089  Sum_probs=40.0

Q ss_pred             HHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCC
Q 042593          142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGM  220 (352)
Q Consensus       142 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~  220 (352)
                      +...+...|++++|...++...+....  +...+..+..++...|++++|.+.|+...... .+..++..+...+...|+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (100)
T cd00189           6 LGNLYYKLGDYDEALEYYEKALELDPD--NADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhcCCc--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHh
Confidence            333344444444444444444433221  22334444444445555555555554443332 222344444445555555


Q ss_pred             HHHHHHHHHHHH
Q 042593          221 GKEAVENFERMQ  232 (352)
Q Consensus       221 ~~~a~~~~~~m~  232 (352)
                      +++|...+.+..
T Consensus        84 ~~~a~~~~~~~~   95 (100)
T cd00189          84 YEEALEAYEKAL   95 (100)
T ss_pred             HHHHHHHHHHHH
Confidence            555555554443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.76  E-value=0.0005  Score=50.02  Aligned_cols=99  Identities=14%  Similarity=-0.000  Sum_probs=77.0

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhH
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEG  248 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a  248 (352)
                      .++-.+...+.+.|++++|.+.|+.+....|+    ...+..+..++.+.|++++|...++.+....  |          
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--p----------   70 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKY--P----------   70 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHC--C----------
Confidence            35567788888999999999999998765443    3466678888999999999999999988642  2          


Q ss_pred             HHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          249 LKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       249 ~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                                 +.+.....+..+..++.+.|+.++|.+.++++...
T Consensus        71 -----------~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        71 -----------KSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             -----------CCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence                       11223456777888889999999999999988766

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.76  E-value=0.0046  Score=62.09  Aligned_cols=242  Identities=12%  Similarity=0.010  Sum_probs=155.6

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCC---CC--chhhHHHHHHHHHhcCChhHHHHHhccCCC-------CCchhH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGF---QS--HVYVNTALGDMYVSLGFLKDSSKLFDELPE-------RNLVTW   93 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~---~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~~~~~~   93 (352)
                      ..+.+...+...|++++|...++......-   .+  -..+...+...+...|++++|...+++...       ++.. .
T Consensus       493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~-~  571 (903)
T PRK04841        493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLP-M  571 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccc-H
Confidence            345566667789999999999988764321   11  123556677788899999999998887643       1111 1


Q ss_pred             HHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc-CCCCC--hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC
Q 042593           94 NVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE-YTEPS--EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF  170 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  170 (352)
                      ...+     +..+...+...|++++|...+.+..... ...+.  ...+..+.......|+.++|...++..........
T Consensus       572 ~~~~-----~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~  646 (903)
T PRK04841        572 HEFL-----LRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGR  646 (903)
T ss_pred             HHHH-----HHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccc
Confidence            1111     4445566777899999999988873221 11122  23455566677889999999999888865321110


Q ss_pred             chhhH-----HHHHHHHHhhCChHHHHHHHHHhccCCC-CH----hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          171 DIHVS-----NCLIDTYAKCGCIFSASKLFEDTSVDRK-NL----VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       171 ~~~~~-----~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                      ....+     ...+..+...|+.+.|.+.+.......+ ..    ..+..+..++...|+.++|...+++.....     
T Consensus       647 ~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~-----  721 (903)
T PRK04841        647 YHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENA-----  721 (903)
T ss_pred             ccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-----
Confidence            11111     1123455668999999999887654321 11    113456677889999999999999877631     


Q ss_pred             chhhhHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          241 SWRIGEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       241 ~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                                     ... +..+ ...+...+..++.+.|+.++|...+.+....
T Consensus       722 ---------------~~~-g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        722 ---------------RSL-RLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             ---------------HHh-CchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                           011 3322 2345667788889999999999888877655

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

Probab=97.76  E-value=0.001  Score=64.34  Aligned_cols=228  Identities=11%  Similarity=-0.039  Sum_probs=153.2

Q ss_pred             CchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           57 SHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        57 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      .+...+..|+..|...+++++|.++.+...+  |+...+         |..+...+.+.++.+.+..+            
T Consensus        29 ~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~---------yy~~G~l~~q~~~~~~~~lv------------   87 (906)
T PRK14720         29 SKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISA---------LYISGILSLSRRPLNDSNLL------------   87 (906)
T ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceeh---------HHHHHHHHHhhcchhhhhhh------------
Confidence            3567899999999999999999999997665  443331         33333356666665444443            


Q ss_pred             ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHH
Q 042593          135 SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIIS  213 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~  213 (352)
                            .++.......++..+..+.+.+...+-   +...+-.+..+|-+.|+.++|..+++++.+.. .|+...|.+.-
T Consensus        88 ------~~l~~~~~~~~~~~ve~~~~~i~~~~~---~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY  158 (906)
T PRK14720         88 ------NLIDSFSQNLKWAIVEHICDKILLYGE---NKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLAT  158 (906)
T ss_pred             ------hhhhhcccccchhHHHHHHHHHHhhhh---hhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHH
Confidence                  334444455566666666666666543   55678899999999999999999999988774 57899999999


Q ss_pred             HHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          214 GFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      .|... +.++|.+++.+.+..-+.-    -.+..+.++|.++...  .+-+...+-.+.+.....-...           
T Consensus       159 ~~ae~-dL~KA~~m~~KAV~~~i~~----kq~~~~~e~W~k~~~~--~~~d~d~f~~i~~ki~~~~~~~-----------  220 (906)
T PRK14720        159 SYEEE-DKEKAITYLKKAIYRFIKK----KQYVGIEEIWSKLVHY--NSDDFDFFLRIERKVLGHREFT-----------  220 (906)
T ss_pred             HHHHh-hHHHHHHHHHHHHHHHHhh----hcchHHHHHHHHHHhc--CcccchHHHHHHHHHHhhhccc-----------
Confidence            99999 9999999999987751100    0167788888888874  2223333333333332221111           


Q ss_pred             CCCCchhhHHHHHHHHhcccccCcccccccchhhhhhHHHH
Q 042593          294 QITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYA  334 (352)
Q Consensus       294 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  334 (352)
                        .-..++-.+...|-...++.+++.+++..+...|.+-.+
T Consensus       221 --~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a  259 (906)
T PRK14720        221 --RLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKA  259 (906)
T ss_pred             --hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhh
Confidence              133445556666777777888888887777666655444

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=97.76  E-value=0.0013  Score=62.77  Aligned_cols=165  Identities=17%  Similarity=0.095  Sum_probs=119.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhh
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEIT  138 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t  138 (352)
                      ...|..|...|+...+...|.+.|++..+-|..-+.+       +....+.|+...+++.|..+.-..-+......-...
T Consensus       492 apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaea-------aaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~n  564 (1238)
T KOG1127|consen  492 APAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEA-------AAASADTYAEESTWEEAFEICLRAAQKAPAFACKEN  564 (1238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhh-------HHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhh
Confidence            4678889999999889999999999988755554444       888999999999999999984443111111111122


Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHH--HHHHHH
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTT--IISGFA  216 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~--li~~~~  216 (352)
                      |...--.+-+.++..++..-++......+.  |...|..+..+|.++|++..|.++|.+...-.|+. +|..  ....-|
T Consensus       565 W~~rG~yyLea~n~h~aV~~fQsALR~dPk--D~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s-~y~~fk~A~~ec  641 (1238)
T KOG1127|consen  565 WVQRGPYYLEAHNLHGAVCEFQSALRTDPK--DYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLS-KYGRFKEAVMEC  641 (1238)
T ss_pred             hhhccccccCccchhhHHHHHHHHhcCCch--hHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHh-HHHHHHHHHHHH
Confidence            333444456778888888888877766544  88999999999999999999999999876555643 2222  222357


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 042593          217 MHGMGKEAVENFERMQK  233 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (352)
                      ..|++.+|...+.....
T Consensus       642 d~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  642 DNGKYKEALDALGLIIY  658 (1238)
T ss_pred             HhhhHHHHHHHHHHHHH
Confidence            78889999888887654

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.74  E-value=0.0019  Score=59.81  Aligned_cols=169  Identities=16%  Similarity=0.134  Sum_probs=116.3

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDG  109 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~  109 (352)
                      .+.+....+.|..|+.+++.+....  .-..-|..+.+.|+..|+++.|+++|-+..     .          ++-.|..
T Consensus       738 aieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~----------~~dai~m  800 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEAD-----L----------FKDAIDM  800 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhcc-----h----------hHHHHHH
Confidence            3445556677888888888776654  234457778888899999999999987753     2          6667788


Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChH
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIF  189 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  189 (352)
                      |.++|+|+.|.++-.+-   .|.......|.+-..-+-+.|++.+|+++|-.+   |.+       ...|..|-+.|..+
T Consensus       801 y~k~~kw~da~kla~e~---~~~e~t~~~yiakaedldehgkf~eaeqlyiti---~~p-------~~aiqmydk~~~~d  867 (1636)
T KOG3616|consen  801 YGKAGKWEDAFKLAEEC---HGPEATISLYIAKAEDLDEHGKFAEAEQLYITI---GEP-------DKAIQMYDKHGLDD  867 (1636)
T ss_pred             HhccccHHHHHHHHHHh---cCchhHHHHHHHhHHhHHhhcchhhhhheeEEc---cCc-------hHHHHHHHhhCcch
Confidence            89999999888875554   444445556777777777888888888777532   221       25577888888888


Q ss_pred             HHHHHHHHhccCCCCH--hhHHHHHHHHHcCCCHHHHHHHHHHH
Q 042593          190 SASKLFEDTSVDRKNL--VSWTTIISGFAMHGMGKEAVENFERM  231 (352)
Q Consensus       190 ~a~~~~~~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m  231 (352)
                      +.+++.++-   .|+.  .|--.+..-|-..|+.++|+.-|-+.
T Consensus       868 dmirlv~k~---h~d~l~dt~~~f~~e~e~~g~lkaae~~flea  908 (1636)
T KOG3616|consen  868 DMIRLVEKH---HGDHLHDTHKHFAKELEAEGDLKAAEEHFLEA  908 (1636)
T ss_pred             HHHHHHHHh---ChhhhhHHHHHHHHHHHhccChhHHHHHHHhh
Confidence            888887765   3332  34444555666777777777766553

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

Probab=97.72  E-value=0.0031  Score=59.64  Aligned_cols=207  Identities=14%  Similarity=0.081  Sum_probs=128.7

Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHH--HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCCh
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPA--IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCI  188 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  188 (352)
                      ...+++.+|++...++.++.   |+. .|..++.+  +.+.|+.++|..+++.....+..  |..+...+-.+|...|+.
T Consensus        20 ld~~qfkkal~~~~kllkk~---Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~--D~~tLq~l~~~y~d~~~~   93 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKKH---PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT--DDLTLQFLQNVYRDLGKL   93 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHHC---CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC--chHHHHHHHHHHHHHhhh
Confidence            45678888888888885644   332 23444444  45889999999888887666554  788888999999999999


Q ss_pred             HHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---------------------hHh
Q 042593          189 FSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---------------------GEE  247 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---------------------~~~  247 (352)
                      ++|..+|++.....|+......+..+|.+.+.+.+-.+.--+|-+. +.-+..+++                     ...
T Consensus        94 d~~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~L  172 (932)
T KOG2053|consen   94 DEAVHLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLAL  172 (932)
T ss_pred             hHHHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHH
Confidence            9999999998877888888888888888888776544433333331 222222222                     555


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHH-hcCCCC--CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA-SGIPSQ--ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~-~~m~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      |.+.++.+.+..|.--+..-.......+...|++++|++++ ....+.  +-+...-+--+.-+...+++.+-.++..+-
T Consensus       173 A~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  173 AEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            66667777666321112222223344556778888888887 233222  223333333444455555555544444443

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

Probab=97.72  E-value=0.0056  Score=55.98  Aligned_cols=191  Identities=12%  Similarity=-0.008  Sum_probs=133.8

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCC---CchhHHHHHHHHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPER---NLVTWNVIITGLV  101 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~~i~~~~  101 (352)
                      ..|..+++ |-..+++...+++.+...+ +.+-...|.....-.++..|+-++|......-...   +.++         
T Consensus         9 ~lF~~~lk-~yE~kQYkkgLK~~~~iL~-k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vC---------   77 (700)
T KOG1156|consen    9 ALFRRALK-CYETKQYKKGLKLIKQILK-KFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVC---------   77 (700)
T ss_pred             HHHHHHHH-HHHHHHHHhHHHHHHHHHH-hCCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchh---------
Confidence            34444554 4466788888888888877 44556677766666777889999998888776653   4455         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                       |..+.-.+-...++++|++.|....+   +.|| ...+.-+----++.++++.......++.+....  ....|..+..
T Consensus        78 -wHv~gl~~R~dK~Y~eaiKcy~nAl~---~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~--~ra~w~~~Av  151 (700)
T KOG1156|consen   78 -WHVLGLLQRSDKKYDEAIKCYRNALK---IEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPS--QRASWIGFAV  151 (700)
T ss_pred             -HHHHHHHHhhhhhHHHHHHHHHHHHh---cCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh--hHHHHHHHHH
Confidence             77777777778899999999998844   3454 345665555567778888888888877776443  5667788888


Q ss_pred             HHHhhCChHHHHHHHHHhccC---CCCHhhHHHHHH------HHHcCCCHHHHHHHHHHHH
Q 042593          181 TYAKCGCIFSASKLFEDTSVD---RKNLVSWTTIIS------GFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~---~~~~~~~~~li~------~~~~~~~~~~a~~~~~~m~  232 (352)
                      ++--.|+...|..+.++..+.   .|+...|.....      .....|..++|.+-+..-.
T Consensus       152 s~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e  212 (700)
T KOG1156|consen  152 AQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNE  212 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhh
Confidence            888899999999998887655   366655554332      2455666666666665543

>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=9.4e-05  Score=50.36  Aligned_cols=82  Identities=13%  Similarity=0.157  Sum_probs=44.3

Q ss_pred             cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHH
Q 042593          113 MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSAS  192 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  192 (352)
                      .|+++.|+.+++++.......|+...+..+..++.+.|++++|..+++. .+.+..  +....-.+..++.+.|++++|+
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~--~~~~~~l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPS--NPDIHYLLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHC--HHHHHHHHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCC--CHHHHHHHHHHHHHhCCHHHHH
Confidence            4566677777777633322122333444466666777777777777766 222222  3333334466666677777776


Q ss_pred             HHHHH
Q 042593          193 KLFED  197 (352)
Q Consensus       193 ~~~~~  197 (352)
                      ++|++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            66654

>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=97.71  E-value=0.00057  Score=46.85  Aligned_cols=97  Identities=13%  Similarity=0.063  Sum_probs=78.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...+++..+..  +.+...+..+...+...+++++|...++...+....  +..++..+..++
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~~~~   78 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD--PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD--NAKAYYNLGLAY   78 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc--chhHHHHHHHHH
Confidence            6667778888999999999999984422  223467788888899999999999999998887644  557888899999


Q ss_pred             HhhCChHHHHHHHHHhccCCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      ...|+.+.|...+.......|
T Consensus        79 ~~~~~~~~a~~~~~~~~~~~~   99 (100)
T cd00189          79 YKLGKYEEALEAYEKALELDP   99 (100)
T ss_pred             HHHHhHHHHHHHHHHHHccCC
Confidence            999999999999988754433

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

Probab=97.69  E-value=0.00058  Score=60.67  Aligned_cols=130  Identities=12%  Similarity=0.079  Sum_probs=101.9

Q ss_pred             hHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHh--CCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593            4 YKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV--GFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus         4 ~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      +..|.+-+.  .+..-   +......+++.+....+++.+.+++-.....  ....-+.|..++|+.|.+.|..+.+..+
T Consensus        51 ~~~l~~k~~--~~~~v---S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~  125 (429)
T PF10037_consen   51 YSELDKKFE--RKKPV---SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLEL  125 (429)
T ss_pred             HHHHHHHHh--cCCCC---cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHH
Confidence            455665444  23333   6677888889999888999999888877754  2223345667999999999999999999


Q ss_pred             hccCCC----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC
Q 042593           82 FDELPE----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN  149 (352)
Q Consensus        82 ~~~m~~----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~  149 (352)
                      ++.=.+    ||..+          +|.||+.+.+.|++..|.++..+| .....-.+..|+...+.+|.+-
T Consensus       126 L~n~~~yGiF~D~~s----------~n~Lmd~fl~~~~~~~A~~V~~~~-~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  126 LKNRLQYGIFPDNFS----------FNLLMDHFLKKGNYKSAAKVATEM-MLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HhChhhcccCCChhh----------HHHHHHHHhhcccHHHHHHHHHHH-HHhhccCCchHHHHHHHHHHHh
Confidence            988655    88888          999999999999999999999999 5555557778888888887766

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 [].

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

Probab=97.69  E-value=0.0068  Score=52.33  Aligned_cols=110  Identities=15%  Similarity=0.051  Sum_probs=79.9

Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHH
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFD  253 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~  253 (352)
                      +.+..|.-+...|+...|.++-.+.  .-|+-.-|...+.+++..++|++-..+... ++                    
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F--kv~dkrfw~lki~aLa~~~~w~eL~~fa~s-kK--------------------  235 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF--KVPDKRFWWLKIKALAENKDWDELEKFAKS-KK--------------------  235 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc--CCcHHHHHHHHHHHHHhcCCHHHHHHHHhC-CC--------------------
Confidence            4455566777788888888888777  568888888888899998888887765432 11                    


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                                .+.-|...+.+|.+.|+..+|...+.++.        +..-+..|++.|++.+|.+...+.
T Consensus       236 ----------sPIGyepFv~~~~~~~~~~eA~~yI~k~~--------~~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  236 ----------SPIGYEPFVEACLKYGNKKEASKYIPKIP--------DEERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             ----------CCCChHHHHHHHHHCCCHHHHHHHHHhCC--------hHHHHHHHHHCCCHHHHHHHHHHc
Confidence                      23456667788888888888888877743        255677778888888887765554

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

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

Probab=97.67  E-value=0.00029  Score=59.96  Aligned_cols=146  Identities=14%  Similarity=0.044  Sum_probs=101.1

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh-hCChHHHHHHHHHhccC-CCCHhhHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK-CGCIFSASKLFEDTSVD-RKNLVSWTTIISG  214 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~-~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~  214 (352)
                      .+|..+++...+.+..+.|..+|.+..+.+..  +.++|-.....-.+ .++.+.|.++|+...+. ..+...|..-+.-
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRC--TYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS---THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            46888889999999999999999999866543  45555555555333 56677799999987665 6677888888999


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      +...++.+.|..+|++.... +.++                       . ....|...++.=.+.|+.+.+.++.+++..
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~-----------------------~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKE-----------------------KQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCH-----------------------HHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCch-----------------------hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999998864 1111                       1 234777778878888888888888777655


Q ss_pred             CCCCchhhHHHHHHH
Q 042593          294 QITNVVVWRTGFLRL  308 (352)
Q Consensus       294 ~~~~~~~~~~li~~~  308 (352)
                      ..|+......++.-|
T Consensus       136 ~~~~~~~~~~f~~ry  150 (280)
T PF05843_consen  136 LFPEDNSLELFSDRY  150 (280)
T ss_dssp             HTTTS-HHHHHHCCT
T ss_pred             HhhhhhHHHHHHHHh
Confidence            434444444444433

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.

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

Probab=97.63  E-value=0.055  Score=51.65  Aligned_cols=191  Identities=13%  Similarity=0.073  Sum_probs=116.7

Q ss_pred             HHHHHHHHH--hcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHh
Q 042593           27 YSFLIRTCV--TLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVK  102 (352)
Q Consensus        27 ~~~ll~~~~--~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~  102 (352)
                      |..+++++.  +.|+.++|..+++.....+.. |..|...+-.+|...++.++|..+|++..+  |+...          
T Consensus        44 ~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~P~eel----------  112 (932)
T KOG2053|consen   44 YAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQKYPSEEL----------  112 (932)
T ss_pred             HHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhhCCcHHH----------
Confidence            666666655  678888888888777665533 778888888888888888888888888876  44333          


Q ss_pred             HHHHHHHHHhcCCHHH----HHHHHHHhHhccCCCCChhhHHHHHHHHHhCC----------ChhhHHHHHHHHHhcC-C
Q 042593          103 WTGIIDGYSRMNRSNE----ALALFRRMAACEYTEPSEITILAVLPAIWKNG----------EVRNCQLIHGYGEKRG-F  167 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~----a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~----------~~~~a~~~~~~~~~~~-~  167 (352)
                      ...+..+|++.+++.+    |+++++..      +-+.+.|-+++.......          -..-|.+..+.+.+.+ .
T Consensus       113 l~~lFmayvR~~~yk~qQkaa~~LyK~~------pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk  186 (932)
T KOG2053|consen  113 LYHLFMAYVREKSYKKQQKAALQLYKNF------PKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGK  186 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhC------CcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCc
Confidence            4445556666665544    44444422      223444444444443321          1233555666555444 2


Q ss_pred             CCCchhhHHHHHHHHHhhCChHHHHHHHHH-hccC--CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          168 NAFDIHVSNCLIDTYAKCGCIFSASKLFED-TSVD--RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       168 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~-~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      .. +..-.-.-...+...|++++|.+++.. .-..  ..+...-+.-+..+...++|.+..++-.++...|
T Consensus       187 ~~-s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~  256 (932)
T KOG2053|consen  187 IE-SEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG  256 (932)
T ss_pred             cc-hHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC
Confidence            21 333333444556677888888888843 2222  2244444556677778888888888888887765

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.62  E-value=0.0045  Score=48.54  Aligned_cols=129  Identities=12%  Similarity=0.035  Sum_probs=86.1

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc-hhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD-IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISG  214 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~  214 (352)
                      ..+..+...+...|++++|...+++..+....+++ ...+..+..++.+.|++++|...+++.....| +...+..+...
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~  115 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVI  115 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            45777788888899999999999998876544312 46788889999999999999999998776655 56667777777


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCC
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGR  280 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  280 (352)
                      +...|+...+..-++.....          .++|.+++++....     ++..|..++..+...|+
T Consensus       116 ~~~~g~~~~a~~~~~~A~~~----------~~~A~~~~~~a~~~-----~p~~~~~~~~~~~~~~~  166 (172)
T PRK02603        116 YHKRGEKAEEAGDQDEAEAL----------FDKAAEYWKQAIRL-----APNNYIEAQNWLKTTGR  166 (172)
T ss_pred             HHHcCChHhHhhCHHHHHHH----------HHHHHHHHHHHHhh-----CchhHHHHHHHHHhcCc
Confidence            77777655444433332221          34455555555543     33335555555555544

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=97.62  E-value=0.0043  Score=57.79  Aligned_cols=240  Identities=14%  Similarity=0.064  Sum_probs=152.1

Q ss_pred             HHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhH
Q 042593           51 SKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMA  127 (352)
Q Consensus        51 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  127 (352)
                      ....+..+...|..|.-+...+|+++.+.+.|++...   .....          |+.+-..|...|.-..|..+.+.-.
T Consensus       315 r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~----------w~~~als~saag~~s~Av~ll~~~~  384 (799)
T KOG4162|consen  315 RLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHER----------WYQLALSYSAAGSDSKAVNLLRESL  384 (799)
T ss_pred             HHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHH----------HHHHHHHHHHhccchHHHHHHHhhc
Confidence            3345667888999999999999999999999998764   22233          8888889999999999999888763


Q ss_pred             hccCCCCChh-hHHHHHHHHH-hCCChhhHHHHHHHHHhc--CCC-CCchhhHHHHHHHHHhh-----------CChHHH
Q 042593          128 ACEYTEPSEI-TILAVLPAIW-KNGEVRNCQLIHGYGEKR--GFN-AFDIHVSNCLIDTYAKC-----------GCIFSA  191 (352)
Q Consensus       128 ~~~~~~p~~~-t~~~ll~~~~-~~~~~~~a~~~~~~~~~~--~~~-~~~~~~~~~li~~~~~~-----------g~~~~a  191 (352)
                      ... ..|+.. .+...-..|. +.+..+++..+-.+....  +.. ...+..|..+.-+|...           ....++
T Consensus       385 ~~~-~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~ks  463 (799)
T KOG4162|consen  385 KKS-EQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKS  463 (799)
T ss_pred             ccc-cCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHH
Confidence            322 234433 3333333343 457777777777666651  111 00234455555555422           234567


Q ss_pred             HHHHHHhccC---CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhH
Q 042593          192 SKLFEDTSVD---RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHY  268 (352)
Q Consensus       192 ~~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~  268 (352)
                      .+.+++..+.   .|++.-|-++  -|+..++++.|.+..++..+.+                         -.-+...|
T Consensus       464 lqale~av~~d~~dp~~if~lal--q~A~~R~l~sAl~~~~eaL~l~-------------------------~~~~~~~w  516 (799)
T KOG4162|consen  464 LQALEEAVQFDPTDPLVIFYLAL--QYAEQRQLTSALDYAREALALN-------------------------RGDSAKAW  516 (799)
T ss_pred             HHHHHHHHhcCCCCchHHHHHHH--HHHHHHhHHHHHHHHHHHHHhc-------------------------CCccHHHH
Confidence            7777776544   3444444333  3667778999999988888752                         23367788


Q ss_pred             HHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhh
Q 042593          269 GCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       269 ~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      ..|.-.+...+++.+|+.+.+..... +.|...-..-+.--..-++.++|+....+++-.+
T Consensus       517 hLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~w  577 (799)
T KOG4162|consen  517 HLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREEALDTCIHKLALW  577 (799)
T ss_pred             HHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHH
Confidence            88888888899999998887765444 2222222222222334666666666666665433

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

Probab=97.57  E-value=0.00092  Score=46.97  Aligned_cols=80  Identities=10%  Similarity=0.170  Sum_probs=64.6

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCC-CCCchhhHHHHHHHHHhhC--------ChHHHHHHHHHhccC--CCCHh
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGF-NAFDIHVSNCLIDTYAKCG--------CIFSASKLFEDTSVD--RKNLV  206 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~li~~~~~~g--------~~~~a~~~~~~~~~~--~~~~~  206 (352)
                      |-...|..+...+++.....+|+.++..|+ .| +..+|+.++.+.++..        ++-..+.+++.|...  +|+..
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lP-sv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~e  105 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLP-SVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDE  105 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCC-cHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHH
Confidence            344566777777999999999999999999 66 9999999999988764        344567788887655  79999


Q ss_pred             hHHHHHHHHHcC
Q 042593          207 SWTTIISGFAMH  218 (352)
Q Consensus       207 ~~~~li~~~~~~  218 (352)
                      +|+.++..+.+.
T Consensus       106 tYnivl~~Llkg  117 (120)
T PF08579_consen  106 TYNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHHh
Confidence            999999887653

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 [, , ].

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

Probab=97.55  E-value=0.00024  Score=48.34  Aligned_cols=81  Identities=16%  Similarity=0.072  Sum_probs=62.3

Q ss_pred             CCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHH
Q 042593          149 NGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVEN  227 (352)
Q Consensus       149 ~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  227 (352)
                      .|+++.|..+++.+.+.... + +...+-.+..+|.+.|++++|.++++.......+....-.+..+|.+.|++++|.+.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~-~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNP-NSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTH-HHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCCh-hHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            57899999999999988653 3 445555689999999999999999988322233445555668899999999999999


Q ss_pred             HHH
Q 042593          228 FER  230 (352)
Q Consensus       228 ~~~  230 (352)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            976

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.55  E-value=0.0053  Score=48.13  Aligned_cols=84  Identities=13%  Similarity=-0.052  Sum_probs=66.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |..+...+...|++++|...|++......-.++ ...+..+...+.+.|++++|...+++..+....  +...+..+..+
T Consensus        38 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg~~  115 (172)
T PRK02603         38 YYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPK--QPSALNNIAVI  115 (172)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc--cHHHHHHHHHH
Confidence            777888899999999999999998443221222 357888899999999999999999999886543  66777778888


Q ss_pred             HHhhCCh
Q 042593          182 YAKCGCI  188 (352)
Q Consensus       182 ~~~~g~~  188 (352)
                      +...|+.
T Consensus       116 ~~~~g~~  122 (172)
T PRK02603        116 YHKRGEK  122 (172)
T ss_pred             HHHcCCh
Confidence            8887774

>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=97.52  E-value=0.00045  Score=44.70  Aligned_cols=63  Identities=16%  Similarity=0.143  Sum_probs=42.8

Q ss_pred             HhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHH
Q 042593          147 WKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTI  211 (352)
Q Consensus       147 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l  211 (352)
                      ...|++++|...++.+.+....  +..++..+..+|.+.|++++|.++++.+....|+-..|..+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~--~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l   64 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPD--NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQL   64 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTT--SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            3567777777777777766544  66666677777777777777777777776666665444444

...

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=97.44  E-value=0.018  Score=51.57  Aligned_cols=190  Identities=11%  Similarity=0.052  Sum_probs=119.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCch---hHHHHHHHHHhH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLV---TWNVIITGLVKW  103 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~---~~~~~i~~~~~~  103 (352)
                      ...+.++..+..++..+++-++...+..  -+..-++....+|...|...++...-+.-.+.+..   .++-+-.+   +
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~---~  301 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKA---L  301 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHH---H
Confidence            5667788888889999999998888766  56666788888899988888877776665543322   22222211   3


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ..+-++|.+.++++.|...|.+.+. ....|+.         ..+....+++....+...-.+...  ..-...-.+.+.
T Consensus       302 ~r~g~a~~k~~~~~~ai~~~~kaLt-e~Rt~~~---------ls~lk~~Ek~~k~~e~~a~~~pe~--A~e~r~kGne~F  369 (539)
T KOG0548|consen  302 ARLGNAYTKREDYEGAIKYYQKALT-EHRTPDL---------LSKLKEAEKALKEAERKAYINPEK--AEEEREKGNEAF  369 (539)
T ss_pred             HHhhhhhhhHHhHHHHHHHHHHHhh-hhcCHHH---------HHHHHHHHHHHHHHHHHHhhChhH--HHHHHHHHHHHH
Confidence            3455577778889999999888622 2222322         223333444444444333333221  222223355666


Q ss_pred             hhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          184 KCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +.|++..|.+.+.++....| |...|....-+|.+.|.+..|..--+.-.+
T Consensus       370 k~gdy~~Av~~YteAIkr~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ie  420 (539)
T KOG0548|consen  370 KKGDYPEAVKHYTEAIKRDPEDARLYSNRAACYLKLGEYPEALKDAKKCIE  420 (539)
T ss_pred             hccCHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            77777777777777665544 567777777777777777777766555554

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.43  E-value=0.0071  Score=45.72  Aligned_cols=95  Identities=5%  Similarity=-0.129  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~  216 (352)
                      ..-.+..-+...|++++|..+|+.+......  +..-|-.|.-++-..|++++|+..|....... -|+..+-.+-.++.
T Consensus        37 ~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~--~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L  114 (157)
T PRK15363         37 TLYRYAMQLMEVKEFAGAARLFQLLTIYDAW--SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYL  114 (157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc--cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            4445566677889999999999988887654  67777888888899999999999998865554 46778888888999


Q ss_pred             cCCCHHHHHHHHHHHHhc
Q 042593          217 MHGMGKEAVENFERMQKV  234 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~  234 (352)
                      ..|+.+.|.+.|+..+..
T Consensus       115 ~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        115 ACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HcCCHHHHHHHHHHHHHH
Confidence            999999999999987764

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.41  E-value=0.0092  Score=46.58  Aligned_cols=97  Identities=8%  Similarity=-0.087  Sum_probs=70.5

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC-chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF-DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIIS  213 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~  213 (352)
                      ...+..+...+...|++++|...++........+. ...++..+..++...|+.++|.+.++......| ...+++.+..
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~  114 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            34567777778888999999999998876643321 235788888899999999999999988765544 4555666666


Q ss_pred             HHH-------cCCCHHHHHHHHHHHH
Q 042593          214 GFA-------MHGMGKEAVENFERMQ  232 (352)
Q Consensus       214 ~~~-------~~~~~~~a~~~~~~m~  232 (352)
                      .+.       ..|++++|...+++-.
T Consensus       115 i~~~~~~~~~~~g~~~~A~~~~~~a~  140 (168)
T CHL00033        115 ICHYRGEQAIEQGDSEIAEAWFDQAA  140 (168)
T ss_pred             HHHHhhHHHHHcccHHHHHHHHHHHH
Confidence            666       7778777776666543

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.41  E-value=0.032  Score=43.23  Aligned_cols=129  Identities=13%  Similarity=0.016  Sum_probs=97.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      -..|..+....|+..+|...|++. -..-..-|......+.++....++...|...++.+-+.....-++..--.+.+.|
T Consensus        92 r~rLa~al~elGr~~EA~~hy~qa-lsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~aR~l  170 (251)
T COG4700          92 RYRLANALAELGRYHEAVPHYQQA-LSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLLFARTL  170 (251)
T ss_pred             HHHHHHHHHHhhhhhhhHHHHHHH-hccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHHHHHHH
Confidence            667888999999999999999998 6666667788888999999999999999999999887764322455566788999


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      ...|+..+|+.-|+...+..|+...----..-+.++|+.+++..-+.++.
T Consensus       171 aa~g~~a~Aesafe~a~~~ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v~  220 (251)
T COG4700         171 AAQGKYADAESAFEVAISYYPGPQARIYYAEMLAKQGRLREANAQYVAVV  220 (251)
T ss_pred             HhcCCchhHHHHHHHHHHhCCCHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence            99999999999999887776655332222233566776666655444443

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.40  E-value=0.023  Score=43.06  Aligned_cols=91  Identities=9%  Similarity=0.019  Sum_probs=63.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      ...+...+...|++++|.++|+-+..   +.|.. .-|..+.-++-..|++++|...|.......+.  ++..+-.+..+
T Consensus        38 lY~~A~~ly~~G~l~~A~~~f~~L~~---~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d--dp~~~~~ag~c  112 (157)
T PRK15363         38 LYRYAMQLMEVKEFAGAARLFQLLTI---YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID--APQAPWAAAEC  112 (157)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC--CchHHHHHHHH
Confidence            44455556677888888888877733   23433 35666666777778888888888877776643  67777777788


Q ss_pred             HHhhCChHHHHHHHHHh
Q 042593          182 YAKCGCIFSASKLFEDT  198 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~  198 (352)
                      +...|+.+.|.+.|+..
T Consensus       113 ~L~lG~~~~A~~aF~~A  129 (157)
T PRK15363        113 YLACDNVCYAIKALKAV  129 (157)
T ss_pred             HHHcCCHHHHHHHHHHH
Confidence            88888888888877765

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.38  E-value=0.0012  Score=52.23  Aligned_cols=82  Identities=13%  Similarity=0.097  Sum_probs=48.1

Q ss_pred             HHHHHHHHHh-----cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCC----------------ChhhHHHHHHH
Q 042593          103 WTGIIDGYSR-----MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNG----------------EVRNCQLIHGY  161 (352)
Q Consensus       103 ~~~li~~~~~-----~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~----------------~~~~a~~~~~~  161 (352)
                      |..++..|.+     .|..+-...-+..| .+.|+.-|..+|+.||+.+=+..                +-+-|.+++++
T Consensus        50 F~~~V~~f~~~~~~RRGHVeFI~aAL~~M-~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~q  128 (228)
T PF06239_consen   50 FLEAVDIFKQRDVRRRGHVEFIYAALKKM-DEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQ  128 (228)
T ss_pred             HHHHHHHHHhcCCCCcChHHHHHHHHHHH-HHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHH
Confidence            4444444433     35555555666667 66777777777777777665422                22445566666


Q ss_pred             HHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          162 GEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       162 ~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      |+..|+-| |..++..+++.+++.+
T Consensus       129 ME~~gV~P-d~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  129 MENNGVMP-DKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHHcCCCC-cHHHHHHHHHHhcccc
Confidence            66666666 6666666666665544

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.37  E-value=0.0058  Score=47.71  Aligned_cols=64  Identities=9%  Similarity=-0.122  Sum_probs=53.5

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ....|..+...+...|++++|...|+......|+    ..+|..+...+...|++++|...+++..+.
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4667788888899999999999999998644332    357888999999999999999999998863

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

Probab=97.37  E-value=0.0039  Score=55.04  Aligned_cols=102  Identities=10%  Similarity=-0.105  Sum_probs=81.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      ...+...|++++|++.|++.....  +-+...|..+..++.+.|++++|...++.+.+....  +...|..+..+|...|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~--P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~--~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD--PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS--LAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC--CHHHHHHHHHHHHHhC
Confidence            455677899999999999994432  134567888889999999999999999999887644  7788889999999999


Q ss_pred             ChHHHHHHHHHhccCCCCHhhHHHHH
Q 042593          187 CIFSASKLFEDTSVDRKNLVSWTTII  212 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~~~~~~~~~~li  212 (352)
                      ++++|...|++.....|+-......+
T Consensus        85 ~~~eA~~~~~~al~l~P~~~~~~~~l  110 (356)
T PLN03088         85 EYQTAKAALEKGASLAPGDSRFTKLI  110 (356)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            99999999999877766544444433

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.35  E-value=0.061  Score=44.70  Aligned_cols=58  Identities=17%  Similarity=0.133  Sum_probs=41.8

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcC
Q 042593          212 ISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGI  291 (352)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  291 (352)
                      ..-|.+.|.+..|..-++.+.+.=  |                     +.+........++.+|.+.|..++|..+...+
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v~~~Y--p---------------------~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l  238 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQMLRDY--P---------------------DTQATRDALPLMENAYRQLQLNAQADKVAKII  238 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHHHHHC--C---------------------CCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            344777777877777777777631  1                     33445667778999999999999998877654


Q ss_pred             C
Q 042593          292 P  292 (352)
Q Consensus       292 ~  292 (352)
                      .
T Consensus       239 ~  239 (243)
T PRK10866        239 A  239 (243)
T ss_pred             h
Confidence            3

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.31  E-value=0.026  Score=49.71  Aligned_cols=136  Identities=16%  Similarity=0.134  Sum_probs=87.2

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---  244 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---  244 (352)
                      -..+|-..|++-.+...++.|..+|-+..+.   .+++..++++|..++. |+..-|..+|+-=...  -||...|.   
T Consensus       396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~ky  472 (660)
T COG5107         396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKY  472 (660)
T ss_pred             hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHH
Confidence            4567778888888888888888888887665   5788888888887665 5677788887753321  24444443   


Q ss_pred             ---------hHhHHHHHHHHHHhcCCCCC--hhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhc
Q 042593          245 ---------GEEGLKFFDKMVEECEVLPD--IKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLIN  311 (352)
Q Consensus       245 ---------~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~  311 (352)
                               -..|..+|+.-+.+  +.-+  ...|..+|+.-.+.|++..+..+-++|...-|...+-..+...|...
T Consensus       473 l~fLi~inde~naraLFetsv~r--~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQen~~evF~Sry~ik  548 (660)
T COG5107         473 LLFLIRINDEENARALFETSVER--LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQENLIEVFTSRYAIK  548 (660)
T ss_pred             HHHHHHhCcHHHHHHHHHHhHHH--HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCcHhHHHHHHHHHhhh
Confidence                     45566666644432  2222  45677777777788888777666666554434444444444444433

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

Probab=97.26  E-value=0.033  Score=50.19  Aligned_cols=128  Identities=12%  Similarity=0.044  Sum_probs=102.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |-..++.--+..-+..|..+|.+. ++.+..+ ++...++++.-+|. +|.+-|.++|+.-.+.-..  ++.--...+..
T Consensus       369 ~~~~mn~irR~eGlkaaR~iF~ka-R~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d--~p~yv~~Yldf  444 (656)
T KOG1914|consen  369 YCQYMNFIRRAEGLKAARKIFKKA-REDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGD--SPEYVLKYLDF  444 (656)
T ss_pred             hhHHHHHHHHhhhHHHHHHHHHHH-hhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCC--ChHHHHHHHHH
Confidence            777788888888899999999999 6666666 67788888887775 7889999999876554222  34445677888


Q ss_pred             HHhhCChHHHHHHHHHhccC--CC--CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          182 YAKCGCIFSASKLFEDTSVD--RK--NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~--~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +...++-..|..+|+.....  .|  ....|..+|+.=..-|+...+.++-+++...
T Consensus       445 L~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~a  501 (656)
T KOG1914|consen  445 LSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTA  501 (656)
T ss_pred             HHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            99999999999999988655  33  4588999999999999999999998887653

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.24  E-value=0.025  Score=46.96  Aligned_cols=57  Identities=11%  Similarity=0.109  Sum_probs=45.6

Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+.+.|.+.|.+..|..-|+.+...-|+    ......++.+|...|..++|.++...+..
T Consensus       180 ~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        180 SVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            4556688999999999999998877554    35566888999999999999988776543

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.22  E-value=0.0035  Score=49.74  Aligned_cols=101  Identities=16%  Similarity=0.159  Sum_probs=72.5

Q ss_pred             chhhHHHHHHHHHhh-----CChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchh
Q 042593          171 DIHVSNCLIDTYAKC-----GCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWR  243 (352)
Q Consensus       171 ~~~~~~~li~~~~~~-----g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~  243 (352)
                      +..+|..+++.|.+.     |.++-....+..|.+.  ..|..+|+.|++.+=+. .+. -..+|+.+--.      ...
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg-~fv-p~n~fQ~~F~h------yp~  117 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKG-KFV-PRNFFQAEFMH------YPR  117 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCC-Ccc-cccHHHHHhcc------CcH
Confidence            788899999998754     6777777777777655  67999999999988763 322 22222222210      000


Q ss_pred             hhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCC
Q 042593          244 IGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGR  280 (352)
Q Consensus       244 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  280 (352)
                      --+-|.+++++|... |+.||..++..|++.+++.+.
T Consensus       118 Qq~c~i~lL~qME~~-gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  118 QQECAIDLLEQMENN-GVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHHHHHHHHc-CCCCcHHHHHHHHHHhccccH
Confidence            056678888888888 999999999999999988775

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

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

Probab=97.21  E-value=0.0061  Score=53.84  Aligned_cols=91  Identities=7%  Similarity=-0.113  Sum_probs=79.8

Q ss_pred             HHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCH
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMG  221 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~  221 (352)
                      ...+...|++++|...+++..+....  +...|..+..+|.+.|++++|+..++......| +...|..+..+|...|++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~--~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPN--NAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCH
Confidence            45567889999999999999987654  788899999999999999999999999876655 678889999999999999


Q ss_pred             HHHHHHHHHHHhcC
Q 042593          222 KEAVENFERMQKVG  235 (352)
Q Consensus       222 ~~a~~~~~~m~~~~  235 (352)
                      ++|...|++..+..
T Consensus        87 ~eA~~~~~~al~l~  100 (356)
T PLN03088         87 QTAKAALEKGASLA  100 (356)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999998743

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

Probab=97.17  E-value=0.0014  Score=41.89  Aligned_cols=54  Identities=20%  Similarity=0.177  Sum_probs=28.2

Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..+.+.|++++|.+.|+.+.+..| +...+..+..++...|++++|...|++..+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445555555555555555554433 344455555555555555555555555544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.16  E-value=0.02  Score=53.04  Aligned_cols=130  Identities=9%  Similarity=-0.043  Sum_probs=88.1

Q ss_pred             HHHHHHHHHhc-----CCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCC--------ChhhHHHHHHHHHhcCCC
Q 042593          103 WTGIIDGYSRM-----NRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNG--------EVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus       103 ~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~--------~~~~a~~~~~~~~~~~~~  168 (352)
                      |...+.+....     ++...|..+|++..+   ..|+- ..|..+..++....        ++..+.+..+........
T Consensus       340 y~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~---ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al~~~  416 (517)
T PRK10153        340 LTLFYQAHHYLNSGDAKSLNKASDLLEEILK---SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVALPEL  416 (517)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhcccC
Confidence            55555554332     247799999999855   34664 34444433333221        122333333333333223


Q ss_pred             CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          169 AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       169 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      +.+...|.++.-.....|++++|...+++.....|+...|..+...+...|+.++|.+.+++.....
T Consensus       417 ~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~  483 (517)
T PRK10153        417 NVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLR  483 (517)
T ss_pred             cCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            3256777777666777899999999999988778899999999999999999999999999988743

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=97.14  E-value=0.13  Score=43.83  Aligned_cols=263  Identities=10%  Similarity=0.009  Sum_probs=182.0

Q ss_pred             CcccHHHHH---HHHHhcCCcchHHHHHHHHHHhCCCCchhh-HHHHHHHHHhcCChhHHHHHhccCCCCCc--------
Q 042593           23 DSFTYSFLI---RTCVTLSYPNLGTQLHAVFSKVGFQSHVYV-NTALGDMYVSLGFLKDSSKLFDELPERNL--------   90 (352)
Q Consensus        23 ~~~~~~~ll---~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~-~~~li~~~~~~g~~~~a~~~~~~m~~~~~--------   90 (352)
                      |+..|-++.   ..|...|+-..|+.-++...+.  +||-.. -.--...+.+.|.++.|+.=|+.+.+.++        
T Consensus        68 dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg~vllK~Gele~A~~DF~~vl~~~~s~~~~~ea  145 (504)
T KOG0624|consen   68 DPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEA  145 (504)
T ss_pred             CchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhchhhhhcccHHHHHHHHHHHHhcCCCcchhHHH
Confidence            555555554   5677888888888777777664  466432 22234466799999999999999875222        


Q ss_pred             hhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC
Q 042593           91 VTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF  170 (352)
Q Consensus        91 ~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  170 (352)
                      ..-.+++.-....-..+..+...||...|+.....++.-.  +.|...|..-..+|...|+...|..=++...+..-.  
T Consensus       146 qskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~--~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~D--  221 (504)
T KOG0624|consen  146 QSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ--PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQD--  221 (504)
T ss_pred             HHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC--cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcccc--
Confidence            1122222222123445667778899999999999884421  346677888889999999999998877777665544  


Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHh----hHHHH---------HHHHHcCCCHHHHHHHHHHHHhcCCC
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLV----SWTTI---------ISGFAMHGMGKEAVENFERMQKVGLK  237 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~l---------i~~~~~~~~~~~a~~~~~~m~~~~~~  237 (352)
                      +...+-.+-..+-..|+.+.++...++..+..||-.    .|-.|         +......++|.++.+..+...+....
T Consensus       222 nTe~~ykis~L~Y~vgd~~~sL~~iRECLKldpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~  301 (504)
T KOG0624|consen  222 NTEGHYKISQLLYTVGDAENSLKEIRECLKLDPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPE  301 (504)
T ss_pred             chHHHHHHHHHHHhhhhHHHHHHHHHHHHccCcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCc
Confidence            556666778888999999999999999887766542    22221         23356778899999999888776544


Q ss_pred             CCcchhh--------------hHhHHHHHHHHHHhcCCCCC-hhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          238 PNRSWRI--------------GEEGLKFFDKMVEECEVLPD-IKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       238 p~~~~~~--------------~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      .....+.              ..+|++.-.+...   +.|| +.++.--..+|.-...++.|..-|+...+.
T Consensus       302 ~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~---~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  302 ETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLD---IDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             ccceeeeeeheeeecccccCCHHHHHHHHHHHHh---cCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc
Confidence            3333333              6667766666664   4554 778888888888888899998888877766

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.10  E-value=0.021  Score=52.90  Aligned_cols=140  Identities=9%  Similarity=-0.099  Sum_probs=88.8

Q ss_pred             CCChhhHHHHHHHHHhCC-----ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC--------ChHHHHHHHHHhc
Q 042593          133 EPSEITILAVLPAIWKNG-----EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG--------CIFSASKLFEDTS  199 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g--------~~~~a~~~~~~~~  199 (352)
                      +.|...|...+++.....     +.+.|..++++..+....  ....+..+..++....        +++.+.+..+...
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~--~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPD--FTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCC--cHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            455667887777754432     256778888888776543  5555555544443321        2233344443322


Q ss_pred             c---CCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042593          200 V---DRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILE  276 (352)
Q Consensus       200 ~---~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~  276 (352)
                      .   ...+...|.++.......|++++|...+++..+.                           .|+...|..+...+.
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L---------------------------~ps~~a~~~lG~~~~  464 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL---------------------------EMSWLNYVLLGKVYE  464 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc---------------------------CCCHHHHHHHHHHHH
Confidence            2   2335566777766666678888888888887754                           356778888888888


Q ss_pred             HcCChhHHHHHHhcCCCCCCCchhh
Q 042593          277 RAGRLEQAEEVASGIPSQITNVVVW  301 (352)
Q Consensus       277 ~~g~~~~A~~~~~~m~~~~~~~~~~  301 (352)
                      ..|+.++|.+.+++.....|...+|
T Consensus       465 ~~G~~~eA~~~~~~A~~L~P~~pt~  489 (517)
T PRK10153        465 LKGDNRLAADAYSTAFNLRPGENTL  489 (517)
T ss_pred             HcCCHHHHHHHHHHHHhcCCCCchH
Confidence            8888888888888776554444443

>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=97.10  E-value=0.002  Score=41.61  Aligned_cols=64  Identities=17%  Similarity=0.144  Sum_probs=48.3

Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCC
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQI  295 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~  295 (352)
                      ...|++++|.++|+++.+..                          +-+...+..+..+|.+.|++++|..+++.+....
T Consensus         2 l~~~~~~~A~~~~~~~l~~~--------------------------p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~   55 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN--------------------------PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD   55 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT--------------------------TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred             hhccCHHHHHHHHHHHHHHC--------------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            45788888888888877631                          2267778889999999999999999999998775


Q ss_pred             CCchhhHHHH
Q 042593          296 TNVVVWRTGF  305 (352)
Q Consensus       296 ~~~~~~~~li  305 (352)
                      |+...|..+.
T Consensus        56 ~~~~~~~~l~   65 (68)
T PF14559_consen   56 PDNPEYQQLL   65 (68)
T ss_dssp             TTHHHHHHHH
T ss_pred             cCHHHHHHHH
Confidence            5545555443

...

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

Probab=97.09  E-value=0.0053  Score=52.40  Aligned_cols=191  Identities=13%  Similarity=0.007  Sum_probs=114.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhc---cCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHh----cCCCCCchhh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAAC---EYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEK----RGFNAFDIHV  174 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~  174 (352)
                      |....+.|-..+++++|.+.|.+....   .+-..+ ...|.....++.+. +.++|...++...+    .|-...-...
T Consensus        38 y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA~~  116 (282)
T PF14938_consen   38 YEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAAKC  116 (282)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHHHH
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            555666777888888888888776211   111111 12455555655554 88888877777654    3322213456


Q ss_pred             HHHHHHHHHhh-CChHHHHHHHHHhccC----C-C--CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhH
Q 042593          175 SNCLIDTYAKC-GCIFSASKLFEDTSVD----R-K--NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGE  246 (352)
Q Consensus       175 ~~~li~~~~~~-g~~~~a~~~~~~~~~~----~-~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  246 (352)
                      +..+...|... |+++.|.+.|++....    . +  -...+..+...+.+.|++++|.++|+++...-...+       
T Consensus       117 ~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~-------  189 (282)
T PF14938_consen  117 LKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENN-------  189 (282)
T ss_dssp             HHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHC-------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhccc-------
Confidence            77778888888 8999999999875433    1 1  135567778889999999999999999877533211       


Q ss_pred             hHHHHHHHHHHhcCCCCChh-hHHHHHHHHHHcCChhHHHHHHhcCCCC------CCCchhhHHHHHHHHhccccc
Q 042593          247 EGLKFFDKMVEECEVLPDIK-HYGCLIDILERAGRLEQAEEVASGIPSQ------ITNVVVWRTGFLRLLINSYFF  315 (352)
Q Consensus       247 ~a~~~~~~m~~~~~~~p~~~-~~~~li~~~~~~g~~~~A~~~~~~m~~~------~~~~~~~~~li~~~~~~g~~~  315 (352)
                                   ..+++.. .|-..+-++...||...|.+.+++....      +........|+.++ ..|+.+
T Consensus       190 -------------l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~-~~~D~e  251 (282)
T PF14938_consen  190 -------------LLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAY-EEGDVE  251 (282)
T ss_dssp             -------------TTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHH-HTT-CC
T ss_pred             -------------ccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH-HhCCHH
Confidence                         1122232 2334455777789999999999887654      12233445556654 444444

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.07  E-value=0.048  Score=44.00  Aligned_cols=182  Identities=9%  Similarity=-0.000  Sum_probs=106.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCC--CCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCch--hHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGF--QSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLV--TWNVI   96 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~--~~~~~   96 (352)
                      +...+-.....+...|++.+|.+.|+.+...--  +-.....-.++.++-+.|++++|...++...+  |+..  .+--.
T Consensus         4 ~~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y   83 (203)
T PF13525_consen    4 TAEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALY   83 (203)
T ss_dssp             -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHH
Confidence            444455556677889999999999999997631  12234555678899999999999999999765  4332  22222


Q ss_pred             HHHHHhHHHHHHH---HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchh
Q 042593           97 ITGLVKWTGIIDG---YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus        97 i~~~~~~~~li~~---~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                      +.+.+.|+..-..   ....+...+|...                +..++.-|-......+|...+..+.+.     -..
T Consensus        84 ~~g~~~~~~~~~~~~~~~D~~~~~~A~~~----------------~~~li~~yP~S~y~~~A~~~l~~l~~~-----la~  142 (203)
T PF13525_consen   84 MLGLSYYKQIPGILRSDRDQTSTRKAIEE----------------FEELIKRYPNSEYAEEAKKRLAELRNR-----LAE  142 (203)
T ss_dssp             HHHHHHHHHHHHHH-TT---HHHHHHHHH----------------HHHHHHH-TTSTTHHHHHHHHHHHHHH-----HHH
T ss_pred             HHHHHHHHhCccchhcccChHHHHHHHHH----------------HHHHHHHCcCchHHHHHHHHHHHHHHH-----HHH
Confidence            2221111111111   1111122233333                444445555556666666666655443     111


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccCCCCH----hhHHHHHHHHHcCCCHHHHH
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL----VSWTTIISGFAMHGMGKEAV  225 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~  225 (352)
                      .--.+.+.|.+.|.+..|..-++.+.+.-|++    ...-.++.+|.+.|..+.+.
T Consensus       143 ~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  143 HELYIARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            22246788999999999999999988776655    34567788888888877543

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

Probab=97.00  E-value=0.009  Score=49.69  Aligned_cols=95  Identities=15%  Similarity=0.059  Sum_probs=60.3

Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHH
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEA  224 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a  224 (352)
                      +.+.+++.+|...|.+..+....  +...|..-..+|++.|.++.|.+=.+......| -..+|..|-.+|...|++++|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~--nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPT--NAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCC--cchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHH
Confidence            44566677777777766665433  566666666777777777776666665544444 356677777777777777777


Q ss_pred             HHHHHHHHhcCCCCCcchhh
Q 042593          225 VENFERMQKVGLKPNRSWRI  244 (352)
Q Consensus       225 ~~~~~~m~~~~~~p~~~~~~  244 (352)
                      .+.|++.++  +.|+..++.
T Consensus       169 ~~aykKaLe--ldP~Ne~~K  186 (304)
T KOG0553|consen  169 IEAYKKALE--LDPDNESYK  186 (304)
T ss_pred             HHHHHhhhc--cCCCcHHHH
Confidence            777766655  456555444

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

Probab=96.99  E-value=0.01  Score=49.40  Aligned_cols=97  Identities=11%  Similarity=0.060  Sum_probs=62.0

Q ss_pred             HHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHH
Q 042593           69 YVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLP  144 (352)
Q Consensus        69 ~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~  144 (352)
                      ..+.+++++|+..|.+..+  | |.+-          |..-..+|++.|+++.|++=-+....   +.|. ..+|..|-.
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~nAVy----------ycNRAAAy~~Lg~~~~AVkDce~Al~---iDp~yskay~RLG~  157 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPTNAVY----------YCNRAAAYSKLGEYEDAVKDCESALS---IDPHYSKAYGRLGL  157 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCCcchH----------HHHHHHHHHHhcchHHHHHHHHHHHh---cChHHHHHHHHHHH
Confidence            3467777777777777665  3 3343          66677777888877777776665522   3343 237777778


Q ss_pred             HHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          145 AIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       145 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      +|...|++++|.+.|+...+.  .| +..+|..=+..
T Consensus       158 A~~~~gk~~~A~~aykKaLel--dP-~Ne~~K~nL~~  191 (304)
T KOG0553|consen  158 AYLALGKYEEAIEAYKKALEL--DP-DNESYKSNLKI  191 (304)
T ss_pred             HHHccCcHHHHHHHHHhhhcc--CC-CcHHHHHHHHH
Confidence            888888888888777766654  44 33344433333

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

Probab=96.96  E-value=0.0045  Score=39.53  Aligned_cols=61  Identities=11%  Similarity=0.035  Sum_probs=52.7

Q ss_pred             HHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       142 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      +...+.+.|++++|...++.+.+....  +...+..+..++...|++++|...|++..+..|+
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~--~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~   63 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPD--NPEAWYLLGRILYQQGRYDEALAYYERALELDPD   63 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTT--HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence            456788999999999999999998744  8899999999999999999999999998665554

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.96  E-value=0.015  Score=42.32  Aligned_cols=91  Identities=15%  Similarity=0.078  Sum_probs=62.0

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCc--hhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSH--VYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~  105 (352)
                      ...++-..|+.++|..+|+.....|....  ...+-.+...+...|++++|..++++...  |+......+      ...
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l------~~f   80 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAAL------RVF   80 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHH------HHH
Confidence            34566678888889999988888876543  34566777788888888888888887653  442211111      222


Q ss_pred             HHHHHHhcCCHHHHHHHHHHh
Q 042593          106 IIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m  126 (352)
                      +.-++...|+.++|++.+-..
T Consensus        81 ~Al~L~~~gr~~eAl~~~l~~  101 (120)
T PF12688_consen   81 LALALYNLGRPKEALEWLLEA  101 (120)
T ss_pred             HHHHHHHCCCHHHHHHHHHHH
Confidence            334667778888888887765

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

Probab=96.89  E-value=0.012  Score=43.15  Aligned_cols=102  Identities=11%  Similarity=0.063  Sum_probs=70.5

Q ss_pred             CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhH
Q 042593          204 NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQ  283 (352)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  283 (352)
                      |..++.++|.++++.|+.+....+.+..-.  +.++...-...        ........|+..+..+++.+|+..|++..
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~Wg--I~~~~~~~~~~--------~~~~spl~Pt~~lL~AIv~sf~~n~~i~~   70 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWG--IDVNGKKKEGD--------YPPSSPLYPTSRLLIAIVHSFGYNGDIFS   70 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcC--CCCCCccccCc--------cCCCCCCCCCHHHHHHHHHHHHhcccHHH
Confidence            456677788888888888888877776542  22211000000        00111677999999999999999999999


Q ss_pred             HHHHHhcCCCC---CCCchhhHHHHHHHHhccccc
Q 042593          284 AEEVASGIPSQ---ITNVVVWRTGFLRLLINSYFF  315 (352)
Q Consensus       284 A~~~~~~m~~~---~~~~~~~~~li~~~~~~g~~~  315 (352)
                      |.++++...+.   +-+..+|..|+.-.....+..
T Consensus        71 al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~~~  105 (126)
T PF12921_consen   71 ALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSSKR  105 (126)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcCCc
Confidence            99999888776   445789999998665555533

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

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.89  E-value=0.091  Score=43.13  Aligned_cols=132  Identities=12%  Similarity=0.041  Sum_probs=97.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH----
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL----  178 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l----  178 (352)
                      -+.++..+...|++.-.+.++++. .+...+-+......+.+.--+.||.+.|...++...+..-.. +...++.+    
T Consensus       180 my~~~~~llG~kEy~iS~d~~~~v-i~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL-~~~q~~~~V~~n  257 (366)
T KOG2796|consen  180 MYSMANCLLGMKEYVLSVDAYHSV-IKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKL-DGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHhcchhhhhhHHHHHHH-HHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhh-hccchhHHHHhh
Confidence            566777777888898899999998 555555667777888888889999999999999777654333 44444333    


Q ss_pred             -HHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCC
Q 042593          179 -IDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGL  236 (352)
Q Consensus       179 -i~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  236 (352)
                       -..|.-++++..|...|+++... ..|+..-|.-.-+..-.|+...|.+.++.|+..-.
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P  317 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDP  317 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence             33455667888889999887655 44666666666666677899999999999987543

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.85  E-value=0.057  Score=41.89  Aligned_cols=128  Identities=16%  Similarity=0.079  Sum_probs=96.8

Q ss_pred             CCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC---CHhhH
Q 042593          132 TEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK---NLVSW  208 (352)
Q Consensus       132 ~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~~~  208 (352)
                      ..|+...-..+.+++.+.|+..+|...|++...--... +....-.+.++....++...|...++.+....|   ++.+-
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~-d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~  163 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAH-DAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH  163 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCC-CHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch
Confidence            45777777889999999999999999999987644444 888888899999999999999999998765533   33444


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHH
Q 042593          209 TTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEV  287 (352)
Q Consensus       209 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~  287 (352)
                      -.+...+...|+...|+.-|+...+.                           -|+...-......+.++|+.++|..-
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~~~---------------------------ypg~~ar~~Y~e~La~qgr~~ea~aq  215 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAISY---------------------------YPGPQARIYYAEMLAKQGRLREANAQ  215 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHh---------------------------CCCHHHHHHHHHHHHHhcchhHHHHH
Confidence            55667889999999999999988763                           24444433445667778877666543

>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=96.83  E-value=0.004  Score=40.31  Aligned_cols=62  Identities=23%  Similarity=0.183  Sum_probs=33.8

Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC-CHHHHHHHHHHHHh
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG-MGKEAVENFERMQK  233 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~  233 (352)
                      +.+|..+...+...|++++|+..|++..+..| +...|..+..+|...| ++++|...+++..+
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            44555555555556666666666655443333 3455555555555555 45666655555443

...

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

Probab=96.78  E-value=0.18  Score=43.68  Aligned_cols=57  Identities=12%  Similarity=0.072  Sum_probs=49.3

Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCccccccc
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQ  323 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  323 (352)
                      |+...|...+.+|+..|+|++-.++...  ++  .+.-|..++..|...|+..+|..+...
T Consensus       206 ~dkrfw~lki~aLa~~~~w~eL~~fa~s--kK--sPIGyepFv~~~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  206 PDKRFWWLKIKALAENKDWDELEKFAKS--KK--SPIGYEPFVEACLKYGNKKEASKYIPK  262 (319)
T ss_pred             cHHHHHHHHHHHHHhcCCHHHHHHHHhC--CC--CCCChHHHHHHHHHCCCHHHHHHHHHh
Confidence            7888999999999999999999987654  33  669999999999999999988876655

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

>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=96.77  E-value=0.0079  Score=45.70  Aligned_cols=63  Identities=16%  Similarity=0.244  Sum_probs=51.8

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      -..+...++..+...|+++.|.++.+.+....| |...|..+|.+|...|+..+|.+.|+++.+
T Consensus        61 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~  124 (146)
T PF03704_consen   61 YLDALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRR  124 (146)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            345567788888999999999999999876654 788999999999999999999999999865

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

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.73  E-value=0.015  Score=48.82  Aligned_cols=104  Identities=13%  Similarity=-0.046  Sum_probs=76.3

Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH----hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHh
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL----VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEE  247 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~  247 (352)
                      ...|...+..+.+.|++++|...|+.+....|+.    ..+-.+..+|...|++++|...|+.+.+.-  |         
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~y--P---------  211 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNY--P---------  211 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--C---------
Confidence            4556666666677799999999999987776654    467778888999999999999999988642  1         


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCc
Q 042593          248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNV  298 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~  298 (352)
                                  +-+.....+-.+..++...|+.++|.++++.+....|+.
T Consensus       212 ------------~s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~yP~s  250 (263)
T PRK10803        212 ------------KSPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKYPGT  250 (263)
T ss_pred             ------------CCcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence                        112234455556777888999999999998877654443

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.69  E-value=0.029  Score=54.11  Aligned_cols=171  Identities=12%  Similarity=-0.035  Sum_probs=115.7

Q ss_pred             hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          152 VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       152 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      ...+...+-+....  .+.-...|..|...|+...+...|.+.|+...+-. -+...+......|++..+++.|..+.-.
T Consensus       474 ~~~al~ali~alrl--d~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~  551 (1238)
T KOG1127|consen  474 SALALHALIRALRL--DVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLR  551 (1238)
T ss_pred             HHHHHHHHHHHHhc--ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHH
Confidence            44444444433333  33256789999999999999999999999876554 4678888999999999999999998333


Q ss_pred             HHhcCCCCCcchhh---------------hHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          231 MQKVGLKPNRSWRI---------------GEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       231 m~~~~~~p~~~~~~---------------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      .-+.   ....+..               ...+...|+...+   +.| |...|..+..+|.++|+...|.++|.+....
T Consensus       552 ~~qk---a~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR---~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L  625 (1238)
T KOG1127|consen  552 AAQK---APAFACKENWVQRGPYYLEAHNLHGAVCEFQSALR---TDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLL  625 (1238)
T ss_pred             Hhhh---chHHHHHhhhhhccccccCccchhhHHHHHHHHhc---CCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhc
Confidence            2211   1111110               5555555655543   344 7788999999999999999999999888766


Q ss_pred             CCCchhhHHHH--HHHHhcccccCcccccccchhhhhhH
Q 042593          295 ITNVVVWRTGF--LRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       295 ~~~~~~~~~li--~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      .|+. .|...-  ...+..|.+++|+......++.+...
T Consensus       626 rP~s-~y~~fk~A~~ecd~GkYkeald~l~~ii~~~s~e  663 (1238)
T KOG1127|consen  626 RPLS-KYGRFKEAVMECDNGKYKEALDALGLIIYAFSLE  663 (1238)
T ss_pred             CcHh-HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence            3322 222222  22467888888888877776655433

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

Probab=96.68  E-value=0.027  Score=41.38  Aligned_cols=44  Identities=11%  Similarity=-0.047  Sum_probs=21.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAI  146 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~  146 (352)
                      ..+++.+|+..|++..|+++.+...+..+++.+..+|..|++-+
T Consensus        55 L~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   55 LIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            44444445555555555555555444444444444444444443

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

>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=96.68  E-value=0.0062  Score=39.37  Aligned_cols=64  Identities=14%  Similarity=0.019  Sum_probs=56.7

Q ss_pred             ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC-ChHHHHHHHHHhcc
Q 042593          135 SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG-CIFSASKLFEDTSV  200 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~  200 (352)
                      +..+|..+...+...|++++|...|++..+....  +...|..+..+|.+.| ++++|.+.++...+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~--~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPN--NAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--CHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            4567889999999999999999999999998644  8889999999999999 79999999987643

...

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.66  E-value=0.13  Score=47.92  Aligned_cols=23  Identities=26%  Similarity=0.330  Sum_probs=18.3

Q ss_pred             HHHHHHcCChhHHHHHHhcCCCC
Q 042593          272 IDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       272 i~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      |..+.++|+.-+|-+++..|.++
T Consensus       930 Ie~~Rka~~~~daarll~qmae~  952 (1189)
T KOG2041|consen  930 IEKDRKAGRHLDAARLLSQMAER  952 (1189)
T ss_pred             HHHhhhcccchhHHHHHHHHhHH
Confidence            66778888888888888887655

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.64  E-value=0.27  Score=40.51  Aligned_cols=140  Identities=12%  Similarity=-0.046  Sum_probs=93.2

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHH----
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTI----  211 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~l----  211 (352)
                      ..+.+++.+.-.|.+.-....+.+..+..... ++.....|++.-.+.||.+.|...|++..+.  ..|..+++.+    
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~-~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQ-EPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcc-cHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            34566666666777777788888888876555 7888888888888999999999999876543  2333333333    


Q ss_pred             -HHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhc
Q 042593          212 -ISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASG  290 (352)
Q Consensus       212 -i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  290 (352)
                       ...|.-.+++.+|...+.+.....                          ..|...-|.-.-+..-.|+..+|.+.++.
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D--------------------------~~~~~a~NnKALcllYlg~l~DAiK~~e~  311 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMD--------------------------PRNAVANNNKALCLLYLGKLKDALKQLEA  311 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccC--------------------------CCchhhhchHHHHHHHHHHHHHHHHHHHH
Confidence             334566678888888887766532                          12333444444444556888888888888


Q ss_pred             CCCCCCCchhhHHH
Q 042593          291 IPSQITNVVVWRTG  304 (352)
Q Consensus       291 m~~~~~~~~~~~~l  304 (352)
                      |...-|...+-+++
T Consensus       312 ~~~~~P~~~l~es~  325 (366)
T KOG2796|consen  312 MVQQDPRHYLHESV  325 (366)
T ss_pred             HhccCCccchhhhH
Confidence            87764444444443

>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=96.60  E-value=0.38  Score=40.96  Aligned_cols=167  Identities=10%  Similarity=-0.033  Sum_probs=98.5

Q ss_pred             HhcCChhHHHHHhccCCC----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHh-------ccCCCCCh--
Q 042593           70 VSLGFLKDSSKLFDELPE----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAA-------CEYTEPSE--  136 (352)
Q Consensus        70 ~~~g~~~~a~~~~~~m~~----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~~~~~p~~--  136 (352)
                      .+.|+++.|..++.+.+.    .++...-.+-+.+  ||.-...+.+..+++.|...+++...       .....|+.  
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~--yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~e   81 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVC--YNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSE   81 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHH--HHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHH
Confidence            456777777777777653    1222211221111  55555555444377777666665411       12233443  


Q ss_pred             ---hhHHHHHHHHHhCCChhh---HHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHH
Q 042593          137 ---ITILAVLPAIWKNGEVRN---CQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWT  209 (352)
Q Consensus       137 ---~t~~~ll~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~  209 (352)
                         .++..++.++...+..+.   |..+++.+.+....  .+.++-.-++++.+.++.+.+.+++.+|....+ ....+.
T Consensus        82 lr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~--~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~  159 (278)
T PF08631_consen   82 LRLSILRLLANAYLEWDTYESVEKALNALRLLESEYGN--KPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFD  159 (278)
T ss_pred             HHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC--CcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHH
Confidence               356677777877776544   55566666544333  456666778888889999999999999876633 344455


Q ss_pred             HHHHHH---HcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          210 TIISGF---AMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       210 ~li~~~---~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      ..+..+   .. .....|...++.+....+.|...
T Consensus       160 ~~l~~i~~l~~-~~~~~a~~~ld~~l~~r~~~~~~  193 (278)
T PF08631_consen  160 SILHHIKQLAE-KSPELAAFCLDYLLLNRFKSSED  193 (278)
T ss_pred             HHHHHHHHHHh-hCcHHHHHHHHHHHHHHhCCChh
Confidence            555544   33 33456777777776665655554

It is also involved in sporulation [].

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.53  E-value=0.053  Score=45.51  Aligned_cols=97  Identities=9%  Similarity=-0.045  Sum_probs=72.5

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC-chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF-DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTII  212 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li  212 (352)
                      .|...+....+.|++++|...|+.+.+.-...+ ....+--+..+|...|++++|...|+.+....|+    ...+-.+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            455555555667899999999999888754320 1356667888899999999999999998765443    44555566


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhc
Q 042593          213 SGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+...|+.++|..+|+++.+.
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            6788889999999999988874

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.51  E-value=0.016  Score=37.92  Aligned_cols=52  Identities=8%  Similarity=-0.102  Sum_probs=22.3

Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                      +.+.++++.|..+++.+.+.+..  +...+.....++.+.|++++|.+.|+...
T Consensus         5 ~~~~~~~~~A~~~~~~~l~~~p~--~~~~~~~~a~~~~~~g~~~~A~~~l~~~l   56 (73)
T PF13371_consen    5 YLQQEDYEEALEVLERALELDPD--DPELWLQRARCLFQLGRYEEALEDLERAL   56 (73)
T ss_pred             HHhCCCHHHHHHHHHHHHHhCcc--cchhhHHHHHHHHHhccHHHHHHHHHHHH
Confidence            33444444444444444443322  33444444444444444444444444443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.49  E-value=0.11  Score=37.67  Aligned_cols=108  Identities=12%  Similarity=0.107  Sum_probs=63.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCC--hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHH
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPS--EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTY  182 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~  182 (352)
                      +..++-..|+.++|+.+|++. ...|....  ...+..+..++...|+.++|..+++........ +.+......+.-++
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~A-l~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L   85 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRA-LAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALAL   85 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHH-HHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHH
Confidence            345566778888888888887 44554433  235666777777788888888888877665322 10112222233466


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFA  216 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~  216 (352)
                      ...|+.++|.+.+-...  .++...|..-|..|.
T Consensus        86 ~~~gr~~eAl~~~l~~l--a~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   86 YNLGRPKEALEWLLEAL--AETLPRYRRAIRFYA  117 (120)
T ss_pred             HHCCCHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence            67778887777775542  233334555554443

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.058  Score=45.15  Aligned_cols=100  Identities=10%  Similarity=-0.041  Sum_probs=69.1

Q ss_pred             CChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC---ChHHHHHHHHHhccCCC-CHhhHH
Q 042593          134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG---CIFSASKLFEDTSVDRK-NLVSWT  209 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~-~~~~~~  209 (352)
                      -|...|..|..+|...|+.+.|...|....+...+  ++..+..+..++..+.   ...++.++|++.....| |+.+..
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 GDAEGWDLLGRAYMALGRASDALLAYRNALRLAGD--NPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHH
Confidence            35567778888888888888888777777665433  6666666666665543   34567777777766544 555566


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          210 TIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      -|...+...|++.+|...|+.|.+..
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcC
Confidence            66667777888888888888887764

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

Probab=96.42  E-value=0.0075  Score=40.14  Aligned_cols=62  Identities=16%  Similarity=0.145  Sum_probs=38.2

Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccC-------CCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVD-------RKN-LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-------~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..+++.+..+|...|++++|++.|++....       .|+ ..+++.+..+|...|++++|++.+++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            345666666677777777776666654321       122 45566677777777777777777776543

...

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.38  E-value=0.2  Score=42.06  Aligned_cols=115  Identities=12%  Similarity=-0.008  Sum_probs=90.0

Q ss_pred             CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCC---CHHHHHHHHHHHHhcCCCCCcchhh
Q 042593          169 AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHG---MGKEAVENFERMQKVGLKPNRSWRI  244 (352)
Q Consensus       169 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~  244 (352)
                      |.|..-|-.|..+|...|+.+.|..-|....+. ++|...+..+..++..+.   ...++..+|+++...          
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~----------  222 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL----------  222 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc----------
Confidence            448999999999999999999999999987655 567777777766654332   457888888888863          


Q ss_pred             hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHH
Q 042593          245 GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLL  309 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~  309 (352)
                                      -+-|+.+...|...+...|++.+|...|+.|.+.-|....|..+|....
T Consensus       223 ----------------D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie~~i  271 (287)
T COG4235         223 ----------------DPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIERSI  271 (287)
T ss_pred             ----------------CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHHHHH
Confidence                            2236777778889999999999999999999988566667777776543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.34  E-value=0.33  Score=45.77  Aligned_cols=114  Identities=11%  Similarity=0.000  Sum_probs=88.0

Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHH
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKF  251 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~  251 (352)
                      .-+.+--+.-+...|+..+|.++-.+.  .-||-..|-.-+.+++..++|++-+++-+.++.                  
T Consensus       684 dlSl~dTv~~li~~g~~k~a~ql~~~F--kipdKr~~wLk~~aLa~~~kweeLekfAkskks------------------  743 (829)
T KOG2280|consen  684 DLSLHDTVTTLILIGQNKRAEQLKSDF--KIPDKRLWWLKLTALADIKKWEELEKFAKSKKS------------------  743 (829)
T ss_pred             cCcHHHHHHHHHHccchHHHHHHHHhc--CCcchhhHHHHHHHHHhhhhHHHHHHHHhccCC------------------
Confidence            344455566677788888888888877  578888888888888888888887777665442                  


Q ss_pred             HHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          252 FDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       252 ~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                                   +.-|.-.+.+|.+.|+.++|.+.+.+....       .-...+|++.|++.+|..+..+..
T Consensus       744 -------------PIGy~PFVe~c~~~~n~~EA~KYiprv~~l-------~ekv~ay~~~~~~~eAad~A~~~r  797 (829)
T KOG2280|consen  744 -------------PIGYLPFVEACLKQGNKDEAKKYIPRVGGL-------QEKVKAYLRVGDVKEAADLAAEHR  797 (829)
T ss_pred             -------------CCCchhHHHHHHhcccHHHHhhhhhccCCh-------HHHHHHHHHhccHHHHHHHHHHhc
Confidence                         233444788899999999999999888754       167889999999999998887764

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.25  E-value=0.45  Score=38.35  Aligned_cols=157  Identities=15%  Similarity=0.028  Sum_probs=91.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      .....+...|++++|.+.|+++.....-.|- ......+..++.+.|+++.|...++.+.+.-+.. ...-+...+.+.+
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~-~~~~~A~Y~~g~~   88 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNS-PKADYALYMLGLS   88 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT--TTHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC-cchhhHHHHHHHH
Confidence            3445567889999999999999444332232 2356788889999999999999999998775543 2222322333322


Q ss_pred             h-------------hCChHHHHHHHHHhccCCCCHhh-----------HH-------HHHHHHHcCCCHHHHHHHHHHHH
Q 042593          184 K-------------CGCIFSASKLFEDTSVDRKNLVS-----------WT-------TIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       184 ~-------------~g~~~~a~~~~~~~~~~~~~~~~-----------~~-------~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      .             .+....|...|+.+...-|+..-           .+       .+...|.+.|.+..|..-++.++
T Consensus        89 ~~~~~~~~~~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~~r~~~v~  168 (203)
T PF13525_consen   89 YYKQIPGILRSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAIIRFQYVI  168 (203)
T ss_dssp             HHHHHHHHH-TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHH
T ss_pred             HHHhCccchhcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            1             12234566667766555443311           01       12344666777777777777766


Q ss_pred             hcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHH
Q 042593          233 KVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAE  285 (352)
Q Consensus       233 ~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~  285 (352)
                      +.=  |                     +.+........++.+|.+.|..+.|.
T Consensus       169 ~~y--p---------------------~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  169 ENY--P---------------------DTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHS--T---------------------TSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHC--C---------------------CCchHHHHHHHHHHHHHHhCChHHHH
Confidence            531  1                     11223346678899999999988554

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.05  E-value=0.1  Score=46.60  Aligned_cols=64  Identities=16%  Similarity=0.035  Sum_probs=35.9

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH----hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL----VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +...++.+..+|.+.|++++|...|++.....|+.    .+|..+..+|...|+.++|...+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            45555555566666666666666665544444432    23555555666666666666666655553

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.05  E-value=0.027  Score=36.77  Aligned_cols=57  Identities=18%  Similarity=0.137  Sum_probs=49.7

Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      -..|.+.+++++|.++++.+....| ++..|.....++.+.|++++|.+.+++..+.+
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            3578899999999999999877755 67778888899999999999999999999754

>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=96.02  E-value=0.019  Score=38.11  Aligned_cols=63  Identities=14%  Similarity=0.264  Sum_probs=47.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHh
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      ..+++.+...|...|++++|++.|++..+     ++...  .++.   +++.+..++...|++++|++.+++.
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~--~~a~---~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHP--DTAN---TLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHH--HHHH---HHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCH--HHHH---HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45788888999999999999998888753     22111  1111   1899999999999999999999886

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.99  E-value=0.13  Score=45.05  Aligned_cols=157  Identities=11%  Similarity=-0.037  Sum_probs=101.1

Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH--HHhhCChHHHHHHHHHhccCCCCHhhHH------------
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT--YAKCGCIFSASKLFEDTSVDRKNLVSWT------------  209 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~--~~~~g~~~~a~~~~~~~~~~~~~~~~~~------------  209 (352)
                      .++.-.|+.++|..+--..++....    ..+..++++  +--.++.+.|...|++-....|+-..--            
T Consensus       177 ~cl~~~~~~~~a~~ea~~ilkld~~----n~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~~~~k~le~~  252 (486)
T KOG0550|consen  177 ECLAFLGDYDEAQSEAIDILKLDAT----NAEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSASMMPKKLEVK  252 (486)
T ss_pred             hhhhhcccchhHHHHHHHHHhcccc----hhHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHhhhHHHHHHH
Confidence            3456778899988887777766432    233344444  3356788999999998765555432211            


Q ss_pred             -HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHH
Q 042593          210 -TIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA  288 (352)
Q Consensus       210 -~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~  288 (352)
                       .=-.-..++|++..|.+.|.+.+.  +.|+                    ...|+...|.....+..+.|+.++|..-.
T Consensus       253 k~~gN~~fk~G~y~~A~E~Yteal~--idP~--------------------n~~~naklY~nra~v~~rLgrl~eaisdc  310 (486)
T KOG0550|consen  253 KERGNDAFKNGNYRKAYECYTEALN--IDPS--------------------NKKTNAKLYGNRALVNIRLGRLREAISDC  310 (486)
T ss_pred             HhhhhhHhhccchhHHHHHHHHhhc--CCcc--------------------ccchhHHHHHHhHhhhcccCCchhhhhhh
Confidence             112224678999999999999775  4555                    66777888888888888888888888887


Q ss_pred             hcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          289 SGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       289 ~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      ++.... +.-+..+-.-..++...+++++|.+.+...++
T Consensus       311 ~~Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a~q  349 (486)
T KOG0550|consen  311 NEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKAMQ  349 (486)
T ss_pred             hhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            777665 11112222223345566667766666655543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.84  E-value=0.34  Score=45.01  Aligned_cols=62  Identities=13%  Similarity=0.201  Sum_probs=36.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHH--HHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQL--HAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE   87 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~--~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   87 (352)
                      +.-.++..=++|.+-++..--.-+  +++++++|-.|+...   +...++-.|++.+|.++|.+--.
T Consensus       597 eAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~G~  660 (1081)
T KOG1538|consen  597 EALDFETARKAYIRVRDLRYLELISELEERKKRGETPNDLL---LADVFAYQGKFHEAAKLFKRSGH  660 (1081)
T ss_pred             hhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHH---HHHHHHhhhhHHHHHHHHHHcCc
Confidence            334455555666655554322222  345566676676653   45566777888888888877543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.82  E-value=0.42  Score=43.98  Aligned_cols=164  Identities=15%  Similarity=0.058  Sum_probs=87.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-----hHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-----TILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-----t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                      ...++...+-.||-+.+++.+.+-.+..++.-...     +|+.++..++.    ..+.+.|.++++.+.+.  -| +..
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP-~s~  267 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YP-NSA  267 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CC-CcH
Confidence            44455555556677777777666633333322211     24444443332    34556666777666655  23 333


Q ss_pred             hHH-HHHHHHHhhCChHHHHHHHHHhccC-----CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHh
Q 042593          174 VSN-CLIDTYAKCGCIFSASKLFEDTSVD-----RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEE  247 (352)
Q Consensus       174 ~~~-~li~~~~~~g~~~~a~~~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~  247 (352)
                      .|. .-.+.+...|++++|.+.|+.....     +.....+--+.-.+.-..+|++|.+.|.++.+..            
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s------------  335 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES------------  335 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc------------
Confidence            332 2345556667777777777754322     1122223334444556667777777777766532            


Q ss_pred             HHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCCh-------hHHHHHHhcCCCC
Q 042593          248 GLKFFDKMVEECEVLPDIKHYGCLIDILERAGRL-------EQAEEVASGIPSQ  294 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~-------~~A~~~~~~m~~~  294 (352)
                                  .+.+..++| ....++...|+.       ++|.++|.+....
T Consensus       336 ------------~WSka~Y~Y-~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~l  376 (468)
T PF10300_consen  336 ------------KWSKAFYAY-LAAACLLMLGREEEAKEHKKEAEELFRKVPKL  376 (468)
T ss_pred             ------------ccHHHHHHH-HHHHHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence                        333333333 223444567777       8888888876544

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.81  E-value=1.2  Score=39.22  Aligned_cols=166  Identities=14%  Similarity=0.057  Sum_probs=98.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCC-C-ChhhHHHHHHHHHh---CCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTE-P-SEITILAVLPAIWK---NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~-p-~~~t~~~ll~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      ++-+|-...+++...++++.+....... + ....--...-|+.+   .|+.++|.+++..+......+ ++.+|..+.+
T Consensus       147 lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~-~~d~~gL~GR  225 (374)
T PF13281_consen  147 LLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENP-DPDTLGLLGR  225 (374)
T ss_pred             HHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCC-ChHHHHHHHH
Confidence            3445888999999999999994322111 1 12222344555666   899999999999966665556 8888988888


Q ss_pred             HHHhh---------CChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCC-HH---HHHHHH---HH-HHhcCCCCCcchh
Q 042593          181 TYAKC---------GCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGM-GK---EAVENF---ER-MQKVGLKPNRSWR  243 (352)
Q Consensus       181 ~~~~~---------g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~---~a~~~~---~~-m~~~~~~p~~~~~  243 (352)
                      .|-..         ..++.|.+.|.+--...||..+=-.+...+...|. .+   +..++-   .. ..+.|..      
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~------  299 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSL------  299 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHHHcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccc------
Confidence            87532         23667777777654334443221111222222222 11   222221   11 1111111      


Q ss_pred             hhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          244 IGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       244 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                                      .-..+--.+..+..+..-.|+.++|.+..+.|...
T Consensus       300 ----------------~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  300 ----------------EKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             ----------------cccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence                            11234455677889999999999999999998876

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.71  E-value=0.45  Score=45.49  Aligned_cols=169  Identities=11%  Similarity=0.028  Sum_probs=109.4

Q ss_pred             CCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHH----HhC------------CCCchhhHHHHHHHHHhcCChhHH
Q 042593           15 HSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFS----KVG------------FQSHVYVNTALGDMYVSLGFLKDS   78 (352)
Q Consensus        15 ~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~----~~~------------~~~~~~~~~~li~~~~~~g~~~~a   78 (352)
                      +|..|..++..+.+.+++++...+.+-.-.-+++...    ..+            .....-+...-++..++...++-|
T Consensus       274 ~~~~~~s~s~ss~~~i~~~~d~~n~~v~ys~vl~~l~d~l~~w~~~~~vltsdg~~~~L~ek~le~kL~iL~kK~ly~~A  353 (933)
T KOG2114|consen  274 KGTENTSLSNSSSNRIFKAYDLRNRYVLYSSVLEDLSDNLIEWSFDCLVLTSDGVVHELIEKDLETKLDILFKKNLYKVA  353 (933)
T ss_pred             CCCCCcccCccchhheeehhhhcCcccchHHhHHHHHHHHHhcCCcEEEEecCCceeeeeeccHHHHHHHHHHhhhHHHH
Confidence            3444444566778888899988888765444444433    333            112233455667788888888888


Q ss_pred             HHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHH
Q 042593           79 SKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLI  158 (352)
Q Consensus        79 ~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~  158 (352)
                      ..+-+.-..+....-+.       .-.-.+-+-+.|++++|...|-+- - .-++|+     .++.-|-...++..--.+
T Consensus       354 i~LAk~~~~d~d~~~~i-------~~kYgd~Ly~Kgdf~~A~~qYI~t-I-~~le~s-----~Vi~kfLdaq~IknLt~Y  419 (933)
T KOG2114|consen  354 INLAKSQHLDEDTLAEI-------HRKYGDYLYGKGDFDEATDQYIET-I-GFLEPS-----EVIKKFLDAQRIKNLTSY  419 (933)
T ss_pred             HHHHHhcCCCHHHHHHH-------HHHHHHHHHhcCCHHHHHHHHHHH-c-ccCChH-----HHHHHhcCHHHHHHHHHH
Confidence            88877654322222111       222334466789999999888776 1 112333     345556666777777788


Q ss_pred             HHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          159 HGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                      ++.+.+.|+.  +...-..|+.+|.+.++.++-.++.+...
T Consensus       420 Le~L~~~gla--~~dhttlLLncYiKlkd~~kL~efI~~~~  458 (933)
T KOG2114|consen  420 LEALHKKGLA--NSDHTTLLLNCYIKLKDVEKLTEFISKCD  458 (933)
T ss_pred             HHHHHHcccc--cchhHHHHHHHHHHhcchHHHHHHHhcCC
Confidence            8888888887  56666788999999988888777777654

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.64  E-value=0.66  Score=42.21  Aligned_cols=158  Identities=10%  Similarity=0.019  Sum_probs=84.9

Q ss_pred             HHHHhcCCcchHHHHHHHHH-HhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHH
Q 042593           32 RTCVTLSYPNLGTQLHAVFS-KVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGY  110 (352)
Q Consensus        32 ~~~~~~g~~~~a~~~~~~m~-~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~  110 (352)
                      +...-.++++++.+..+.-. -..++  ....+.++..+-+.|..+.|+.+-.+-   +..               ....
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D~---~~r---------------FeLA  328 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVTDP---DHR---------------FELA  328 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-H---HHH---------------HHHH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcCCh---HHH---------------hHHH
Confidence            33445566766655553111 11112  344677777777788888887775442   111               1334


Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS  190 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  190 (352)
                      .+.|+++.|.++.++.       .+...|..|.....+.|+++-|+..+++..          -|..|+-.|.-.|+.+.
T Consensus       329 l~lg~L~~A~~~a~~~-------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~----------d~~~L~lLy~~~g~~~~  391 (443)
T PF04053_consen  329 LQLGNLDIALEIAKEL-------DDPEKWKQLGDEALRQGNIELAEECYQKAK----------DFSGLLLLYSSTGDREK  391 (443)
T ss_dssp             HHCT-HHHHHHHCCCC-------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT-----------HHHHHHHHHHCT-HHH
T ss_pred             HhcCCHHHHHHHHHhc-------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhc----------CccccHHHHHHhCCHHH
Confidence            5677777777665544       355677777777777777777777776432          24566667777777766


Q ss_pred             HHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          191 ASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       191 a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      -.++.+.......    +|....++.-.|+.++..+++.+
T Consensus       392 L~kl~~~a~~~~~----~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  392 LSKLAKIAEERGD----INIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHHHHHHHHTT-----HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHccC----HHHHHHHHHHcCCHHHHHHHHHH
Confidence            6666554432211    44445555556666666666654

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.

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=95.63  E-value=0.38  Score=42.24  Aligned_cols=255  Identities=11%  Similarity=0.045  Sum_probs=126.8

Q ss_pred             ccHHHHH--HHHHhcCCcchHHHHHHHHHHhCCCCch----hhHHHHHHHHHhcCChhHHHHHhccCC-------C--CC
Q 042593           25 FTYSFLI--RTCVTLSYPNLGTQLHAVFSKVGFQSHV----YVNTALGDMYVSLGFLKDSSKLFDELP-------E--RN   89 (352)
Q Consensus        25 ~~~~~ll--~~~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~-------~--~~   89 (352)
                      ..|...+  .-+|+.|+.+....+|+..++.|- -|.    .+|.-|.++|.-.+++++|.++...=.       .  ..
T Consensus        16 SCleLalEGERLck~gdcraGv~ff~aA~qvGT-eDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGE   94 (639)
T KOG1130|consen   16 SCLELALEGERLCKMGDCRAGVDFFKAALQVGT-EDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGE   94 (639)
T ss_pred             HHHHHHHHHHHHHhccchhhhHHHHHHHHHhcc-hHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhcc
Confidence            3444444  458899999999999999999883 333    357777778888888999887654311       0  00


Q ss_pred             chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhH---hccC-CCCChhhHHHHHHHHHhCCC--------------
Q 042593           90 LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMA---ACEY-TEPSEITILAVLPAIWKNGE--------------  151 (352)
Q Consensus        90 ~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~-~~p~~~t~~~ll~~~~~~~~--------------  151 (352)
                      ..+          ...|-+.+--.|.+++|+-.-.+-+   +.-| .......+..+.+.|...|+              
T Consensus        95 AKs----------sgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~  164 (639)
T KOG1130|consen   95 AKS----------SGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFN  164 (639)
T ss_pred             ccc----------cccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhccccc
Confidence            000          1111111222233333322211100   0000 00111223333333332221              


Q ss_pred             ------hhhHHHHHHHH----HhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhc---cC----CCCHhhHHHHHHH
Q 042593          152 ------VRNCQLIHGYG----EKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTS---VD----RKNLVSWTTIISG  214 (352)
Q Consensus       152 ------~~~a~~~~~~~----~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~---~~----~~~~~~~~~li~~  214 (352)
                            ++.|.++|.+-    .+.|-...-...|..|-+.|--.|+++.|+..-+.-.   +.    ...-..+..+-.+
T Consensus       165 ~ev~~al~~Av~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~  244 (639)
T KOG1130|consen  165 AEVTSALENAVKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNC  244 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchh
Confidence                  23334443322    2222221123456666666666777777665544311   11    1223445666666


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcch------hh----------hHhHHHHHHHHHHh----cCCCCChhhHHHHHHH
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSW------RI----------GEEGLKFFDKMVEE----CEVLPDIKHYGCLIDI  274 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~------~~----------~~~a~~~~~~m~~~----~~~~p~~~~~~~li~~  274 (352)
                      +.-.|+++.|.+.|+.-...-++....+      |+          ++.|+.++.+-..-    ....-....+.+|..+
T Consensus       245 hiflg~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna  324 (639)
T KOG1130|consen  245 HIFLGNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNA  324 (639)
T ss_pred             hhhhcccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            6667777777776665433222111111      11          55555555443321    0112245677888999


Q ss_pred             HHHcCChhHHHHHHhc
Q 042593          275 LERAGRLEQAEEVASG  290 (352)
Q Consensus       275 ~~~~g~~~~A~~~~~~  290 (352)
                      |...|..++|..+.+.
T Consensus       325 ~~alg~h~kAl~fae~  340 (639)
T KOG1130|consen  325 FNALGEHRKALYFAEL  340 (639)
T ss_pred             HHhhhhHHHHHHHHHH
Confidence            9999998888776543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.63  E-value=0.11  Score=42.87  Aligned_cols=102  Identities=11%  Similarity=0.009  Sum_probs=63.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCC-CCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC-CCchhhHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYT-EPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLID  180 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~  180 (352)
                      |+.-+..+ +.|++..|..-|....+...- .-....+--|..++...|++++|..+|..+.+.-.. |.-+...-.|..
T Consensus       145 Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~  223 (262)
T COG1729         145 YNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGV  223 (262)
T ss_pred             HHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHH
Confidence            55555543 456677777777777333211 112234556777777777777777777777654332 223455666777


Q ss_pred             HHHhhCChHHHHHHHHHhccCCCCH
Q 042593          181 TYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      +..+.|+.++|..+|+++.+..|+.
T Consensus       224 ~~~~l~~~d~A~atl~qv~k~YP~t  248 (262)
T COG1729         224 SLGRLGNTDEACATLQQVIKRYPGT  248 (262)
T ss_pred             HHHHhcCHHHHHHHHHHHHHHCCCC
Confidence            7777777788888877777666654

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.62  E-value=0.7  Score=42.06  Aligned_cols=134  Identities=17%  Similarity=0.148  Sum_probs=100.3

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKW  103 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~  103 (352)
                      ....+.+++-+-+.|..+.|+++-         .|+.+   --+...+.|+++.|.++-++..  +...          |
T Consensus       295 ~~~~~~i~~fL~~~G~~e~AL~~~---------~D~~~---rFeLAl~lg~L~~A~~~a~~~~--~~~~----------W  350 (443)
T PF04053_consen  295 KDQGQSIARFLEKKGYPELALQFV---------TDPDH---RFELALQLGNLDIALEIAKELD--DPEK----------W  350 (443)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHS---------S-HHH---HHHHHHHCT-HHHHHHHCCCCS--THHH----------H
T ss_pred             hhHHHHHHHHHHHCCCHHHHHhhc---------CChHH---HhHHHHhcCCHHHHHHHHHhcC--cHHH----------H
Confidence            344788888888999999998863         33332   2455678999999999998886  3445          9


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA  183 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  183 (352)
                      ..|.....+.|+++-|.+.|.+. +         -+..++--|.-.|+.++..++.+...+.|-       +|....++.
T Consensus       351 ~~Lg~~AL~~g~~~lAe~c~~k~-~---------d~~~L~lLy~~~g~~~~L~kl~~~a~~~~~-------~n~af~~~~  413 (443)
T PF04053_consen  351 KQLGDEALRQGNIELAEECYQKA-K---------DFSGLLLLYSSTGDREKLSKLAKIAEERGD-------INIAFQAAL  413 (443)
T ss_dssp             HHHHHHHHHTTBHHHHHHHHHHC-T----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT--------HHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhh-c---------CccccHHHHHHhCCHHHHHHHHHHHHHccC-------HHHHHHHHH
Confidence            99999999999999999999998 4         255677778888999888888887776653       456667777


Q ss_pred             hhCChHHHHHHHHHh
Q 042593          184 KCGCIFSASKLFEDT  198 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~  198 (352)
                      -.|+.+++.+++.+-
T Consensus       414 ~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  414 LLGDVEECVDLLIET  428 (443)
T ss_dssp             HHT-HHHHHHHHHHT
T ss_pred             HcCCHHHHHHHHHHc
Confidence            789999988888765

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.

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=95.62  E-value=0.51  Score=36.41  Aligned_cols=125  Identities=12%  Similarity=-0.002  Sum_probs=59.8

Q ss_pred             CCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC--hhHHHHHhccCCCCCchh
Q 042593           15 HSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF--LKDSSKLFDELPERNLVT   92 (352)
Q Consensus        15 ~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~--~~~a~~~~~~m~~~~~~~   92 (352)
                      .++.|   +...|..++..+.+.|++.    .+.++...++-+|.......+-.+.....  ..-|.+++.++.    ..
T Consensus        23 ~~i~~---~~~L~~lli~lLi~~~~~~----~L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~----~~   91 (167)
T PF07035_consen   23 HNIPV---QHELYELLIDLLIRNGQFS----QLHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG----TA   91 (167)
T ss_pred             cCCCC---CHHHHHHHHHHHHHcCCHH----HHHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh----hh
Confidence            56666   6666666666666666643    33334445554444443333322222110  222333333332    11


Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhc
Q 042593           93 WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKR  165 (352)
Q Consensus        93 ~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  165 (352)
                                +..++..+...|++-+|+++..+..+     .+...-..++.+..+.+|...-..+++-..+.
T Consensus        92 ----------~~~iievLL~~g~vl~ALr~ar~~~~-----~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~  149 (167)
T PF07035_consen   92 ----------YEEIIEVLLSKGQVLEALRYARQYHK-----VDSVPARKFLEAAANSNDDQLFYAVFRFFEER  149 (167)
T ss_pred             ----------HHHHHHHHHhCCCHHHHHHHHHHcCC-----cccCCHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                      45555666666666666666655411     12222344555555555555545555444443

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

Probab=95.61  E-value=0.094  Score=43.48  Aligned_cols=106  Identities=13%  Similarity=0.101  Sum_probs=75.2

Q ss_pred             CCCcccHHHHHHHHHhc-----CCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHH
Q 042593           21 LFDSFTYSFLIRTCVTL-----SYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNV   95 (352)
Q Consensus        21 ~~~~~~~~~ll~~~~~~-----g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~   95 (352)
                      .+|-.+|-..+..+...     +.++-.-..+..|.+.|+..|..+|+.|++.+-+..-+..           |     .
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~-----------n-----v  127 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQ-----------N-----V  127 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccH-----------H-----H
Confidence            44777788887777643     5666666778889999999999999999988765322111           1     1


Q ss_pred             HHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCCh
Q 042593           96 IITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEV  152 (352)
Q Consensus        96 ~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~  152 (352)
                             +..+.-.|-  .+-+-+++++++| ...|+.||..+-..+++++.+.+..
T Consensus       128 -------fQ~~F~HYP--~QQ~C~I~vLeqM-E~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  128 -------FQKVFLHYP--QQQNCAIKVLEQM-EWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             -------HHHHHhhCc--hhhhHHHHHHHHH-HHcCCCCchHHHHHHHHHhcccccc
Confidence                   111111122  2344578999999 9999999999999999999887753

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.54  E-value=0.75  Score=42.85  Aligned_cols=199  Identities=12%  Similarity=0.098  Sum_probs=118.5

Q ss_pred             hHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhc
Q 042593            4 YKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFD   83 (352)
Q Consensus         4 ~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~   83 (352)
                      +++|++     .|-.|   +...   +...|+-.|.+.+|-++|..   .|..      |..+..|.....++.|.+++.
T Consensus       623 L~~~k~-----rge~P---~~iL---lA~~~Ay~gKF~EAAklFk~---~G~e------nRAlEmyTDlRMFD~aQE~~~  682 (1081)
T KOG1538|consen  623 LEERKK-----RGETP---NDLL---LADVFAYQGKFHEAAKLFKR---SGHE------NRALEMYTDLRMFDYAQEFLG  682 (1081)
T ss_pred             HHHHHh-----cCCCc---hHHH---HHHHHHhhhhHHHHHHHHHH---cCch------hhHHHHHHHHHHHHHHHHHhh
Confidence            356666     78888   6553   34567778888888887753   3432      123444555555555555544


Q ss_pred             cCCCCCchhHHHHHHHHHhH-------HHHHHHHHhcCCHHHHHHHHH-----HhHhccCC---CCChhhHHHHHHHHHh
Q 042593           84 ELPERNLVTWNVIITGLVKW-------TGIIDGYSRMNRSNEALALFR-----RMAACEYT---EPSEITILAVLPAIWK  148 (352)
Q Consensus        84 ~m~~~~~~~~~~~i~~~~~~-------~~li~~~~~~~~~~~a~~~~~-----~m~~~~~~---~p~~~t~~~ll~~~~~  148 (352)
                      .-..   .+---+++--+.|       -+....+..+|+.++|..+.-     +|.-+-+-   ..+..+...+...+.+
T Consensus       683 ~g~~---~eKKmL~RKRA~WAr~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~  759 (1081)
T KOG1538|consen  683 SGDP---KEKKMLIRKRADWARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKK  759 (1081)
T ss_pred             cCCh---HHHHHHHHHHHHHhhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhh
Confidence            3321   0000000000001       122244566788777776632     22121111   2234466666666777


Q ss_pred             CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhh-----------HHHHHHHHHc
Q 042593          149 NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVS-----------WTTIISGFAM  217 (352)
Q Consensus       149 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----------~~~li~~~~~  217 (352)
                      ......|-++|..|-.          ...+++.....+++++|..+-+...+..||+..           |.-.=.+|.+
T Consensus       760 l~~~gLAaeIF~k~gD----------~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhk  829 (1081)
T KOG1538|consen  760 LDSPGLAAEIFLKMGD----------LKSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHK  829 (1081)
T ss_pred             ccccchHHHHHHHhcc----------HHHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHH
Confidence            7888888888886632          236678888999999999999988766666532           3334467889


Q ss_pred             CCCHHHHHHHHHHHHhcC
Q 042593          218 HGMGKEAVENFERMQKVG  235 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~~~  235 (352)
                      .|+-.+|.++++++....
T Consensus       830 AGr~~EA~~vLeQLtnna  847 (1081)
T KOG1538|consen  830 AGRQREAVQVLEQLTNNA  847 (1081)
T ss_pred             hcchHHHHHHHHHhhhhh
Confidence            999999999998876643

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

Probab=95.52  E-value=0.06  Score=40.79  Aligned_cols=55  Identities=15%  Similarity=0.104  Sum_probs=26.4

Q ss_pred             HHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       142 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      ++..+...|+++.|..+.+.+....+.  +...|..+|.+|...|+...|.++|+.+
T Consensus        68 l~~~~~~~~~~~~a~~~~~~~l~~dP~--~E~~~~~lm~~~~~~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   68 LAEALLEAGDYEEALRLLQRALALDPY--DEEAYRLLMRALAAQGRRAEALRVYERY  122 (146)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHHHSTT---HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHhccCHHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            333444455555555555555544322  4555555555555555555555555544

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

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.51  E-value=0.73  Score=34.51  Aligned_cols=126  Identities=18%  Similarity=0.111  Sum_probs=81.2

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcC
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMH  218 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~  218 (352)
                      ...++..+...+.......+++.+.+.+. . +....+.++..|++.+ .++..+.++.    ..+......++..|.+.
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~-~~~~~~~li~ly~~~~-~~~ll~~l~~----~~~~yd~~~~~~~c~~~   82 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLNS-E-NPALQTKLIELYAKYD-PQKEIERLDN----KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccCc-c-chhHHHHHHHHHHHHC-HHHHHHHHHh----ccccCCHHHHHHHHHHc
Confidence            44667777777788888888888887764 3 7778888888888764 3445555552    22334445577777788


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHc-CChhHHHHHHhcCCCCCCC
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERA-GRLEQAEEVASGIPSQITN  297 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~~~~~  297 (352)
                      +.++++.-++.++...                                  ...+..+... ++.+.|.+.+.+-.    +
T Consensus        83 ~l~~~~~~l~~k~~~~----------------------------------~~Al~~~l~~~~d~~~a~~~~~~~~----~  124 (140)
T smart00299       83 KLYEEAVELYKKDGNF----------------------------------KDAIVTLIEHLGNYEKAIEYFVKQN----N  124 (140)
T ss_pred             CcHHHHHHHHHhhcCH----------------------------------HHHHHHHHHcccCHHHHHHHHHhCC----C
Confidence            8888888888775431                                  1122333333 67777777776632    5


Q ss_pred             chhhHHHHHHHH
Q 042593          298 VVVWRTGFLRLL  309 (352)
Q Consensus       298 ~~~~~~li~~~~  309 (352)
                      ...|..++..+.
T Consensus       125 ~~lw~~~~~~~l  136 (140)
T smart00299      125 PELWAEVLKALL  136 (140)
T ss_pred             HHHHHHHHHHHH
Confidence            567777776654

>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=95.50  E-value=0.54  Score=34.42  Aligned_cols=137  Identities=14%  Similarity=0.102  Sum_probs=78.2

Q ss_pred             hcCChhHHHHHhccCCC-CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC
Q 042593           71 SLGFLKDSSKLFDELPE-RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN  149 (352)
Q Consensus        71 ~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~  149 (352)
                      -.|.+++..++..+... .+..-          ||.+|--....-+-+-..++++.+    |--.|...          .
T Consensus        14 ldG~V~qGveii~k~v~Ssni~E----------~NWvICNiiDaa~C~yvv~~LdsI----GkiFDis~----------C   69 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNSSNIKE----------YNWVICNIIDAADCDYVVETLDSI----GKIFDISK----------C   69 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHHS-HHH----------HTHHHHHHHHH--HHHHHHHHHHH----GGGS-GGG-----------
T ss_pred             HhchHHHHHHHHHHHcCcCCccc----------cceeeeecchhhchhHHHHHHHHH----hhhcCchh----------h
Confidence            35777777777777654 33344          444444444444444445555544    22233322          2


Q ss_pred             CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHH
Q 042593          150 GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENF  228 (352)
Q Consensus       150 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~  228 (352)
                      |++..+...+..   .|.   ........+..+...|+-+.-.++..++.+. .+++...-.+..+|.+.|+..++.+++
T Consensus        70 ~NlKrVi~C~~~---~n~---~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell  143 (161)
T PF09205_consen   70 GNLKRVIECYAK---RNK---LSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELL  143 (161)
T ss_dssp             S-THHHHHHHHH---TT------HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             cchHHHHHHHHH---hcc---hHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHH
Confidence            333332222222   111   4455677788999999999999999887644 788888889999999999999999999


Q ss_pred             HHHHhcCCC
Q 042593          229 ERMQKVGLK  237 (352)
Q Consensus       229 ~~m~~~~~~  237 (352)
                      .+.-+.|++
T Consensus       144 ~~ACekG~k  152 (161)
T PF09205_consen  144 KEACEKGLK  152 (161)
T ss_dssp             HHHHHTT-H
T ss_pred             HHHHHhchH
Confidence            998888753

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.50  E-value=1.7  Score=38.80  Aligned_cols=128  Identities=15%  Similarity=0.039  Sum_probs=95.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccC-CCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEY-TEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |...++.-.+..-++.|..+|-+. ++.+ +.+++..+++++.-++. |+...|.++|+.-...-..  +..--+..+..
T Consensus       400 ~C~~~N~v~r~~Gl~aaR~~F~k~-rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~f~d--~~~y~~kyl~f  475 (660)
T COG5107         400 FCVHLNYVLRKRGLEAARKLFIKL-RKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLKFPD--STLYKEKYLLF  475 (660)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHH-hccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHhCCC--chHHHHHHHHH
Confidence            777777777888889999999999 5555 67888889999887765 7788888888865544222  23333466778


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKN--LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +...++-+.|..+|+.-... ..+  ...|..+|+.=..-|+...+..+=++|.+.
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH
Confidence            88889999999999854322 222  567889998888889988888887777663

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.49  E-value=0.38  Score=44.28  Aligned_cols=183  Identities=14%  Similarity=0.031  Sum_probs=113.7

Q ss_pred             HHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHHHHHHHHHhHHHHHHHHHh----cCCHHH
Q 042593           44 TQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVIITGLVKWTGIIDGYSR----MNRSNE  118 (352)
Q Consensus        44 ~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~~~~~~li~~~~~----~~~~~~  118 (352)
                      .-+|..+... +||   ....++...+=.||-+.+++++.+..+ +++...-+.+. +..|+.++..++.    ..+.+.
T Consensus       177 ~G~f~L~lSl-LPp---~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~-LL~y~~~~~~~~~~~~~~~~~~~  251 (468)
T PF10300_consen  177 FGLFNLVLSL-LPP---KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALV-LLWYHLVVPSFLGIDGEDVPLEE  251 (468)
T ss_pred             HHHHHHHHHh-CCH---HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHH-HHHHHHHHHHHcCCcccCCCHHH
Confidence            4556666553 244   344567777788888888888887654 33322111111 1126666665554    457888


Q ss_pred             HHHHHHHhHhccCCCCChhhHHHH-HHHHHhCCChhhHHHHHHHHHhc--CCCCCchhhHHHHHHHHHhhCChHHHHHHH
Q 042593          119 ALALFRRMAACEYTEPSEITILAV-LPAIWKNGEVRNCQLIHGYGEKR--GFNAFDIHVSNCLIDTYAKCGCIFSASKLF  195 (352)
Q Consensus       119 a~~~~~~m~~~~~~~p~~~t~~~l-l~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  195 (352)
                      |.++++.+.+ .  -|+...|... .+.+...|++++|.+.++.....  .......-.+--+.-++.-.+++++|.+.|
T Consensus       252 a~~lL~~~~~-~--yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f  328 (468)
T PF10300_consen  252 AEELLEEMLK-R--YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYF  328 (468)
T ss_pred             HHHHHHHHHH-h--CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHH
Confidence            9999999843 2  3666655433 34466789999999999975532  221113334446677788899999999999


Q ss_pred             HHhccCCCCHhhHHHHHH--HHHcCCCH-------HHHHHHHHHHHhc
Q 042593          196 EDTSVDRKNLVSWTTIIS--GFAMHGMG-------KEAVENFERMQKV  234 (352)
Q Consensus       196 ~~~~~~~~~~~~~~~li~--~~~~~~~~-------~~a~~~~~~m~~~  234 (352)
                      ..+.+......++-..+.  ++...|+.       ++|.++|.+....
T Consensus       329 ~~L~~~s~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~l  376 (468)
T PF10300_consen  329 LRLLKESKWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPKL  376 (468)
T ss_pred             HHHHhccccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence            998766444333333333  34556666       8888888887553

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.45  E-value=0.77  Score=34.40  Aligned_cols=130  Identities=9%  Similarity=0.064  Sum_probs=81.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      +......++..+.+.+.......+++.+...+ ..++...+.++..|++.+ .++..+.++.  ..+...          
T Consensus         6 ~~~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~~~~yd----------   71 (140)
T smart00299        6 DPIDVSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN--KSNHYD----------   71 (140)
T ss_pred             CcCCHHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh--ccccCC----------
Confidence            34446678888888888888888888888776 467778888888888763 3445555552  122222          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC-CChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN-GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      ...+++.|.+.+-++++.-++.++ ..         +...+..+... ++.+.|.++...      .. +...|..++..
T Consensus        72 ~~~~~~~c~~~~l~~~~~~l~~k~-~~---------~~~Al~~~l~~~~d~~~a~~~~~~------~~-~~~lw~~~~~~  134 (140)
T smart00299       72 IEKVGKLCEKAKLYEEAVELYKKD-GN---------FKDAIVTLIEHLGNYEKAIEYFVK------QN-NPELWAEVLKA  134 (140)
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHhh-cC---------HHHHHHHHHHcccCHHHHHHHHHh------CC-CHHHHHHHHHH
Confidence            445667777777777777777776 21         11222223233 666666666654      11 55566666665


Q ss_pred             HH
Q 042593          182 YA  183 (352)
Q Consensus       182 ~~  183 (352)
                      +.
T Consensus       135 ~l  136 (140)
T smart00299      135 LL  136 (140)
T ss_pred             HH
Confidence            54

>PRK15331 chaperone protein SicA; Provisional

Probab=95.38  E-value=0.15  Score=39.00  Aligned_cols=88  Identities=9%  Similarity=0.017  Sum_probs=56.2

Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHH
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~  222 (352)
                      .-+-..|++++|..+|+-+.-.+..  +..-|..|..++-..+++++|...|...... .-|+..+-..-.++...|+.+
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~~d~~--n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~  122 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCIYDFY--NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAA  122 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcC--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHH
Confidence            3344667777777777777765544  5556666777777777777777777653222 223333444556677777777


Q ss_pred             HHHHHHHHHHh
Q 042593          223 EAVENFERMQK  233 (352)
Q Consensus       223 ~a~~~~~~m~~  233 (352)
                      .|...|....+
T Consensus       123 ~A~~~f~~a~~  133 (165)
T PRK15331        123 KARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHh
Confidence            77777777666

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

Probab=95.31  E-value=0.14  Score=42.55  Aligned_cols=99  Identities=11%  Similarity=0.087  Sum_probs=74.5

Q ss_pred             HHHHHhccCC--CCCchhHHHHHHHHHhHHHHHHHHH-----hcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC
Q 042593           77 DSSKLFDELP--ERNLVTWNVIITGLVKWTGIIDGYS-----RMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN  149 (352)
Q Consensus        77 ~a~~~~~~m~--~~~~~~~~~~i~~~~~~~~li~~~~-----~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~  149 (352)
                      ..++.|....  ++|..+          |-..+..+.     +.+.++-...-++.| +..|+.-|..+|+.|++.+-+.
T Consensus        52 ~~e~~F~aa~~~~RdK~s----------fl~~V~~F~E~sVr~R~HveFIy~ALk~m-~eyGVerDl~vYk~LlnvfPKg  120 (406)
T KOG3941|consen   52 HVEKQFEAAEPEKRDKDS----------FLAAVATFKEKSVRGRTHVEFIYTALKYM-KEYGVERDLDVYKGLLNVFPKG  120 (406)
T ss_pred             chhhhhhccCcccccHHH----------HHHHHHHHHHhhhcccchHHHHHHHHHHH-HHhcchhhHHHHHHHHHhCccc
Confidence            3455666655  355555          444444443     345677777778889 9999999999999999988665


Q ss_pred             CC----------------hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          150 GE----------------VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       150 ~~----------------~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      .-                -.-+.+++++|...|+.| |..+-..|++++++.+-
T Consensus       121 kfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmP-dkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  121 KFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMP-DKEIEDILVNAFGRWNF  173 (406)
T ss_pred             ccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCC-chHHHHHHHHHhccccc
Confidence            42                244779999999999999 99999999999998875

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=95.31  E-value=1.4  Score=36.42  Aligned_cols=172  Identities=15%  Similarity=0.067  Sum_probs=114.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |+.-+ .-.+.|++++|.+.|+.+..+....| ...+...++.++-+.++.+.|....++....-... ...-|..-|.+
T Consensus        38 Y~~g~-~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~-~n~dY~~Ylkg  115 (254)
T COG4105          38 YNEGL-TELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTH-PNADYAYYLKG  115 (254)
T ss_pred             HHHHH-HHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCC-CChhHHHHHHH
Confidence            44433 35678999999999999955544433 34477788888889999999999999998876665 44556666666


Q ss_pred             HHhh-------CChHHHHHHHH---HhccCCCCH------hh-----------H-HHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          182 YAKC-------GCIFSASKLFE---DTSVDRKNL------VS-----------W-TTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       182 ~~~~-------g~~~~a~~~~~---~~~~~~~~~------~~-----------~-~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ++.-       .|...+.+-|.   ++...-||.      ..           + -.+...|.+.|.+..|..-+++|++
T Consensus       116 Ls~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e  195 (254)
T COG4105         116 LSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLE  195 (254)
T ss_pred             HHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHh
Confidence            6642       34444444444   443333432      11           1 1234568888999999999999888


Q ss_pred             cCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCch
Q 042593          234 VGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVV  299 (352)
Q Consensus       234 ~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~  299 (352)
                      .  -|                     ...-.....-.+..+|...|-.++|.+.-.-+....|+..
T Consensus       196 ~--y~---------------------~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N~p~s~  238 (254)
T COG4105         196 N--YP---------------------DTSAVREALARLEEAYYALGLTDEAKKTAKVLGANYPDSQ  238 (254)
T ss_pred             c--cc---------------------cccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhcCCCCc
Confidence            5  11                     1112344566788899999999999887776665544443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=95.31  E-value=1.8  Score=37.92  Aligned_cols=183  Identities=15%  Similarity=0.069  Sum_probs=109.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh--hHHHHHHHHH--h-CCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI--TILAVLPAIW--K-NGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~--t~~~ll~~~~--~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                      +.+.+...|..|||+.|+++++.-....-+.++..  .-..++.+-+  . ..+...|...-.+..+....  -...--.
T Consensus       191 ~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pd--lvPaav~  268 (531)
T COG3898         191 ARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPD--LVPAAVV  268 (531)
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCc--cchHHHH
Confidence            77889999999999999999998755555667654  2233333322  1 12344455554444444322  2333345


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc-CCCCCcchhh------------
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKV-GLKPNRSWRI------------  244 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~------------  244 (352)
                      -..++.+.|++.++-.+++.+-+..|.+..+..-+  +.+.|+  .+..-+++..+. .++||..--.            
T Consensus       269 AAralf~d~~~rKg~~ilE~aWK~ePHP~ia~lY~--~ar~gd--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e  344 (531)
T COG3898         269 AARALFRDGNLRKGSKILETAWKAEPHPDIALLYV--RARSGD--TALDRLKRAKKLESLKPNNAESSLAVAEAALDAGE  344 (531)
T ss_pred             HHHHHHhccchhhhhhHHHHHHhcCCChHHHHHHH--HhcCCC--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccc
Confidence            56788999999999999999877766665544322  345554  444444444432 3556543332            


Q ss_pred             hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH-cCChhHHHHHHhcCCCC
Q 042593          245 GEEGLKFFDKMVEECEVLPDIKHYGCLIDILER-AGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       245 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~-~g~~~~A~~~~~~m~~~  294 (352)
                      +..|..--+...   ...|....|..|.+.-.. .||-.++...+-+....
T Consensus       345 ~~~ARa~Aeaa~---r~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         345 FSAARAKAEAAA---REAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             hHHHHHHHHHHh---hhCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            222222222221   456777888877776654 49999888887665443

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=95.26  E-value=0.69  Score=43.48  Aligned_cols=129  Identities=12%  Similarity=-0.041  Sum_probs=69.0

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      .|.+..|..|.......-.++-|+..|-+... +++...--+-.-+..=-.-...-+--|++++|.++|-+| .+..   
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~-drrD---  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDA-DRRD---  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhcc-chhh---
Confidence            47888899888888888888888888887764 332110000000000000001112247888888888888 4332   


Q ss_pred             ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC---chhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          135 SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF---DIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                            ..+....+.||+-.+.++++.   -|-...   -...|+.+.+.+.....++.|.+.+..
T Consensus       765 ------LAielr~klgDwfrV~qL~r~---g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~  821 (1189)
T KOG2041|consen  765 ------LAIELRKKLGDWFRVYQLIRN---GGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSY  821 (1189)
T ss_pred             ------hhHHHHHhhhhHHHHHHHHHc---cCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                  234555566776555444432   221110   123555666666666666666655554

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.14  E-value=2.8  Score=39.88  Aligned_cols=129  Identities=12%  Similarity=0.102  Sum_probs=95.4

Q ss_pred             HHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          120 LALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       120 ~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                      +.+.+.+..+.|..-..-+.+--+.-+...|+...|.++-.+.+    .| +...|-.-+.+++..+++++-+++-+..+
T Consensus       668 l~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ip-dKr~~wLk~~aLa~~~kweeLekfAkskk  742 (829)
T KOG2280|consen  668 LKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IP-DKRLWWLKLTALADIKKWEELEKFAKSKK  742 (829)
T ss_pred             HHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----Cc-chhhHHHHHHHHHhhhhHHHHHHHHhccC
Confidence            33444444444544555567777778888999999988877653    23 88889999999999999999888777553


Q ss_pred             cCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcC
Q 042593          200 VDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAG  279 (352)
Q Consensus       200 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g  279 (352)
                          .+.-|.-...+|.+.|+.++|..++.+.-.                           .   +    -.+.+|.+.|
T Consensus       743 ----sPIGy~PFVe~c~~~~n~~EA~KYiprv~~---------------------------l---~----ekv~ay~~~~  784 (829)
T KOG2280|consen  743 ----SPIGYLPFVEACLKQGNKDEAKKYIPRVGG---------------------------L---Q----EKVKAYLRVG  784 (829)
T ss_pred             ----CCCCchhHHHHHHhcccHHHHhhhhhccCC---------------------------h---H----HHHHHHHHhc
Confidence                267788899999999999999988876432                           1   1    4577888888


Q ss_pred             ChhHHHHHHhcC
Q 042593          280 RLEQAEEVASGI  291 (352)
Q Consensus       280 ~~~~A~~~~~~m  291 (352)
                      ++.+|.++--+-
T Consensus       785 ~~~eAad~A~~~  796 (829)
T KOG2280|consen  785 DVKEAADLAAEH  796 (829)
T ss_pred             cHHHHHHHHHHh
Confidence            888887765443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.04  E-value=0.39  Score=35.81  Aligned_cols=78  Identities=9%  Similarity=-0.073  Sum_probs=54.4

Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      ....+.|++++|.+.|+.+.......|- ...-..++.++.+.+++++|...+++..+..... ...-|...+.+++.-.
T Consensus        18 ~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~h-p~vdYa~Y~~gL~~~~   96 (142)
T PF13512_consen   18 QEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTH-PNVDYAYYMRGLSYYE   96 (142)
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC-CCccHHHHHHHHHHHH
Confidence            3455778899999998888444332222 3366778888888899999998888888887765 4455666666655443

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.99  E-value=0.032  Score=42.15  Aligned_cols=131  Identities=10%  Similarity=0.040  Sum_probs=91.3

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      ...++..+.+.+.++....+++.+...+...+....+.++..|++.++.++..++++....-|             ...+
T Consensus        10 ~~~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~yd-------------~~~~   76 (143)
T PF00637_consen   10 ISEVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNNYD-------------LDKA   76 (143)
T ss_dssp             SCCCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSSS--------------CTHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccccC-------------HHHH
Confidence            345678888899999999999999987766778899999999999999999999999554322             4456


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      +..|.+.|.+++|.-++.++ ....-..+         .+...++++.|.++...   .   . +..+|..+++.+...+
T Consensus        77 ~~~c~~~~l~~~a~~Ly~~~-~~~~~al~---------i~~~~~~~~~a~e~~~~---~---~-~~~l~~~l~~~~l~~~  139 (143)
T PF00637_consen   77 LRLCEKHGLYEEAVYLYSKL-GNHDEALE---------ILHKLKDYEEAIEYAKK---V---D-DPELWEQLLKYCLDSK  139 (143)
T ss_dssp             HHHHHTTTSHHHHHHHHHCC-TTHTTCSS---------TSSSTHCSCCCTTTGGG---C---S-SSHHHHHHHHHHCTST
T ss_pred             HHHHHhcchHHHHHHHHHHc-ccHHHHHH---------HHHHHccHHHHHHHHHh---c---C-cHHHHHHHHHHHHhcC
Confidence            67788888888888888887 43221111         13344566666633332   1   2 5677888887776665


Q ss_pred             C
Q 042593          187 C  187 (352)
Q Consensus       187 ~  187 (352)
                      +
T Consensus       140 ~  140 (143)
T PF00637_consen  140 P  140 (143)
T ss_dssp             C
T ss_pred             c
Confidence            4

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.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.76  E-value=0.74  Score=41.31  Aligned_cols=63  Identities=8%  Similarity=-0.125  Sum_probs=47.5

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch---hhHHHHHHHHHhhCChHHHHHHHHHhcc
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI---HVSNCLIDTYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~~~~  200 (352)
                      ...++.+..++.+.|++++|...+++..+.+..  +.   .+|..+..+|...|+.++|.+.+++...
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd--~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALELNPN--PDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC--chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            446778888888888888888888887776544  33   3577888888888888888888887654

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=94.67  E-value=0.015  Score=50.58  Aligned_cols=254  Identities=11%  Similarity=0.065  Sum_probs=147.9

Q ss_pred             HHHHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHh---HhccCCCC-Chhh
Q 042593           66 GDMYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM---AACEYTEP-SEIT  138 (352)
Q Consensus        66 i~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m---~~~~~~~p-~~~t  138 (352)
                      ..-+|+.|+.+....+|+...+   .|..+.+++      |..|-++|.-.+++++|++.-..=   .+.-|-+. ....
T Consensus        24 GERLck~gdcraGv~ff~aA~qvGTeDl~tLSAI------YsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKs   97 (639)
T KOG1130|consen   24 GERLCKMGDCRAGVDFFKAALQVGTEDLSTLSAI------YSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKS   97 (639)
T ss_pred             HHHHHhccchhhhHHHHHHHHHhcchHHHHHHHH------HHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccc
Confidence            3457899999999999998876   455554444      999999999999999999864321   01111111 1122


Q ss_pred             HHHHHHHHHhCCChhhHHHH----HHHHHhcCCCCCchhhHHHHHHHHHhhC--------------------ChHHHHHH
Q 042593          139 ILAVLPAIWKNGEVRNCQLI----HGYGEKRGFNAFDIHVSNCLIDTYAKCG--------------------CIFSASKL  194 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~~~~~~~li~~~~~~g--------------------~~~~a~~~  194 (352)
                      -..+-+.+.-.|.+++|.-.    +.-..+.|-.......+-.+.+.|...|                    .++.|.++
T Consensus        98 sgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~f  177 (639)
T KOG1130|consen   98 SGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKF  177 (639)
T ss_pred             cccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHH
Confidence            23344444455666655422    2222233322212334445556665444                    24567777


Q ss_pred             HHH---hccC----CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHH----hcCCCC----------Ccchhh--hHhHHHH
Q 042593          195 FED---TSVD----RKNLVSWTTIISGFAMHGMGKEAVENFERMQ----KVGLKP----------NRSWRI--GEEGLKF  251 (352)
Q Consensus       195 ~~~---~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~~~~p----------~~~~~~--~~~a~~~  251 (352)
                      |.+   |...    ..--..|..|-..|.-.|+++.|+..-+.-.    +-|-+.          +...+.  ++.|.+.
T Consensus       178 y~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~eh  257 (639)
T KOG1130|consen  178 YMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEH  257 (639)
T ss_pred             HHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHH
Confidence            765   2211    1233567777777777888988877655422    122211          112222  6666666


Q ss_pred             HHHHHHh---cCC-CCChhhHHHHHHHHHHcCChhHHHHHHhc-------CCCCCCCchhhHHHHHHHHhcccccCcccc
Q 042593          252 FDKMVEE---CEV-LPDIKHYGCLIDILERAGRLEQAEEVASG-------IPSQITNVVVWRTGFLRLLINSYFFSPITL  320 (352)
Q Consensus       252 ~~~m~~~---~~~-~p~~~~~~~li~~~~~~g~~~~A~~~~~~-------m~~~~~~~~~~~~li~~~~~~g~~~~a~~~  320 (352)
                      |..-...   .|- ........+|...|.-..++++|...+.+       +........++.+|..+|...|..++|+.+
T Consensus       258 YK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~f  337 (639)
T KOG1130|consen  258 YKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYF  337 (639)
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHH
Confidence            6553322   011 11223445677777777788888776543       222255678899999999999999999987


Q ss_pred             cccch
Q 042593          321 NSQRL  325 (352)
Q Consensus       321 ~~~~~  325 (352)
                      ..+.+
T Consensus       338 ae~hl  342 (639)
T KOG1130|consen  338 AELHL  342 (639)
T ss_pred             HHHHH
Confidence            77664

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.58  E-value=1.5  Score=37.68  Aligned_cols=132  Identities=9%  Similarity=0.086  Sum_probs=74.8

Q ss_pred             cchHHHHHHHHHHhCCCCchhhHHHHHHHHHh--cC----ChhHHHHHhccCCC-------CCchhHHHHHHHHHhHHHH
Q 042593           40 PNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS--LG----FLKDSSKLFDELPE-------RNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        40 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~--~g----~~~~a~~~~~~m~~-------~~~~~~~~~i~~~~~~~~l  106 (352)
                      ++....+++.|.+.|+..+..+|-+..-....  ..    ...+|..+|+.|++       ++-.+          +..+
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~----------~a~l  147 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYP----------FAAL  147 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchh----------HHHH
Confidence            34567888999999999888777553333333  12    35568888888875       22233          4444


Q ss_pred             HHHHHhcCC----HHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCC-C--hhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          107 IDGYSRMNR----SNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNG-E--VRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       107 i~~~~~~~~----~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~-~--~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                      +..  ...+    .+.+...|+.+ ...|...+.. .+.+-+-++.... .  ...+..+++.+.+.|+.. ....|. .
T Consensus       148 LA~--~~~~~e~l~~~~E~~Y~~L-~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~ki-k~~~yp-~  222 (297)
T PF13170_consen  148 LAM--TSEDVEELAERMEQCYQKL-ADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKI-KYMHYP-T  222 (297)
T ss_pred             Hhc--ccccHHHHHHHHHHHHHHH-HHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCcc-cccccc-H
Confidence            333  2333    34566677777 5556544432 3333333333222 1  346777888888888876 554453 3


Q ss_pred             HHHHHhhC
Q 042593          179 IDTYAKCG  186 (352)
Q Consensus       179 i~~~~~~g  186 (352)
                      +..++-.+
T Consensus       223 lGlLall~  230 (297)
T PF13170_consen  223 LGLLALLE  230 (297)
T ss_pred             HHHHHhcC
Confidence            34444333

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.41  E-value=0.0028  Score=48.00  Aligned_cols=87  Identities=13%  Similarity=0.106  Sum_probs=60.3

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCC
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGM  220 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~  220 (352)
                      .++..+.+.+..+....+++.+.+.+... +....+.++..|++.++.++..++++....     .-...++..|.+.|.
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~-~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~-----yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKEN-NPDLHTLLLELYIKYDPYEKLLEFLKTSNN-----YDLDKALRLCEKHGL   85 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC--SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS-----S-CTHHHHHHHTTTS
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhccccc-CHHHHHHHHHHHHhcCCchHHHHHcccccc-----cCHHHHHHHHHhcch
Confidence            45666777788888888888888766555 788888888999988887888877773321     233455666777777


Q ss_pred             HHHHHHHHHHHHh
Q 042593          221 GKEAVENFERMQK  233 (352)
Q Consensus       221 ~~~a~~~~~~m~~  233 (352)
                      +++|.-++.++-.
T Consensus        86 ~~~a~~Ly~~~~~   98 (143)
T PF00637_consen   86 YEEAVYLYSKLGN   98 (143)
T ss_dssp             HHHHHHHHHCCTT
T ss_pred             HHHHHHHHHHccc
Confidence            7777777766443

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.

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=94.33  E-value=3.4  Score=36.33  Aligned_cols=28  Identities=18%  Similarity=0.112  Sum_probs=23.3

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      ...+.+++...|..|+++.|+++.+.-+
T Consensus       188 ~WA~~AtLe~r~~~gdWd~AlkLvd~~~  215 (531)
T COG3898         188 PWAARATLEARCAAGDWDGALKLVDAQR  215 (531)
T ss_pred             chHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence            4567788999999999999999988654

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=94.30  E-value=1.1  Score=34.12  Aligned_cols=66  Identities=6%  Similarity=-0.085  Sum_probs=29.5

Q ss_pred             hCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHH
Q 042593          148 KNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGF  215 (352)
Q Consensus       148 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~  215 (352)
                      +.++.++++.++..+.-..+..+...++.  ...+.+.|++.+|.++|+++....|....-..|+..|
T Consensus        22 ~~~~~~D~e~lL~ALrvLRP~~~e~~~~~--~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~C   87 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLRPEFPELDLFD--GWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALC   87 (160)
T ss_pred             ccCChHHHHHHHHHHHHhCCCchHHHHHH--HHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHH
Confidence            44455555555555544433321222222  2234455555555555555544444333333333333

>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=94.27  E-value=0.9  Score=35.69  Aligned_cols=97  Identities=19%  Similarity=0.129  Sum_probs=68.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh--hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH--H
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI--TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC--L  178 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~--l  178 (352)
                      +..+..-|++.|+.++|++.|.++ ......+...  .+..+|+.....+++..+...+.+....-....+...-|.  .
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~-~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~  117 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRA-RDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKV  117 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHH-hhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            888889999999999999999999 6665555543  6788889999999999999888877654333212222211  1


Q ss_pred             HH--HHHhhCChHHHHHHHHHhcc
Q 042593          179 ID--TYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       179 i~--~~~~~g~~~~a~~~~~~~~~  200 (352)
                      ..  .+...|++..|-+.|-+...
T Consensus       118 ~~gL~~l~~r~f~~AA~~fl~~~~  141 (177)
T PF10602_consen  118 YEGLANLAQRDFKEAAELFLDSLS  141 (177)
T ss_pred             HHHHHHHHhchHHHHHHHHHccCc
Confidence            11  23356789888888877643

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.23  E-value=0.79  Score=39.29  Aligned_cols=25  Identities=16%  Similarity=0.337  Sum_probs=13.3

Q ss_pred             HhHHHHHHHHHHhcCCCCChhhHHHH
Q 042593          246 EEGLKFFDKMVEECEVLPDIKHYGCL  271 (352)
Q Consensus       246 ~~a~~~~~~m~~~~~~~p~~~~~~~l  271 (352)
                      ..+.++++.+.+. |+++....|..+
T Consensus       199 ~r~~~l~~~l~~~-~~kik~~~yp~l  223 (297)
T PF13170_consen  199 ARVIELYNALKKN-GVKIKYMHYPTL  223 (297)
T ss_pred             HHHHHHHHHHHHc-CCccccccccHH
Confidence            3444555555555 666655555444

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.19  E-value=2  Score=33.18  Aligned_cols=136  Identities=14%  Similarity=0.050  Sum_probs=84.8

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI  137 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  137 (352)
                      +...|..-++. ++.+..++|+.-|.++.+-+...|..+-     --.......+.|+...|..-|+++ ......|-..
T Consensus        58 sgd~flaAL~l-A~~~k~d~Alaaf~~lektg~g~YpvLA-----~mr~at~~a~kgdta~AV~aFdei-a~dt~~P~~~  130 (221)
T COG4649          58 SGDAFLAALKL-AQENKTDDALAAFTDLEKTGYGSYPVLA-----RMRAATLLAQKGDTAAAVAAFDEI-AADTSIPQIG  130 (221)
T ss_pred             chHHHHHHHHH-HHcCCchHHHHHHHHHHhcCCCcchHHH-----HHHHHHHHhhcccHHHHHHHHHHH-hccCCCcchh
Confidence            34455555543 4567788888888888776655544433     223334567788888888888888 5544445433


Q ss_pred             -hHHHHH--HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          138 -TILAVL--PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       138 -t~~~ll--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                       -..-+=  -.+...|.++.+..-.+-+...+-.. ....-..|--+--+.|++.+|.+.|..+...
T Consensus       131 rd~ARlraa~lLvD~gsy~dV~srvepLa~d~n~m-R~sArEALglAa~kagd~a~A~~~F~qia~D  196 (221)
T COG4649         131 RDLARLRAAYLLVDNGSYDDVSSRVEPLAGDGNPM-RHSAREALGLAAYKAGDFAKAKSWFVQIAND  196 (221)
T ss_pred             hHHHHHHHHHHHhccccHHHHHHHhhhccCCCChh-HHHHHHHHhHHHHhccchHHHHHHHHHHHcc
Confidence             111121  22446677777777766665544333 4455566766777888888888888887543

>PRK15331 chaperone protein SicA; Provisional

Probab=94.13  E-value=0.83  Score=35.01  Aligned_cols=92  Identities=11%  Similarity=-0.091  Sum_probs=70.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  184 (352)
                      .....+-..|++++|..+|.-+ ...+ .-+..-+..|..++-..+++++|...|...-..+..  |+..+--...+|..
T Consensus        42 ~~Ay~~y~~Gk~~eA~~~F~~L-~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~--dp~p~f~agqC~l~  117 (165)
T PRK15331         42 AHAYEFYNQGRLDEAETFFRFL-CIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKN--DYRPVFFTGQCQLL  117 (165)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH-HHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC--CCCccchHHHHHHH
Confidence            3344556789999999999998 3322 123345666777777889999999999988877654  55556677889999


Q ss_pred             hCChHHHHHHHHHhcc
Q 042593          185 CGCIFSASKLFEDTSV  200 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~  200 (352)
                      .|+.+.|.+.|.....
T Consensus       118 l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        118 MRKAAKARQCFELVNE  133 (165)
T ss_pred             hCCHHHHHHHHHHHHh
Confidence            9999999999998764

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=93.99  E-value=3.1  Score=37.89  Aligned_cols=168  Identities=11%  Similarity=-0.054  Sum_probs=83.7

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGF  215 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~  215 (352)
                      .....+++..+.....+.-++.+-.+|...|-   +...|..++.+|..+ .-+.-..+|+++....-|-.....-+..+
T Consensus        66 d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~e---~kmal~el~q~y~en-~n~~l~~lWer~ve~dfnDvv~~ReLa~~  141 (711)
T COG1747          66 DSCLVTLLTIFGDNHKNQIVEHLCTRVLEYGE---SKMALLELLQCYKEN-GNEQLYSLWERLVEYDFNDVVIGRELADK  141 (711)
T ss_pred             chHHHHHHHHhccchHHHHHHHHHHHHHHhcc---hHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcchhHHHHHHHHHH
Confidence            33444555555555555555555555555442   344455555555555 33444455554433322222222222222


Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhh--------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCCh
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRI--------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRL  281 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~--------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  281 (352)
                      ...++.+.+...|......=+......-.              .+....+..++....|...-...+.-+-.-|....++
T Consensus       142 yEkik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~~eN~  221 (711)
T COG1747         142 YEKIKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELIGDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSENENW  221 (711)
T ss_pred             HHHhchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhccccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhccccCH
Confidence            22244445555554444321110000000              3344444555555445555566777777888888899


Q ss_pred             hHHHHHHhcCCCC-CCCchhhHHHHHH
Q 042593          282 EQAEEVASGIPSQ-ITNVVVWRTGFLR  307 (352)
Q Consensus       282 ~~A~~~~~~m~~~-~~~~~~~~~li~~  307 (352)
                      ++|.+++..+.++ ..|...-..++.-
T Consensus       222 ~eai~Ilk~il~~d~k~~~ar~~~i~~  248 (711)
T COG1747         222 TEAIRILKHILEHDEKDVWARKEIIEN  248 (711)
T ss_pred             HHHHHHHHHHhhhcchhhhHHHHHHHH
Confidence            9999998877666 4455555555543

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.91  E-value=4.6  Score=36.29  Aligned_cols=115  Identities=14%  Similarity=0.079  Sum_probs=73.7

Q ss_pred             ChHHHHHHHHHhccCC-CCHhhHHHHHH----HHH---cCCCHHHHHHHHHHHHhcCCCCCcchhh-----hHhHHHHHH
Q 042593          187 CIFSASKLFEDTSVDR-KNLVSWTTIIS----GFA---MHGMGKEAVENFERMQKVGLKPNRSWRI-----GEEGLKFFD  253 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~~-~~~~~~~~li~----~~~---~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----~~~a~~~~~  253 (352)
                      .-++|.++++.+.... -|...=|.+..    +|.   ....+.+-..+-+-+.+.|++|-...-.     ..+|..+|.
T Consensus       395 ~dekalnLLk~il~ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLys  474 (549)
T PF07079_consen  395 CDEKALNLLKLILQFTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYS  474 (549)
T ss_pred             ccHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHh
Confidence            3778888888876653 35544443322    222   2234566666666677788877654433     444444332


Q ss_pred             H----------HHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHH
Q 042593          254 K----------MVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGF  305 (352)
Q Consensus       254 ~----------m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li  305 (352)
                      .          +--. .+.|++.+|..+.-++....++++|+..+..+.   ||..+|++-+
T Consensus       475 qgey~kc~~ys~WL~-~iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~LP---~n~~~~dskv  532 (549)
T PF07079_consen  475 QGEYHKCYLYSSWLT-KIAPSPQAYRLLGLCLMENKRYQEAWEYLQKLP---PNERMRDSKV  532 (549)
T ss_pred             cccHHHHHHHHHHHH-HhCCcHHHHHHHHHHHHHHhhHHHHHHHHHhCC---CchhhHHHHH
Confidence            1          1111 578999999999999999999999999999886   4666665533

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.90  E-value=1.6  Score=36.31  Aligned_cols=97  Identities=15%  Similarity=0.086  Sum_probs=76.2

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC-CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC----CHhhHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA-FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK----NLVSWTTI  211 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----~~~~~~~l  211 (352)
                      ..|+.-+. +.+.|++..|...|....+..... .....+-=|.+++...|++++|..+|..+.+..|    -+..+-.|
T Consensus       143 ~~Y~~A~~-~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         143 KLYNAALD-LYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHHHH-HHHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            35666555 457788999999999999875431 0223344588999999999999999999876633    34677888


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhc
Q 042593          212 ISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+..+.|+.++|..+|+++.+.
T Consensus       222 g~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHH
Confidence            88999999999999999999875

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=93.82  E-value=4.5  Score=35.81  Aligned_cols=70  Identities=6%  Similarity=-0.072  Sum_probs=48.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhC---CCCchhhHHHHHHHHHh---cCChhHHHHHhccCC-C---CCchh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVG---FQSHVYVNTALGDMYVS---LGFLKDSSKLFDELP-E---RNLVT   92 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~~~~~li~~~~~---~g~~~~a~~~~~~m~-~---~~~~~   92 (352)
                      +..+.-.++-+|....+++...++.+.+....   +.-++..--...-++.+   .|+.++|++++..+. +   ++..+
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            44555566778999999999999999998752   22233333344556667   899999999998843 2   45556

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=93.79  E-value=2.8  Score=33.44  Aligned_cols=199  Identities=14%  Similarity=0.023  Sum_probs=80.1

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHh-CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKV-GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWT  104 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~  104 (352)
                      .+......+...+.+..+...+...... ........+......+...++...+.+.+......+......       ..
T Consensus        61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~  133 (291)
T COG0457          61 LLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLA-------EA  133 (291)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcchH-------HH
Confidence            3444444444455555444444444331 112233344444444444444555555555443311100000       11


Q ss_pred             HHHH-HHHhcCCHHHHHHHHHHhHhccCC--CCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          105 GIID-GYSRMNRSNEALALFRRMAACEYT--EPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       105 ~li~-~~~~~~~~~~a~~~~~~m~~~~~~--~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      .... .+...|+++.|...+.+. .....  ......+......+...++.+.+...+....+..... ....+..+...
T Consensus       134 ~~~~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~  211 (291)
T COG0457         134 LLALGALYELGDYEEALELYEKA-LELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDD-DAEALLNLGLL  211 (291)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHH-HhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCccc-chHHHHHhhHH
Confidence            1111 444555555555555554 11110  0111222222223344455555555555544443221 23344444445


Q ss_pred             HHhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +...++.+.|...+.......|+ ...+..+...+...+..+++...+.+...
T Consensus       212 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (291)
T COG0457         212 YLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALE  264 (291)
T ss_pred             HHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55555555555555554433333 22222222222244444555444444443

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

Probab=93.72  E-value=0.65  Score=39.09  Aligned_cols=64  Identities=13%  Similarity=0.223  Sum_probs=56.3

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      -..++..++..+...|+.+.+.+.++++.... -+...|..+|.+|.+.|+...|...|+.+.+.
T Consensus       152 ~~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~  216 (280)
T COG3629         152 FIKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKT  216 (280)
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence            35567788999999999999999999987664 48899999999999999999999999998873

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.72  E-value=0.076  Score=30.71  Aligned_cols=40  Identities=18%  Similarity=0.220  Sum_probs=31.3

Q ss_pred             hhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHH
Q 042593          266 KHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGF  305 (352)
Q Consensus       266 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li  305 (352)
                      .++..+...|...|++++|.+++++.... +.|...|..+.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La   42 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALA   42 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhh
Confidence            35677889999999999999999998877 55556665543

>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=93.69  E-value=2.1  Score=31.52  Aligned_cols=129  Identities=8%  Similarity=0.030  Sum_probs=59.9

Q ss_pred             HhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHH---HHHHHHH-------hH
Q 042593           35 VTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWN---VIITGLV-------KW  103 (352)
Q Consensus        35 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~---~~i~~~~-------~~  103 (352)
                      .-.|.+++..++........   +..-+|-+|.-....-+-+-..+.++.+-+ -|.....   .++.+++       ..
T Consensus        13 ildG~V~qGveii~k~v~Ss---ni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n~~se~v   89 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNSS---NIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRNKLSEYV   89 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHHS----HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT---HHH
T ss_pred             HHhchHHHHHHHHHHHcCcC---CccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhcchHHHH
Confidence            34678888888888777653   344455555444444444444444444432 1111100   0000000       13


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  168 (352)
                      +..++.....|+-+...++++++ .. +-++++.....+..||.+.|+..++.+++.+..+.|+.
T Consensus        90 D~ALd~lv~~~kkDqLdki~~~l-~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   90 DLALDILVKQGKKDQLDKIYNEL-KK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHH-------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHhccHHHHHHHHHHH-hh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            44455555566666666666655 22 22455555556666666666666666666666666543

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.67  E-value=0.19  Score=28.95  Aligned_cols=29  Identities=17%  Similarity=0.100  Sum_probs=14.9

Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      +..+..+|...|++++|.++|++..+..|
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~P   32 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALALDP   32 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            44455555555555555555555544433

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.61  E-value=2.8  Score=38.09  Aligned_cols=79  Identities=11%  Similarity=0.018  Sum_probs=57.4

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCC--HhhHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKN--LVSWTTII  212 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~--~~~~~~li  212 (352)
                      ..+-..+..++.+.|+.++|.+.++++.+.........+...|+.++...+.+.++..++.+-.+. -|.  ...|+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            334445667777899999999999999865433214557788999999999999999999887543 233  45677655


Q ss_pred             HH
Q 042593          213 SG  214 (352)
Q Consensus       213 ~~  214 (352)
                      --
T Consensus       339 Lk  340 (539)
T PF04184_consen  339 LK  340 (539)
T ss_pred             HH
Confidence            43

The molecular function of this protein is uncertain.

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=93.58  E-value=2.1  Score=33.63  Aligned_cols=99  Identities=17%  Similarity=0.060  Sum_probs=68.3

Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCC----CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHh
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDR----KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEE  247 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~  247 (352)
                      ...+..+.+.|++.|+.+.|.+.|.++....    .-...+-.+|......+++..+.....+....-..          
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~----------  105 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEK----------  105 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhc----------
Confidence            4567788999999999999999999986652    23455677888888999999999888887663111          


Q ss_pred             HHHHHHHHHHhcCCCCC----hhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          248 GLKFFDKMVEECEVLPD----IKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                                  +-.++    ...|..|  .+...|++.+|-+.|-+....
T Consensus       106 ------------~~d~~~~nrlk~~~gL--~~l~~r~f~~AA~~fl~~~~t  142 (177)
T PF10602_consen  106 ------------GGDWERRNRLKVYEGL--ANLAQRDFKEAAELFLDSLST  142 (177)
T ss_pred             ------------cchHHHHHHHHHHHHH--HHHHhchHHHHHHHHHccCcC
Confidence                        11111    2233322  234578999998888766544

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.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.56  E-value=3  Score=37.41  Aligned_cols=120  Identities=10%  Similarity=-0.035  Sum_probs=78.9

Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH--H
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY--A  183 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~--~  183 (352)
                      +-+.++..+|.++|.+.-++..-.|.    ...-+.+++||.. .+++.....+.+..+....    ..|-.+..++  -
T Consensus        16 Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~~~~----s~~l~LF~~L~~Y   90 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQFGK----SAYLPLFKALVAY   90 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHhcCC----chHHHHHHHHHHH
Confidence            45678999999999998333222222    2345577888765 5677777777777654322    2233333332  3


Q ss_pred             hhCChHHHHHHHHHhccC-----C-----------CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          184 KCGCIFSASKLFEDTSVD-----R-----------KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~-----~-----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +.+++++|.+.+......     .           +|...-++.++++...|++.++..++++|...
T Consensus        91 ~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~  157 (549)
T PF07079_consen   91 KQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIER  157 (549)
T ss_pred             HhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHH
Confidence            677888888887664332     1           22233467788999999999999999998875

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.35  E-value=4.7  Score=40.60  Aligned_cols=30  Identities=17%  Similarity=0.174  Sum_probs=21.1

Q ss_pred             CCchhhHHHHHHHHHhcC--ChhHHHHHhccCC
Q 042593           56 QSHVYVNTALGDMYVSLG--FLKDSSKLFDELP   86 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g--~~~~a~~~~~~m~   86 (352)
                      .|+ .-.-.+|.+|.+.+  .++.|+....+..
T Consensus       788 ~~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~  819 (1265)
T KOG1920|consen  788 APD-KFNLFILTSYVKSNPPEIEEALQKIKELQ  819 (1265)
T ss_pred             Ccc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            455 44556788888887  6777777777766

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=93.21  E-value=2.1  Score=37.68  Aligned_cols=96  Identities=11%  Similarity=0.067  Sum_probs=45.6

Q ss_pred             HHHHHhcCChhHHHHHhccCCC--------CCch--hHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           66 GDMYVSLGFLKDSSKLFDELPE--------RNLV--TWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        66 i~~~~~~g~~~~a~~~~~~m~~--------~~~~--~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      .+.|.+.|++..|...|+....        ++..  ....+...  .++.+.-++.+.+++.+|+..-++.+...  ++|
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~--~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~--~~N  290 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLA--CHLNLAACYLKLKEYKEAIESCNKVLELD--PNN  290 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHH--HhhHHHHHHHhhhhHHHHHHHHHHHHhcC--CCc
Confidence            3456678888888777776432        0000  00000000  14455555555555555555555442211  233


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhc
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKR  165 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  165 (352)
                      ....---..++...|+++.|...|+.+.+.
T Consensus       291 ~KALyRrG~A~l~~~e~~~A~~df~ka~k~  320 (397)
T KOG0543|consen  291 VKALYRRGQALLALGEYDLARDDFQKALKL  320 (397)
T ss_pred             hhHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            334444444555555555555555555544

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.08  E-value=3.3  Score=32.07  Aligned_cols=131  Identities=14%  Similarity=0.077  Sum_probs=73.4

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhH---HHHHH-
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSW---TTIIS-  213 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~---~~li~-  213 (352)
                      +|..-++ +++.+..++|+.-|..+.+.|......-.--.........|+...|...|+++-...|-+...   ..|=. 
T Consensus        61 ~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa  139 (221)
T COG4649          61 AFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAA  139 (221)
T ss_pred             HHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHH
Confidence            4444444 345566777777777777776553111122223344566778888888888876553322222   11111 


Q ss_pred             -HHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          214 -GFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       214 -~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                       .+..+|-++......+-+-..                         +-+.-...-..|.-+-.+.|++.+|.+.|..+.
T Consensus       140 ~lLvD~gsy~dV~srvepLa~d-------------------------~n~mR~sArEALglAa~kagd~a~A~~~F~qia  194 (221)
T COG4649         140 YLLVDNGSYDDVSSRVEPLAGD-------------------------GNPMRHSAREALGLAAYKAGDFAKAKSWFVQIA  194 (221)
T ss_pred             HHHhccccHHHHHHHhhhccCC-------------------------CChhHHHHHHHHhHHHHhccchHHHHHHHHHHH
Confidence             245666666666555544332                         212223334566667778888888888887776


Q ss_pred             CC
Q 042593          293 SQ  294 (352)
Q Consensus       293 ~~  294 (352)
                      ..
T Consensus       195 ~D  196 (221)
T COG4649         195 ND  196 (221)
T ss_pred             cc
Confidence            55

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.69  E-value=2.9  Score=30.70  Aligned_cols=90  Identities=12%  Similarity=0.035  Sum_probs=61.3

Q ss_pred             HHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCH-h---hHHHHHHHHHcCC
Q 042593          145 AIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNL-V---SWTTIISGFAMHG  219 (352)
Q Consensus       145 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~-~---~~~~li~~~~~~~  219 (352)
                      +++..|++++|.+.|.+....-..  ....||.-..++.-.|+.++|++=+++...- .+.. .   .|-.--..|...|
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 ALAEAGDLDGALELFGQALCLAPE--RASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhccc--chHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhC
Confidence            466778888888888877665433  7778888888888888888888777765433 2222 1   2222233466778


Q ss_pred             CHHHHHHHHHHHHhcCC
Q 042593          220 MGKEAVENFERMQKVGL  236 (352)
Q Consensus       220 ~~~~a~~~~~~m~~~~~  236 (352)
                      +.+.|..=|+...+.|-
T Consensus       130 ~dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLGS  146 (175)
T ss_pred             chHHHHHhHHHHHHhCC
Confidence            88888888888777664

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=92.10  E-value=2  Score=37.80  Aligned_cols=124  Identities=9%  Similarity=-0.089  Sum_probs=79.1

Q ss_pred             HHHHhcCCHHHHHHHHHHhHhc----cCCCC---------ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593          108 DGYSRMNRSNEALALFRRMAAC----EYTEP---------SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~----~~~~p---------~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                      +.+.+.|++..|...|++....    .+..+         -...++.+.-++.+.+++..|...-...+..+..  |...
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~--N~KA  293 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPN--NVKA  293 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCC--chhH
Confidence            4577889999999888875221    11111         1224666677777888888888777777766544  5555


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhH-HHHHHHHHcCCCH-HHHHHHHHHHHh
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSW-TTIISGFAMHGMG-KEAVENFERMQK  233 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~li~~~~~~~~~-~~a~~~~~~m~~  233 (352)
                      .-.-..+|...|+++.|+..|+.+.+..|+-..- +-|+..--+.... +...++|..|..
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5566778888888888888888887766644333 3344333333333 344667777755

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=91.95  E-value=6.9  Score=33.08  Aligned_cols=113  Identities=12%  Similarity=0.088  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh-CC-ChhhHHHHHHHHHhc-CCCCCchhhHHHHHHHHHhhCChHHHH
Q 042593          116 SNEALALFRRMAACEYTEPSEITILAVLPAIWK-NG-EVRNCQLIHGYGEKR-GFNAFDIHVSNCLIDTYAKCGCIFSAS  192 (352)
Q Consensus       116 ~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~-~~-~~~~a~~~~~~~~~~-~~~~~~~~~~~~li~~~~~~g~~~~a~  192 (352)
                      +.+|+++|+...-+..+--|..+...+++.... .+ ....-.++.+.+... +-.+ +..+...+|+.+++.+++.+-.
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l-~~~vi~~Il~~L~~~~dW~kl~  222 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSL-TRNVIISILEILAESRDWNKLF  222 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCC-ChhHHHHHHHHHHhcccHHHHH
Confidence            445566666431113344555555666665554 11 222223333333322 2333 5666666677777777777777


Q ss_pred             HHHHHhccC---CCCHhhHHHHHHHHHcCCCHHHHHHHHH
Q 042593          193 KLFEDTSVD---RKNLVSWTTIISGFAMHGMGKEAVENFE  229 (352)
Q Consensus       193 ~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~  229 (352)
                      ++++.....   ..|...|..+|..-...|+..-...+.+
T Consensus       223 ~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  223 QFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             HHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            776664433   3366667777777777776654444443

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=91.92  E-value=7  Score=34.73  Aligned_cols=174  Identities=7%  Similarity=-0.111  Sum_probs=96.2

Q ss_pred             CcccHHHHH-HHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHH--HhcCChhHHHHHhccCCC--CCchh---HH
Q 042593           23 DSFTYSFLI-RTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMY--VSLGFLKDSSKLFDELPE--RNLVT---WN   94 (352)
Q Consensus        23 ~~~~~~~ll-~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~--~~~g~~~~a~~~~~~m~~--~~~~~---~~   94 (352)
                      .-.++..+- ..+.-.|+.++|.++--...+.. ..+.  +..+++..  --.++.+.|...|++-..  |+...   -.
T Consensus       167 ac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld-~~n~--~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~~  243 (486)
T KOG0550|consen  167 ACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD-ATNA--EALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSAS  243 (486)
T ss_pred             hhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc-cchh--HHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhHh
Confidence            334444443 23345788888887755444433 2222  33334433  345788899999998775  33221   11


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhc--cCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC--EYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI  172 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  172 (352)
                      -..+.+-.|..-.+-..+.|.+..|.+.|.+....  .++.|+...|.....+..+.|+.++|..--++..+....  -+
T Consensus       244 ~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~s--yi  321 (486)
T KOG0550|consen  244 MMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSS--YI  321 (486)
T ss_pred             hhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHH--HH
Confidence            11122223444445566778888888888877332  223444555666666777788888877766666554211  22


Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                      ..+..-.+++...+++++|.+-|+...+.
T Consensus       322 kall~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  322 KALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            23333334445556777777777665443

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

Probab=91.90  E-value=0.43  Score=26.08  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=19.0

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          207 SWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      +|+.|...|.+.|++++|.++|++..
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            46677778888888888888888754

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=91.74  E-value=7.4  Score=32.97  Aligned_cols=124  Identities=12%  Similarity=0.121  Sum_probs=85.4

Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      ......|+..+|..+|........  -+...-..+..++...|+.+.|..++..+-..--.. .......-|..+.+...
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~~--~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~-~~~~l~a~i~ll~qaa~  218 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAAP--ENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDK-AAHGLQAQIELLEQAAA  218 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhCc--ccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhh-HHHHHHHHHHHHHHHhc
Confidence            345677888888888888744322  234566778888889999999999988775443222 23333345666777776


Q ss_pred             hHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          188 IFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       188 ~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+...+-...-..+-|...--.+...+...|+.++|.+.+=.+.+.
T Consensus       219 ~~~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~  265 (304)
T COG3118         219 TPEIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRR  265 (304)
T ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66666666666444557777778888888999998888877766654

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.67  E-value=0.25  Score=26.69  Aligned_cols=32  Identities=9%  Similarity=0.178  Sum_probs=24.3

Q ss_pred             HHHHHHhCCCCchhhHHHHHHHHHhcCChhHHH
Q 042593           47 HAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSS   79 (352)
Q Consensus        47 ~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~   79 (352)
                      |+..++.. |-|...|+.|...|...|++++|+
T Consensus         2 y~kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    2 YKKAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             hHHHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            34445544 557888999999999999998886

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=91.37  E-value=7.4  Score=32.25  Aligned_cols=58  Identities=16%  Similarity=0.201  Sum_probs=44.9

Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .+.+.|.+.|.+..|..-+++|.+..|+    ....-.+..+|-..|..++|...-+-+...
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            5567788999999999999998877443    245666778899999988888877766653

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.24  E-value=4.5  Score=30.45  Aligned_cols=54  Identities=11%  Similarity=-0.034  Sum_probs=29.3

Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcC
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRG  166 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  166 (352)
                      ...++++++..+++.|.....-.|...++...+  +...|++++|.++++++.+.+
T Consensus        21 L~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccC
Confidence            346666666666666633222222333444443  455666666666666666554

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=91.10  E-value=7  Score=35.66  Aligned_cols=75  Identities=9%  Similarity=0.012  Sum_probs=53.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                      .+..++-+.|+.++|.+.|.+|.+.....-+......++.++...+.+.++..++.+-.+...+..-...|+..+
T Consensus       264 RLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  264 RLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            355666788999999999999955443222344778899999999999999999998765443321345666544

The molecular function of this protein is uncertain.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.07  E-value=2.4  Score=36.13  Aligned_cols=106  Identities=12%  Similarity=0.063  Sum_probs=78.8

Q ss_pred             HhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCch---hHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhH
Q 042593           52 KVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLV---TWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMA  127 (352)
Q Consensus        52 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~---~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  127 (352)
                      ..|.+.+..+...++..-....++++++..+-++.. |+..   .|+        -...++ .+-.-+.++++.++..= 
T Consensus        57 ~~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~--------~~~~ir-lllky~pq~~i~~l~np-  126 (418)
T KOG4570|consen   57 ERGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWT--------IHTWIR-LLLKYDPQKAIYTLVNP-  126 (418)
T ss_pred             hcCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhcccc--------HHHHHH-HHHccChHHHHHHHhCc-
Confidence            345566777888888888888899999998888764 2211   011        111222 23345677888888877 


Q ss_pred             hccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCC
Q 042593          128 ACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGF  167 (352)
Q Consensus       128 ~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  167 (352)
                      ...|+-||.+++..++..+.+.+++.+|.++.-.|.....
T Consensus       127 IqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~qe~  166 (418)
T KOG4570|consen  127 IQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMMQEA  166 (418)
T ss_pred             chhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence            7899999999999999999999999999998888876653

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

Probab=90.71  E-value=0.53  Score=25.71  Aligned_cols=24  Identities=8%  Similarity=0.191  Sum_probs=17.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      |+.|...|.+.|++++|.++|++.
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            667777777888888888877774

>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=90.69  E-value=9.7  Score=32.42  Aligned_cols=154  Identities=8%  Similarity=-0.010  Sum_probs=95.8

Q ss_pred             HhcCCHHHHHHHHHHhHhcc-CCCCChh-----hHHHHHHHHHhCC-ChhhHHHHHHHHHhc----C----CCCC----c
Q 042593          111 SRMNRSNEALALFRRMAACE-YTEPSEI-----TILAVLPAIWKNG-EVRNCQLIHGYGEKR----G----FNAF----D  171 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~-~~~p~~~-----t~~~ll~~~~~~~-~~~~a~~~~~~~~~~----~----~~~~----~  171 (352)
                      .+.|+.+.|..++.+..... ...|+..     .+..+.......+ +++.|...+++..+.    +    ..+.    .
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            46799999999999984333 3445432     2223333344555 888877666665443    1    1120    1


Q ss_pred             hhhHHHHHHHHHhhCChH---HHHHHHHHhccCCCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---
Q 042593          172 IHVSNCLIDTYAKCGCIF---SASKLFEDTSVDRKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---  244 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~---~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---  244 (352)
                      ..+...++.+|...+..+   +|.++++.+....|+ +.++-.-+..+.+.++.+++.+.+.+|...-..++...-.   
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~  163 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHH
Confidence            346667788888777654   566677777655565 5556566777778999999999999999874323322211   


Q ss_pred             ---------hHhHHHHHHHHHHhcCCCCCh
Q 042593          245 ---------GEEGLKFFDKMVEECEVLPDI  265 (352)
Q Consensus       245 ---------~~~a~~~~~~m~~~~~~~p~~  265 (352)
                               ...+...++.+... .+.|..
T Consensus       164 ~i~~l~~~~~~~a~~~ld~~l~~-r~~~~~  192 (278)
T PF08631_consen  164 HIKQLAEKSPELAAFCLDYLLLN-RFKSSE  192 (278)
T ss_pred             HHHHHHhhCcHHHHHHHHHHHHH-HhCCCh
Confidence                     55666666666655 555544

It is also involved in sporulation [].

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.60  E-value=11  Score=32.73  Aligned_cols=48  Identities=8%  Similarity=-0.038  Sum_probs=21.8

Q ss_pred             hCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          148 KNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       148 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      ..|-+++|++.-++..+.+..  |.-.-.++...+--.|+..++.++..+
T Consensus       187 E~g~y~dAEk~A~ralqiN~~--D~Wa~Ha~aHVlem~~r~Keg~eFM~~  234 (491)
T KOG2610|consen  187 ECGIYDDAEKQADRALQINRF--DCWASHAKAHVLEMNGRHKEGKEFMYK  234 (491)
T ss_pred             HhccchhHHHHHHhhccCCCc--chHHHHHHHHHHHhcchhhhHHHHHHh
Confidence            445555555554444443322  333334444444444555555544444

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=90.52  E-value=9.9  Score=32.25  Aligned_cols=53  Identities=9%  Similarity=0.085  Sum_probs=30.0

Q ss_pred             HHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE   87 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   87 (352)
                      ....|++.+|..+|....... +-+...--.+..+|...|+.+.|..++..++.
T Consensus       144 ~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~  196 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPL  196 (304)
T ss_pred             hhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcc
Confidence            344556666666666555543 22344444556666666666666666666653

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.50  E-value=7.5  Score=33.58  Aligned_cols=116  Identities=14%  Similarity=0.005  Sum_probs=65.6

Q ss_pred             hcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhc-CCCC-CchhhHHHHHHHHHhhCChH
Q 042593          112 RMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKR-GFNA-FDIHVSNCLIDTYAKCGCIF  189 (352)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~-~~~~~~~~li~~~~~~g~~~  189 (352)
                      ..|++.+|-..+++++++  .+-|...+.-.=.+|.-.|+.+.-...++.+.-. +... -...+-..+.-++..+|-++
T Consensus       115 ~~g~~h~a~~~wdklL~d--~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~  192 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD--YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYD  192 (491)
T ss_pred             ccccccHHHHHHHHHHHh--CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccch
Confidence            456677777777777333  2345666777777777777777777777766533 2111 02223334444556777888


Q ss_pred             HHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHH
Q 042593          190 SASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFE  229 (352)
Q Consensus       190 ~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~  229 (352)
                      +|++.-++..+. +-|.-.-.++.+.+-.+|+++++.+++.
T Consensus       193 dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~  233 (491)
T KOG2610|consen  193 DAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMY  233 (491)
T ss_pred             hHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHH
Confidence            887777765443 2344444444444444455544444443

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=90.26  E-value=2.2  Score=31.30  Aligned_cols=89  Identities=10%  Similarity=0.026  Sum_probs=46.4

Q ss_pred             HHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh--hHHHH
Q 042593           68 MYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI--TILAV  142 (352)
Q Consensus        68 ~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~--t~~~l  142 (352)
                      +.+..|+++.|++.|.+...   .+...          ||.-..++--.|+.++|++=+++.....|-+--..  .|..-
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~raSa----------yNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQR  121 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPERASA----------YNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQR  121 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhcccchHh----------hccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHH
Confidence            34556666666666665443   23333          66666666666666666666666544444321111  22222


Q ss_pred             HHHHHhCCChhhHHHHHHHHHhcC
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKRG  166 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~~  166 (352)
                      ...|...|+.+.|..=|+..-+.|
T Consensus       122 g~lyRl~g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  122 GLLYRLLGNDDAARADFEAAAQLG  145 (175)
T ss_pred             HHHHHHhCchHHHHHhHHHHHHhC
Confidence            333445556666655555554444

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=89.76  E-value=4  Score=28.46  Aligned_cols=73  Identities=7%  Similarity=-0.002  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhCCChh--hHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC-HhhHHHHH
Q 042593          139 ILAVLPAIWKNGEVR--NCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN-LVSWTTII  212 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li  212 (352)
                      |..--..+....+.+  +..+-++.+....+.| .+.+..+.+++|.+.+++..|.++|+.++.+..+ ...|..++
T Consensus        11 F~ary~~~F~~~~iD~we~rrglN~l~~~DlVP-~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~l   86 (108)
T PF02284_consen   11 FDARYEKYFNRPDIDGWELRRGLNNLFGYDLVP-EPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYIL   86 (108)
T ss_dssp             HHHHHHHHHH-TT--HHHHHHHHHHHTTSSB----HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHH
T ss_pred             HHHHHHHHhCCccccHHHHHHHHHHHhccccCC-ChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHH
Confidence            333334444433333  4556666666667777 7788888888888888888888888877544222 22555544

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 ....

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

Probab=89.67  E-value=2.8  Score=35.44  Aligned_cols=61  Identities=11%  Similarity=-0.008  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhcc
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  200 (352)
                      ++..++..+...|+.+.+...++++......  +...|..+|.+|.+.|+...|++.|+.+.+
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~--~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPY--DEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCcc--chHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            4456677777888899999999988887544  888999999999999999999999988754

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.45  E-value=10  Score=35.48  Aligned_cols=79  Identities=19%  Similarity=0.172  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..|-++..+.+++..|.+.|.+. +.         |..|+-.+...|+-+....+-+..++.|..       |...-+|
T Consensus       669 w~~Lg~~al~~~~l~lA~EC~~~a-~d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g~~-------N~AF~~~  731 (794)
T KOG0276|consen  669 WRQLGDAALSAGELPLASECFLRA-RD---------LGSLLLLYTSSGNAEGLAVLASLAKKQGKN-------NLAFLAY  731 (794)
T ss_pred             HHHHHHHHhhcccchhHHHHHHhh-cc---------hhhhhhhhhhcCChhHHHHHHHHHHhhccc-------chHHHHH
Confidence            555556666666666666655555 21         224444455555555444444444444432       1222344


Q ss_pred             HhhCChHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDT  198 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~  198 (352)
                      -..|+++++.+++.+-
T Consensus       732 ~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  732 FLSGDYEECLELLIST  747 (794)
T ss_pred             HHcCCHHHHHHHHHhc
Confidence            4556666666655543

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=89.27  E-value=18  Score=33.34  Aligned_cols=178  Identities=11%  Similarity=0.070  Sum_probs=107.9

Q ss_pred             CCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC---CCchhHHHH
Q 042593           20 PLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE---RNLVTWNVI   96 (352)
Q Consensus        20 ~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~   96 (352)
                      .++|-...-+++..++..-.+.-+..+-..|...|  -+...|-.++.+|... .-++-..+++.+.+   .|++     
T Consensus        62 ~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfnDvv-----  133 (711)
T COG1747          62 QLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFNDVV-----  133 (711)
T ss_pred             ccccchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcchhHH-----
Confidence            34678888899999999989888888888898877  5677888889999887 45666666665443   2322     


Q ss_pred             HHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC--C---hhhHHHHHHHHHhCCChhhHHHHHHHHHhc-CCCCC
Q 042593           97 ITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP--S---EITILAVLPAIWKNGEVRNCQLIHGYGEKR-GFNAF  170 (352)
Q Consensus        97 i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p--~---~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~  170 (352)
                            ...-+..+...++..++...|.+. ...-++.  +   ...|..+...-  ..+.+....+...+.+. |... 
T Consensus       134 ------~~ReLa~~yEkik~sk~a~~f~Ka-~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~-  203 (711)
T COG1747         134 ------IGRELADKYEKIKKSKAAEFFGKA-LYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGR-  203 (711)
T ss_pred             ------HHHHHHHHHHHhchhhHHHHHHHH-HHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccch-
Confidence                  222222233336666777777666 2221110  0   11233332211  24555566666665543 2222 


Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHH
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGF  215 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~  215 (352)
                      ....+.-+-.-|....++.+|++++..+.+. ..|+..-..++.-+
T Consensus       204 ~~Vl~qdv~~~Ys~~eN~~eai~Ilk~il~~d~k~~~ar~~~i~~l  249 (711)
T COG1747         204 GSVLMQDVYKKYSENENWTEAIRILKHILEHDEKDVWARKEIIENL  249 (711)
T ss_pred             HHHHHHHHHHHhccccCHHHHHHHHHHHhhhcchhhhHHHHHHHHH
Confidence            4455555667778888899999988876554 45555554554443

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.16  E-value=13  Score=36.16  Aligned_cols=150  Identities=9%  Similarity=-0.008  Sum_probs=75.1

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHH----HHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALG----DMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLV  101 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li----~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~  101 (352)
                      ....-|..+.+...++.|..+   ++..+  .+..+...+.    +.+-+.|++++|...|-+-..--.           
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~L---Ak~~~--~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le-----------  399 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINL---AKSQH--LDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLE-----------  399 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHH---HHhcC--CCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCC-----------
Confidence            344455555555555555443   22333  3333333344    444478999999877766543111           


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                       -..+|.-|..+.........++.+ .+.|+ .+...-+.|+++|.+.++.++...+.+... .|..   ..-....+..
T Consensus       400 -~s~Vi~kfLdaq~IknLt~YLe~L-~~~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~---~fd~e~al~I  472 (933)
T KOG2114|consen  400 -PSEVIKKFLDAQRIKNLTSYLEAL-HKKGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW---FFDVETALEI  472 (933)
T ss_pred             -hHHHHHHhcCHHHHHHHHHHHHHH-HHccc-ccchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce---eeeHHHHHHH
Confidence             112334444455555555555666 44443 344455566777777777666655555433 2211   1112344455


Q ss_pred             HHhhCChHHHHHHHHHh
Q 042593          182 YAKCGCIFSASKLFEDT  198 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~  198 (352)
                      +.+.+-+++|..+-...
T Consensus       473 lr~snyl~~a~~LA~k~  489 (933)
T KOG2114|consen  473 LRKSNYLDEAELLATKF  489 (933)
T ss_pred             HHHhChHHHHHHHHHHh
Confidence            55555555555544443

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=89.13  E-value=0.63  Score=25.10  Aligned_cols=22  Identities=23%  Similarity=0.164  Sum_probs=12.7

Q ss_pred             chhhHHHHHHHHHhhCChHHHH
Q 042593          171 DIHVSNCLIDTYAKCGCIFSAS  192 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~  192 (352)
                      +...|+.+..+|...|++++|+
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            5555556656666666555553

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=89.13  E-value=5.8  Score=33.13  Aligned_cols=200  Identities=10%  Similarity=0.004  Sum_probs=125.3

Q ss_pred             hcCCHHHHHHHHHHhHhccCCCCC--hhhHHHHHHHHHhCCChhhHHHHHHHHHhc---CC--CCCchhhHHHHHHHHHh
Q 042593          112 RMNRSNEALALFRRMAACEYTEPS--EITILAVLPAIWKNGEVRNCQLIHGYGEKR---GF--NAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~~~~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~--~~~~~~~~~~li~~~~~  184 (352)
                      +..++++|+.-|.+.....|-+-+  -...-.++....+.+++++....+.++...   .+  .. +....|++++.-+.
T Consensus        39 ~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNy-SEKsIN~IlDyiSt  117 (440)
T KOG1464|consen   39 KEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNY-SEKSINSILDYIST  117 (440)
T ss_pred             cccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhccc-cHHHHHHHHHHHhh
Confidence            345889999999988665553333  346778899999999999999888888542   11  12 45677888888777


Q ss_pred             hCChHHHHHHHHHhccC-------CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHH
Q 042593          185 CGCIFSASKLFEDTSVD-------RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVE  257 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~  257 (352)
                      +.+.+--.++++.-.+.       ..-..|-+.|-..|...+.+.+...+++++..+--+.+ ..-.          . +
T Consensus       118 S~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~ed-GedD----------~-k  185 (440)
T KOG1464|consen  118 SKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTED-GEDD----------Q-K  185 (440)
T ss_pred             hhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhcccc-Cchh----------h-h
Confidence            77776666665542211       22224445677778888888888888888766421111 0000          0 0


Q ss_pred             hcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CCCchhhHHH----HHHHHhcccccCcccccccchh
Q 042593          258 ECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---ITNVVVWRTG----FLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       258 ~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~~~l----i~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      . |. --...|..=|..|..+.+-.....+++.....   .|.+.....+    ...+++.|++++|..-|.++++
T Consensus       186 K-Gt-QLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlImGvIRECGGKMHlreg~fe~AhTDFFEAFK  259 (440)
T KOG1464|consen  186 K-GT-QLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIMGVIRECGGKMHLREGEFEKAHTDFFEAFK  259 (440)
T ss_pred             c-cc-hhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHHhHHHHcCCccccccchHHHHHhHHHHHHh
Confidence            0 11 12346667788888888877777777654332   4444333322    2335678888888887777754

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=88.90  E-value=2.5  Score=29.05  Aligned_cols=45  Identities=7%  Similarity=-0.049  Sum_probs=27.3

Q ss_pred             hHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          154 NCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       154 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                      ++.+-++.+....+.| ++.+..+.+++|.+.+|+.-|.++|+.++
T Consensus        25 e~rr~mN~l~~~DlVP-~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          25 ELRRGLNNLFGYDLVP-EPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             HHHHHHHHHhccccCC-CcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            4445555555555556 66666666666666666666666666554

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.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=88.75  E-value=8.3  Score=28.88  Aligned_cols=77  Identities=12%  Similarity=0.018  Sum_probs=54.3

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH--hhHHHHHHHHHc
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL--VSWTTIISGFAM  217 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~li~~~~~  217 (352)
                      .-.....+.|++++|.+.|+.+..+=.. +....+--.++.+|-+.|++++|...+++..+..|+-  .-|--.+.+++.
T Consensus        15 ~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~   94 (142)
T PF13512_consen   15 QEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSY   94 (142)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHH
Confidence            3344455779999999999999876322 2245667789999999999999999999987664432  334444444443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.66  E-value=12  Score=30.80  Aligned_cols=205  Identities=12%  Similarity=0.065  Sum_probs=108.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..-..+|-...++++|...+.+..+.  .+-+...|.       ..+.++.|--+.+++.+..  . -...|+.....|
T Consensus        34 yekAAvafRnAk~feKakdcLlkA~~~--yEnnrslfh-------AAKayEqaamLake~~kls--E-vvdl~eKAs~lY  101 (308)
T KOG1585|consen   34 YEKAAVAFRNAKKFEKAKDCLLKASKG--YENNRSLFH-------AAKAYEQAAMLAKELSKLS--E-VVDLYEKASELY  101 (308)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHH--HHhcccHHH-------HHHHHHHHHHHHHHHHHhH--H-HHHHHHHHHHHH
Confidence            666666777788888888877766211  111211111       1233455555555554432  1 345566667777


Q ss_pred             HhhCChHHHHHHHHHhc---cC-CCCH--hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHH--
Q 042593          183 AKCGCIFSASKLFEDTS---VD-RKNL--VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDK--  254 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~---~~-~~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~--  254 (352)
                      ..+|..+.|-..+++.-   +. .|+.  ..|..-+...-..++...|.+++...-..-++...    +.++-..+.+  
T Consensus       102 ~E~GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~k----f~Eaa~a~lKe~  177 (308)
T KOG1585|consen  102 VECGSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEK----FTEAATAFLKEG  177 (308)
T ss_pred             HHhCCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHH----hhHHHHHHHHhh
Confidence            77777666655555421   11 4432  34555555555555556666655554332111111    1111111111  


Q ss_pred             --HHHhcCCCCC-hhhHHHHHHHHHHcCChhHHHHHHhc---CCCC--CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          255 --MVEECEVLPD-IKHYGCLIDILERAGRLEQAEEVASG---IPSQ--ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       255 --m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~---m~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                        ..+- .--++ ...|-..|-.+....|+..|++.++.   +...  +.+..+...|+.+| ..|+.++.-.+..--.
T Consensus       178 ~~~~~~-~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~kvl~sp~  254 (308)
T KOG1585|consen  178 VAADKC-DAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKKVLSSPT  254 (308)
T ss_pred             hHHHHH-hhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHHHHHHcChH
Confidence              1111 11122 24466667777778899999999988   4443  56778888888886 4566666555544443

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.36  E-value=26  Score=34.02  Aligned_cols=149  Identities=9%  Similarity=0.042  Sum_probs=91.8

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCC---chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQS---HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li  107 (352)
                      ++.+.+.+.+++|+++.+...  |..|   -.......|+.+.-.|++++|-...-.|...+..-          |..-+
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~--~~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn~~~e----------We~~V  430 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASI--GNEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGNNAAE----------WELWV  430 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhcc--CCccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcchHHH----------HHHHH
Confidence            566777788888887655443  3344   34567788999999999999999988888777766          66666


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHH------------------HHhcCCCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGY------------------GEKRGFNA  169 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~------------------~~~~~~~~  169 (352)
                      ..+...++...   ++.-+ -......+...|..++..+.. .+..+-.++.++                  ..+.  ..
T Consensus       431 ~~f~e~~~l~~---Ia~~l-Pt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~--Se  503 (846)
T KOG2066|consen  431 FKFAELDQLTD---IAPYL-PTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQN--SE  503 (846)
T ss_pred             HHhccccccch---hhccC-CCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhh--cc
Confidence            66666655543   22333 222223344566666666655 222111111111                  1111  11


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhc
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTS  199 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  199 (352)
                       +...-..|...|...+++++|.+.+-...
T Consensus       504 -~~~L~e~La~LYl~d~~Y~~Al~~ylklk  532 (846)
T KOG2066|consen  504 -STALLEVLAHLYLYDNKYEKALPIYLKLQ  532 (846)
T ss_pred             -chhHHHHHHHHHHHccChHHHHHHHHhcc
Confidence             23344568999999999999999998774

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=88.08  E-value=8.1  Score=39.05  Aligned_cols=20  Identities=20%  Similarity=0.111  Sum_probs=9.0

Q ss_pred             HHHHHhCCChhhHHHHHHHH
Q 042593          143 LPAIWKNGEVRNCQLIHGYG  162 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~  162 (352)
                      +.+|...|+|++|..+..++
T Consensus       972 l~a~~~~~dWr~~l~~a~ql  991 (1265)
T KOG1920|consen  972 LKAYKECGDWREALSLAAQL  991 (1265)
T ss_pred             HHHHHHhccHHHHHHHHHhh
Confidence            33444444444444444433

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

Probab=88.02  E-value=1.4  Score=24.50  Aligned_cols=29  Identities=17%  Similarity=0.266  Sum_probs=22.0

Q ss_pred             HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          205 LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       205 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..+++.|...|...|++++|..++++..+
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            35677888888888888888888888665

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=87.82  E-value=6.3  Score=34.42  Aligned_cols=229  Identities=13%  Similarity=0.062  Sum_probs=132.2

Q ss_pred             HHhcCCcchHHHHHHHHHHhC--CCCchhhHHHHHHHHHhcCChhHHHHHhcc-C---CC--CCchhHHHHHHHHHhHHH
Q 042593           34 CVTLSYPNLGTQLHAVFSKVG--FQSHVYVNTALGDMYVSLGFLKDSSKLFDE-L---PE--RNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~-m---~~--~~~~~~~~~i~~~~~~~~  105 (352)
                      +....+.+.++..+..-..+-  ..-.-.++..+..+.++.|.+++++..--. |   .+  .....+.+       |-.
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea-------~ln   88 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEA-------YLN   88 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHH
Confidence            335566677776666544321  111235677778888888888776543211 1   11  11111111       556


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCCh---hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC----CCchhhHHHH
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPSE---ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN----AFDIHVSNCL  178 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~~l  178 (352)
                      +.+++-+.-++.+++.+-+.-....|..|..   ....++-+++.-.+.++++.+.|+...+....    .....++-.|
T Consensus        89 lar~~e~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~L  168 (518)
T KOG1941|consen   89 LARSNEKLCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSL  168 (518)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhH
Confidence            6666666666666666654433444444421   23445677777778888888888876543221    1145688899


Q ss_pred             HHHHHhhCChHHHHHHHHHhccC----C-CCH------hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHh
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVD----R-KNL------VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEE  247 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~----~-~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~  247 (352)
                      -..|.+..|+++|.-+.......    . .|.      ...-.|..++-..|....|.+.-++..+..+.          
T Consensus       169 gslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~----------  238 (518)
T KOG1941|consen  169 GSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQ----------  238 (518)
T ss_pred             HHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHH----------
Confidence            99999999999987666543221    1 222      12223455677788888888877775543111          


Q ss_pred             HHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhc
Q 042593          248 GLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASG  290 (352)
Q Consensus       248 a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~  290 (352)
                                . |-.| .......+.+.|...|+.+.|+.=++.
T Consensus       239 ----------~-Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~  271 (518)
T KOG1941|consen  239 ----------H-GDRALQARCLLCFADIYRSRGDLERAFRRYEQ  271 (518)
T ss_pred             ----------h-CChHHHHHHHHHHHHHHHhcccHhHHHHHHHH
Confidence                      1 3222 233445667777888887777655543

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=87.59  E-value=16  Score=30.92  Aligned_cols=115  Identities=10%  Similarity=0.030  Sum_probs=83.4

Q ss_pred             cCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhc--CCHHHHHHHHHHhHhccCCCCChhhHHHHHH
Q 042593           72 LGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRM--NRSNEALALFRRMAACEYTEPSEITILAVLP  144 (352)
Q Consensus        72 ~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~--~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~  144 (352)
                      ...+.+|+++|+...-     .|...          -..+++.....  .....-.++.+-+....+..++..+...+++
T Consensus       141 N~~Vv~aL~L~~~~~~~~~Ii~d~ev----------islLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~  210 (292)
T PF13929_consen  141 NKIVVEALKLYDGLNPDESIIFDEEV----------ISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILE  210 (292)
T ss_pred             hHHHHHHHHHhhccCcccceeeChHH----------HHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHH
Confidence            3456778888884321     23333          44455554441  1344445555555445556788899999999


Q ss_pred             HHHhCCChhhHHHHHHHHHhc-CCCCCchhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          145 AIWKNGEVRNCQLIHGYGEKR-GFNAFDIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       145 ~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      .+++.+++....++++..... +... |...|..+|+.-...|+..-..++.++
T Consensus       211 ~L~~~~dW~kl~~fW~~~~~~~~~~~-D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  211 ILAESRDWNKLFQFWEQCIPNSVPGN-DPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHhcccHHHHHHHHHHhcccCCCCC-CCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            999999999999999988766 4555 889999999999999999888888775

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=87.55  E-value=7.6  Score=32.75  Aligned_cols=127  Identities=11%  Similarity=0.074  Sum_probs=78.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-------hHHHHHHHHHhCCChhhHHHHHHHHHhcC---CCCCchhhH
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPSEI-------TILAVLPAIWKNGEVRNCQLIHGYGEKRG---FNAFDIHVS  175 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-------t~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~  175 (352)
                      +.+...+.+++++|...+.++ -..|+..|..       |...+...|.+.|+....-+......+.-   -.|....+.
T Consensus         9 ~a~~~v~~~~~~~ai~~yk~i-L~kg~s~dek~~nEqE~tvlel~~lyv~~g~~~~l~~~i~~sre~m~~ftk~k~~Kii   87 (421)
T COG5159           9 LANNAVKSNDIEKAIGEYKRI-LGKGVSKDEKTLNEQEATVLELFKLYVSKGDYCSLGDTITSSREAMEDFTKPKITKII   87 (421)
T ss_pred             HHHHhhhhhhHHHHHHHHHHH-hcCCCChhhhhhhHHHHHHHHHHHHHHhcCCcchHHHHHHhhHHHHHHhcchhHHHHH
Confidence            345567789999999999999 6667766654       45577778888888766555544333211   112134455


Q ss_pred             HHHHHHHHhh-CChHHHHHHHHHhccC-CC------CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          176 NCLIDTYAKC-GCIFSASKLFEDTSVD-RK------NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       176 ~~li~~~~~~-g~~~~a~~~~~~~~~~-~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..|+.-+... ..++....+.....+. ..      -...=..++..+.+.|.+.+|..+.+.+..
T Consensus        88 rtLiekf~~~~dsl~dqi~v~~~~iewA~rEkr~fLr~~Le~Kli~l~y~~~~YsdalalIn~ll~  153 (421)
T COG5159          88 RTLIEKFPYSSDSLEDQIKVLTALIEWADREKRKFLRLELECKLIYLLYKTGKYSDALALINPLLH  153 (421)
T ss_pred             HHHHHhcCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            5555555433 3466666666554322 11      112234578889999999999887765543

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=87.10  E-value=13  Score=29.36  Aligned_cols=221  Identities=14%  Similarity=0.043  Sum_probs=144.8

Q ss_pred             CCcchHHHHHHHHHHhCCC-CchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcC
Q 042593           38 SYPNLGTQLHAVFSKVGFQ-SHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMN  114 (352)
Q Consensus        38 g~~~~a~~~~~~m~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~  114 (352)
                      +....+...+......... .....+......+...+++..+...+.....  ........       +......+...+
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~  109 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEA-------LLNLGLLLEALG  109 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHH-------HHHHHHHHHHHh
Confidence            4555555555555544322 1357777888888899999988888877643  11111111       666667777788


Q ss_pred             CHHHHHHHHHHhHhccCCCCChhhHHHHHH-HHHhCCChhhHHHHHHHHHhcCC--CCCchhhHHHHHHHHHhhCChHHH
Q 042593          115 RSNEALALFRRMAACEYTEPSEITILAVLP-AIWKNGEVRNCQLIHGYGEKRGF--NAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       115 ~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      +...+...+... ......+ ......... ++...|+.+.+...++.......  .. ....+......+...++.+.+
T Consensus       110 ~~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a  186 (291)
T COG0457         110 KYEEALELLEKA-LALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNE-LAEALLALGALLEALGRYEEA  186 (291)
T ss_pred             hHHHHHHHHHHH-HcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccc-hHHHHHHhhhHHHHhcCHHHH
Confidence            889999999888 4332222 122223333 78899999999999998865332  12 344455555557788899999


Q ss_pred             HHHHHHhccCCCC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHH
Q 042593          192 SKLFEDTSVDRKN--LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYG  269 (352)
Q Consensus       192 ~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~  269 (352)
                      ...+.......++  ...+..+-..+...++++.|...+........                          .....+.
T Consensus       187 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~--------------------------~~~~~~~  240 (291)
T COG0457         187 LELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDP--------------------------DNAEALY  240 (291)
T ss_pred             HHHHHHHHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCc--------------------------ccHHHHh
Confidence            9999988766444  67788888888888888999888888776311                          1233344


Q ss_pred             HHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          270 CLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       270 ~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      .+...+...|..+.+...+......
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         241 NLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             hHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4444444666788888777766555

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=86.97  E-value=1  Score=23.88  Aligned_cols=26  Identities=19%  Similarity=0.303  Sum_probs=11.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          208 WTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      |..+..+|...|++++|...|++.++
T Consensus         4 ~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    4 YYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            44444444444555555554444443

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 ....

>PRK11906 transcriptional regulator; Provisional

Probab=86.70  E-value=25  Score=32.05  Aligned_cols=164  Identities=9%  Similarity=-0.011  Sum_probs=99.5

Q ss_pred             hhH--HHHHHHHHhcC-----ChhHHHHHhccCC---C--CCc-hhHHHHHHHHHhHHHHHHHHHh-cCCHHHHHHHHHH
Q 042593           60 YVN--TALGDMYVSLG-----FLKDSSKLFDELP---E--RNL-VTWNVIITGLVKWTGIIDGYSR-MNRSNEALALFRR  125 (352)
Q Consensus        60 ~~~--~~li~~~~~~g-----~~~~a~~~~~~m~---~--~~~-~~~~~~i~~~~~~~~li~~~~~-~~~~~~a~~~~~~  125 (352)
                      ..|  ...+.+.....     ..+.|..+|.+..   +  |+- ..|..+-  ++++.....++.. ..+..+|.++-++
T Consensus       252 ~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA--~~h~~~~~~g~~~~~~~~~~a~~~A~r  329 (458)
T PRK11906        252 NHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLA--ECHMSLALHGKSELELAAQKALELLDY  329 (458)
T ss_pred             cchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHH--HHHHHHHHhcCCCchHHHHHHHHHHHH
Confidence            455  55565555422     3567888899877   4  332 2322221  1112222222222 3456677777776


Q ss_pred             hHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          126 MAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       126 m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .....  .-|......+..+....++.+.+...|++....+..  ...+|....-...-+|+.++|.+.+++..+-.|.-
T Consensus       330 Aveld--~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn--~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~  405 (458)
T PRK11906        330 VSDIT--TVDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTD--IASLYYYRALVHFHNEKIEEARICIDKSLQLEPRR  405 (458)
T ss_pred             HHhcC--CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCc--cHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchh
Confidence            63322  245566667777777888899999999999887655  56666666666777899999999999965555533


Q ss_pred             ---hhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          206 ---VSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       206 ---~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                         ......+..|+.++ .++|..++-+
T Consensus       406 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~  432 (458)
T PRK11906        406 RKAVVIKECVDMYVPNP-LKNNIKLYYK  432 (458)
T ss_pred             hHHHHHHHHHHHHcCCc-hhhhHHHHhh
Confidence               22333344666664 5666666544

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.56  E-value=8.5  Score=31.73  Aligned_cols=175  Identities=11%  Similarity=0.038  Sum_probs=99.3

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHc
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAM  217 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~  217 (352)
                      .|..-..+|...+++++|...+.+..+.--.  +...|.+       ..-++.|.-+.+++....--+..|+.....|..
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~~~yEn--nrslfhA-------AKayEqaamLake~~klsEvvdl~eKAs~lY~E  103 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKASKGYEN--NRSLFHA-------AKAYEQAAMLAKELSKLSEVVDLYEKASELYVE  103 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHHHHh--cccHHHH-------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            4556667788888999988877666532111  2222211       112333444444443222334455666778888


Q ss_pred             CCCHHHHHHHHHHHHh--cCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-
Q 042593          218 HGMGKEAVENFERMQK--VGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-  294 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~--~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  294 (352)
                      +|..+.|-..+++.-+  .++.|+...-.+.++..+++.--   ..+.-...+..+-..+.+..++++|-..+.+-... 
T Consensus       104 ~GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~d---r~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~  180 (308)
T KOG1585|consen  104 CGSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDD---RDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGVAA  180 (308)
T ss_pred             hCCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccc---hHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhhHH
Confidence            8888888777776544  24566433322333333332211   11223456777788888999998887766544332 


Q ss_pred             -----CCCc-hhhHHHHHHHHhcccccCcccccccc
Q 042593          295 -----ITNV-VVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       295 -----~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                           .++. ..|-..|..|+...++..|...++..
T Consensus       181 ~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~  216 (308)
T KOG1585|consen  181 DKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDC  216 (308)
T ss_pred             HHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcch
Confidence                 1222 34666677777778888887777663

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=86.36  E-value=12  Score=28.21  Aligned_cols=54  Identities=9%  Similarity=0.140  Sum_probs=39.9

Q ss_pred             HHhcCCcchHHHHHHHHHHhCC-CCchhhHHHHHHHHHhcCChhHHHHHhccCCCCC
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGF-QSHVYVNTALGDMYVSLGFLKDSSKLFDELPERN   89 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~   89 (352)
                      -...++++++..+++.|.-..- .+...++.  ...+...|++++|.++|+++.+..
T Consensus        20 aL~~~d~~D~e~lLdALrvLrP~~~e~d~~d--g~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        20 ALRSADPYDAQAMLDALRVLRPNLKELDMFD--GWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HHhcCCHHHHHHHHHHHHHhCCCccccchhH--HHHHHHcCCHHHHHHHHHhhhccC
Confidence            3458899999999999986541 12334453  445678999999999999998744

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=85.47  E-value=2.2  Score=29.36  Aligned_cols=47  Identities=11%  Similarity=0.157  Sum_probs=38.7

Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHH
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFL  306 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~  306 (352)
                      .+.|++....+-+++|.+..|+..|.++|+-++.+ ..+...|..++.
T Consensus        37 DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~lq   84 (103)
T cd00923          37 DLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYILQ   84 (103)
T ss_pred             ccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHHH
Confidence            78899999999999999999999999999988766 334456666554

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.

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=85.44  E-value=1.4  Score=23.24  Aligned_cols=23  Identities=26%  Similarity=0.306  Sum_probs=9.8

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHH
Q 042593          210 TIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      .+-..+...|++++|.+.|++..
T Consensus         6 ~lg~~~~~~~~~~~A~~~~~~al   28 (34)
T PF07719_consen    6 YLGQAYYQLGNYEEAIEYFEKAL   28 (34)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH
Confidence            33444444444444444444443

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=85.20  E-value=8.9  Score=32.23  Aligned_cols=25  Identities=12%  Similarity=-0.048  Sum_probs=11.7

Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      +...-|-.|.|.++...+.++-...
T Consensus       120 IleLCILLysKv~Ep~amlev~~~W  144 (309)
T PF07163_consen  120 ILELCILLYSKVQEPAAMLEVASAW  144 (309)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            3334444455555555554444443

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

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=84.71  E-value=13  Score=32.55  Aligned_cols=64  Identities=11%  Similarity=-0.078  Sum_probs=47.8

Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-----CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-----ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      ....+|..+.+.+.+.|.++.|...+..+...     ...+.+.-.-..-+...|+..+|+....+.+.
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45678899999999999999999999888764     11334444456667788888888887766554

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=84.45  E-value=7  Score=31.60  Aligned_cols=76  Identities=11%  Similarity=0.034  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC--CCchhhHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN--AFDIHVSNCLID  180 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~li~  180 (352)
                      .+..++.+.+.+.+++++....+-.+.+  +-|..+-..++.-+|-.|++++|..-++..-+....  + ...+|..+|+
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkak--Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~-~a~lyr~lir   80 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAK--PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTV-GASLYRHLIR   80 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcC--CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccch-HHHHHHHHHH
Confidence            3455677778888888888777663422  234456677788888888888887766655443322  2 3456666665


Q ss_pred             H
Q 042593          181 T  181 (352)
Q Consensus       181 ~  181 (352)
                      +
T Consensus        81 ~   81 (273)
T COG4455          81 C   81 (273)
T ss_pred             H
Confidence            4

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=84.28  E-value=7.5  Score=31.00  Aligned_cols=75  Identities=11%  Similarity=-0.106  Sum_probs=55.9

Q ss_pred             hCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-----CCCHhhHHHHHHHHHcCCCHH
Q 042593          148 KNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-----RKNLVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       148 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~  222 (352)
                      +.|+ +.|.+.|-.+...+.-. ++.....|...|. ..+.+++..++......     .+|+..+.+|.+.+.+.|+.+
T Consensus       119 r~~d-~~A~~~fL~~E~~~~l~-t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e  195 (203)
T PF11207_consen  119 RFGD-QEALRRFLQLEGTPELE-TAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYE  195 (203)
T ss_pred             ccCc-HHHHHHHHHHcCCCCCC-CHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchh
Confidence            4444 66777777777777655 7777777776666 56788888888765432     578899999999999999998


Q ss_pred             HHH
Q 042593          223 EAV  225 (352)
Q Consensus       223 ~a~  225 (352)
                      .|.
T Consensus       196 ~AY  198 (203)
T PF11207_consen  196 QAY  198 (203)
T ss_pred             hhh
Confidence            874

>PHA02875 ankyrin repeat protein; Provisional

Probab=84.20  E-value=32  Score=31.12  Aligned_cols=206  Identities=12%  Similarity=-0.047  Sum_probs=98.5

Q ss_pred             hhHHHHHHhhccCCCCCCCCCccc--HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchh--hHHHHHHHHHhcCChhHH
Q 042593            3 VYKQLQQIYIHSHSPLPPLFDSFT--YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY--VNTALGDMYVSLGFLKDS   78 (352)
Q Consensus         3 ~~~~M~~~~~~~~g~~P~~~~~~~--~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~--~~~~li~~~~~~g~~~~a   78 (352)
                      +.+.+.+     .|..|   +...  ..+.+..++..|+.+    +.+.+.+.|..|+..  .....+...+..|+.+.+
T Consensus        17 iv~~Ll~-----~g~~~---n~~~~~g~tpL~~A~~~~~~~----~v~~Ll~~ga~~~~~~~~~~t~L~~A~~~g~~~~v   84 (413)
T PHA02875         17 IARRLLD-----IGINP---NFEIYDGISPIKLAMKFRDSE----AIKLLMKHGAIPDVKYPDIESELHDAVEEGDVKAV   84 (413)
T ss_pred             HHHHHHH-----CCCCC---CccCCCCCCHHHHHHHcCCHH----HHHHHHhCCCCccccCCCcccHHHHHHHCCCHHHH
Confidence            4455555     66666   4322  344556666777764    555566667655432  123346666788998888


Q ss_pred             HHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhh--HHHHHHHHHhCCChhhHH
Q 042593           79 SKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEIT--ILAVLPAIWKNGEVRNCQ  156 (352)
Q Consensus        79 ~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t--~~~ll~~~~~~~~~~~a~  156 (352)
                      ..+++.-...+......       -...+...+..|+.+-+..++     +.|..|+...  -.+.+...+..|+.+.+.
T Consensus        85 ~~Ll~~~~~~~~~~~~~-------g~tpL~~A~~~~~~~iv~~Ll-----~~gad~~~~~~~g~tpLh~A~~~~~~~~v~  152 (413)
T PHA02875         85 EELLDLGKFADDVFYKD-------GMTPLHLATILKKLDIMKLLI-----ARGADPDIPNTDKFSPLHLAVMMGDIKGIE  152 (413)
T ss_pred             HHHHHcCCcccccccCC-------CCCHHHHHHHhCCHHHHHHHH-----hCCCCCCCCCCCCCCHHHHHHHcCCHHHHH
Confidence            88887543211100000       011223344556664333333     3344443321  123445555677766555


Q ss_pred             HHHHHHHhcCCCCC--chhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          157 LIHGYGEKRGFNAF--DIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       157 ~~~~~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+++    .|..+.  +..-. ..+...+..|+.+-+.-+++.-... ..+.....+++...+..|+.+    +.+-+.+
T Consensus       153 ~Ll~----~g~~~~~~d~~g~-TpL~~A~~~g~~eiv~~Ll~~ga~~n~~~~~~~~t~l~~A~~~~~~~----iv~~Ll~  223 (413)
T PHA02875        153 LLID----HKACLDIEDCCGC-TPLIIAMAKGDIAICKMLLDSGANIDYFGKNGCVAALCYAIENNKID----IVRLFIK  223 (413)
T ss_pred             HHHh----cCCCCCCCCCCCC-CHHHHHHHcCCHHHHHHHHhCCCCCCcCCCCCCchHHHHHHHcCCHH----HHHHHHH
Confidence            4443    443320  12222 2334455667776665555532111 111111224444445556654    4455556


Q ss_pred             cCCCCCcc
Q 042593          234 VGLKPNRS  241 (352)
Q Consensus       234 ~~~~p~~~  241 (352)
                      .|..++..
T Consensus       224 ~gad~n~~  231 (413)
T PHA02875        224 RGADCNIM  231 (413)
T ss_pred             CCcCcchH
Confidence            67666543

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=84.14  E-value=1.2  Score=23.29  Aligned_cols=25  Identities=20%  Similarity=0.093  Sum_probs=11.7

Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCC
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      ..++.+.|+.++|.+.|+++....|
T Consensus         7 a~~~~~~g~~~~A~~~~~~~~~~~P   31 (33)
T PF13174_consen    7 ARCYYKLGDYDEAIEYFQRLIKRYP   31 (33)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHCc
Confidence            3444445555555555555443333

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=84.06  E-value=3.4  Score=21.79  Aligned_cols=26  Identities=15%  Similarity=0.140  Sum_probs=22.2

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      .+|..+..+|...|++++|+..|++.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~a   27 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRA   27 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHH
Confidence            46888999999999999999999875

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 ....

>PRK11906 transcriptional regulator; Provisional

Probab=84.05  E-value=33  Score=31.25  Aligned_cols=118  Identities=9%  Similarity=0.004  Sum_probs=81.9

Q ss_pred             CHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHh---------CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh
Q 042593          115 RSNEALALFRRMAACEYTEPSEI-TILAVLPAIWK---------NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       115 ~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  184 (352)
                      ..+.|+.+|.+......+.|+-. .|..+..++..         ..+..+|.+.-+...+.+..  |+.....+..++.-
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld~~--Da~a~~~~g~~~~~  350 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDITTV--DGKILAIMGLITGL  350 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHh
Confidence            45688889999854445666643 34433333321         22345566666666666544  78888888888888


Q ss_pred             hCChHHHHHHHHHhccCCCCH-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          185 CGCIFSASKLFEDTSVDRKNL-VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .|+++.|...|++...-.||. .+|...-..+.-.|+.++|.+.+++..+.
T Consensus       351 ~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrL  401 (458)
T PRK11906        351 SGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQL  401 (458)
T ss_pred             hcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc
Confidence            999999999999987667753 44555555567789999999999996653

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

Probab=83.99  E-value=1.5  Score=24.41  Aligned_cols=28  Identities=18%  Similarity=0.277  Sum_probs=22.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      ..+++.|...|...|++++|+.++++..
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            4578889999999999999999888753

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=83.71  E-value=11  Score=34.18  Aligned_cols=127  Identities=10%  Similarity=0.008  Sum_probs=83.8

Q ss_pred             hcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHH
Q 042593          112 RMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      ..||+..|-+-+...++...-.|+....-+.|  +...|+++++...+....+. +.. ...+-.++++..-+.|+++.|
T Consensus       301 ~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i--~~~lg~ye~~~~~~s~~~~~-~~s-~~~~~~~~~r~~~~l~r~~~a  376 (831)
T PRK15180        301 ADGDIIAASQQLFAALRNQQQDPVLIQLRSVI--FSHLGYYEQAYQDISDVEKI-IGT-TDSTLRCRLRSLHGLARWREA  376 (831)
T ss_pred             hccCHHHHHHHHHHHHHhCCCCchhhHHHHHH--HHHhhhHHHHHHHhhchhhh-hcC-CchHHHHHHHhhhchhhHHHH
Confidence            45666655544443335555556665544443  56789999998888766543 223 667788899999999999999


Q ss_pred             HHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          192 SKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       192 ~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      ..+-..|.... .+..........--..|-++++...|+++...+.+.+...
T Consensus       377 ~s~a~~~l~~eie~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~~~~g~  428 (831)
T PRK15180        377 LSTAEMMLSNEIEDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPETQSGW  428 (831)
T ss_pred             HHHHHHHhccccCChhheeeecccHHHHhHHHHHHHHHHHHhccCChhcccc
Confidence            99998887662 3344333333344556778999999999877654444433

>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=83.70  E-value=2.2  Score=21.18  Aligned_cols=22  Identities=18%  Similarity=0.288  Sum_probs=15.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHhc
Q 042593           62 NTALGDMYVSLGFLKDSSKLFD   83 (352)
Q Consensus        62 ~~~li~~~~~~g~~~~a~~~~~   83 (352)
                      ...+..++...|++++|+.+++
T Consensus         4 ~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    4 RLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHh
Confidence            4456667777777777777665

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

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

Probab=83.06  E-value=14  Score=26.23  Aligned_cols=24  Identities=21%  Similarity=0.490  Sum_probs=21.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      |..|+.-|...|..++|++++.+.
T Consensus        42 ~~eL~~lY~~kg~h~~AL~ll~~l   65 (108)
T PF10366_consen   42 YQELVDLYQGKGLHRKALELLKKL   65 (108)
T ss_pred             HHHHHHHHHccCccHHHHHHHHHH
Confidence            888889999999999999999988

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

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=82.67  E-value=1.9  Score=29.94  Aligned_cols=48  Identities=13%  Similarity=0.194  Sum_probs=35.2

Q ss_pred             CCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHH
Q 042593          260 EVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLR  307 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~  307 (352)
                      .+.|++....+-+++|.+..++..|.++|+-++.+ .+....|..++.-
T Consensus        40 DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lqE   88 (108)
T PF02284_consen   40 DLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQE   88 (108)
T ss_dssp             SB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHHH
T ss_pred             ccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHHH
Confidence            78899999999999999999999999999988776 3333367666543

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 ....

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.41  E-value=40  Score=31.82  Aligned_cols=99  Identities=17%  Similarity=0.096  Sum_probs=57.7

Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS  190 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  190 (352)
                      .+.|+++.|.++..+.       -+..-|..|.++....+++..|.+.+....          -|..|+-++...|+.+.
T Consensus       648 l~lgrl~iA~~la~e~-------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~----------d~~~LlLl~t~~g~~~~  710 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEA-------NSEVKWRQLGDAALSAGELPLASECFLRAR----------DLGSLLLLYTSSGNAEG  710 (794)
T ss_pred             hhcCcHHHHHHHHHhh-------cchHHHHHHHHHHhhcccchhHHHHHHhhc----------chhhhhhhhhhcCChhH
Confidence            4556666666665555       244456677777777777777766665332          23455556666666555


Q ss_pred             HHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          191 ASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       191 a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      ...+-....+...+    |...-+|...|+++++.+++.+
T Consensus       711 l~~la~~~~~~g~~----N~AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  711 LAVLASLAKKQGKN----NLAFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             HHHHHHHHHhhccc----chHHHHHHHcCCHHHHHHHHHh
Confidence            44444444333322    3334456677888888777755

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=81.92  E-value=15  Score=25.64  Aligned_cols=85  Identities=14%  Similarity=0.126  Sum_probs=53.5

Q ss_pred             cchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHH
Q 042593           40 PNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEA  119 (352)
Q Consensus        40 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a  119 (352)
                      -++|..+-+.+...+-. ....--+-+..+.+.|++++|..+.+.+.-||...          |-+|-.  -+.|..+++
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlep----------w~ALce--~rlGl~s~l   87 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEP----------WLALCE--WRLGLGSAL   87 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHH----------HHHHHH--HhhccHHHH
Confidence            45666666666655421 22222233445668899999999999888888888          444333  366777777


Q ss_pred             HHHHHHhHhccCCCCChhhH
Q 042593          120 LALFRRMAACEYTEPSEITI  139 (352)
Q Consensus       120 ~~~~~~m~~~~~~~p~~~t~  139 (352)
                      ..-+.+| ...| .|...+|
T Consensus        88 ~~rl~rl-a~sg-~p~lq~F  105 (115)
T TIGR02508        88 ESRLNRL-AASG-DPRLQTF  105 (115)
T ss_pred             HHHHHHH-HhCC-CHHHHHH
Confidence            7777777 5554 3444444

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

---

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	352
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-05

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.5 bits (125), Expect = 1e-07
 Identities = 55/373 (14%), Positives = 107/373 (28%), Gaps = 108/373 (28%)

Query: 28  SFLIRTCVTLSYPNLGTQLHAVFSKVGFQ--SHVYVNTALGDMYVSLGFLKDSSK-LF-- 82
           +F +  C  L    L T+   V   +     +H+ ++      + S+    D  K L   
Sbjct: 261 AFNLS-CKIL----LTTRFKQVTDFLSAATTTHISLD------HHSMTLTPDEVKSLLLK 309

Query: 83  ------DELPER----NLVTWNVIITGLVKWTGIIDGYSRMN---------RSNEAL--A 121
                  +LP      N    ++I   +       D +  +N          S   L  A
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369

Query: 122 LFRRMAACEYTE----PSEITI-LAVLPAIWKNGEVRNCQLI----HGYG--EKRGFNA- 169
            +R+M    +      P    I   +L  IW +    +  ++    H Y   EK+   + 
Sbjct: 370 EYRKM----FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKEST 425

Query: 170 ---FDIHVSNC------------LIDTY--AKCGCIFSASKLFEDTSVDRKNLVSWTTII 212
                I++               ++D Y   K          + D               
Sbjct: 426 ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD-----------QYFY 474

Query: 213 SGFAMHGMGKEAVENFERMQKVGLKPNRSW---RIGEEGLKFFDKMVEECEVLPDIKHYG 269
           S    H    E  E     + V L  +  +   +I  +    ++        L  +K Y 
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFL--DFRFLEQKIRHDSTA-WNASGSILNTLQQLKFYK 531

Query: 270 CLIDILERAGRLEQ-AEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFF 328
               I +   + E+    +   +P    N++   + +  LL             +     
Sbjct: 532 PY--ICDNDPKYERLVNAILDFLPKIEENLI--CSKYTDLL-------------RIALMA 574

Query: 329 P-AALY--ALTQI 338
              A++  A  Q+
Sbjct: 575 EDEAIFEEAHKQV 587

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 45.2 bits (105), Expect = 3e-05
 Identities = 27/171 (15%), Positives = 52/171 (30%), Gaps = 19/171 (11%)

Query: 134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASK 193
           P E  +  +L        +   Q   G   +   +     +             +  A  
Sbjct: 90  PWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRL-LAFFKCCLLTDQLPLAHH 148

Query: 194 LFEDTSVDRK-----NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN--------- 239
           L       R+      L  +  ++ G+A  G  KE V     ++  GL P+         
Sbjct: 149 LLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208

Query: 240 ---RSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEV 287
              R  +      +  ++M +E   L  +     L+   +RA  L+   +V
Sbjct: 209 CMGRQDQDAGTIERCLEQMSQEGLKLQAL-FTAVLLSEEDRATVLKAVHKV 258

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	352
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.95
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.95
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.91
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.88
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.87
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.82
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.82
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.82
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.82
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.8
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.8
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.8
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.78
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.78
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.76
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.76
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.75
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.75
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.72
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.71
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.69
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.68
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.67
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.64
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.63
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.63
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.62
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.61
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.6
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.59
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.58
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.57
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.57
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.57
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.57
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.56
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.56
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.55
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.55
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.55
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.53
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.52
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.5
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.5
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.48
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.47
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.47
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.45
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.44
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.44
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.43
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.43
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.41
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.4
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.38
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.38
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.36
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.33
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.32
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.32
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.31
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.31
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.28
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.28
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.28
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.27
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.26
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.26
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.26
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.23
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.23
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.22
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.2
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.2
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.17
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.14
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.14
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.13
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.12
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.11
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.08
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.08
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.03
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.03
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.02
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.99
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.99
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.98
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.98
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.97
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.92
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.91
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.91
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.89
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.88
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.87
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.87
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.85
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.84
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.83
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.82
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.79
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.79
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.78
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.78
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.77
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.77
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.77
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.76
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.7
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.7
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.69
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.66
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.62
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.58
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.55
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.54
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.53
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.52
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.52
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.51
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.51
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.5
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.5
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.5
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.5
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.49
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.48
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.48
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.48
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.46
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.46
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.46
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.45
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.44
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.44
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.42
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.41
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.4
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.4
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.4
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.37
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.36
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.35
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.33
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.32
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.28
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.27
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.27
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.24
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.24
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.23
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.22
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.22
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.2
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.2
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.2
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.2
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.2
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.19
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.19
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.19
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.18
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.17
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.15
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.12
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.12
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.11
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.09
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.09
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.07
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.06
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.05
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.03
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.02
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.02
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.99
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.97
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.92
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.9
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.88
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.85
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.85
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.83
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.83
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.8
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.8
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.74
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.74
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.62
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.61
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.57
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.53
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.53
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.52
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.52
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.48
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.45
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.25
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.25
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.17
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.07
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.05
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.0
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.98
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.95
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.94
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.91
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.9
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.9
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.87
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.69
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.54
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.42
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.36
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.27
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.17
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.16
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.06
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.86
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.46
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.45
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.42
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.28
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.1
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.07
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.06
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.04
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.51
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.29
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	94.14
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	92.9
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	92.89
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.65
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	92.11
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	91.99
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	91.52
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	90.76
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	90.21
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.84
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.76
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	89.73
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	89.41
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	88.86
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	86.38
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	86.33
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	86.15
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	85.67
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	85.32
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.83
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	84.35
2p58_C	116	Putative type III secretion protein YSCG; type III	84.35
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	83.96
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	83.64
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	83.11
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	82.53
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	82.09
3eiq_C	358	Programmed cell death protein 4; PDCD4, anti-oncog	80.69
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	80.45
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	80.4

>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=2.5e-32  Score=248.90  Aligned_cols=196  Identities=10%  Similarity=0.016  Sum_probs=172.7

Q ss_pred             hhHHHHHHhhccCCCCCCCCCc-ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC-------
Q 042593            3 VYKQLQQIYIHSHSPLPPLFDS-FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF-------   74 (352)
Q Consensus         3 ~~~~M~~~~~~~~g~~P~~~~~-~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~-------   74 (352)
                      +++.|++     +++.+   .+ ..++.+|.+|++.|++++|+++|+.|.+.|++||..|||+||.+|++.+.       
T Consensus        12 L~~~~~~-----k~~~~---spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~   83 (501)
T 4g26_A           12 LSRKAKK-----KAIQQ---SPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPN   83 (501)
T ss_dssp             --------------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCC
T ss_pred             HHHHHHH-----hcccC---CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhc
Confidence            4456666     55555   43 35899999999999999999999999999999999999999999998765       


Q ss_pred             --hhHHHHHhccCCC----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh
Q 042593           75 --LKDSSKLFDELPE----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK  148 (352)
Q Consensus        75 --~~~a~~~~~~m~~----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~  148 (352)
                        +++|.++|++|.+    ||..+          ||+||++|++.|++++|.++|++| ...|+.||..||+++|.+|++
T Consensus        84 ~~l~~A~~lf~~M~~~G~~Pd~~t----------yn~lI~~~~~~g~~~~A~~l~~~M-~~~g~~Pd~~tyn~lI~~~~~  152 (501)
T 4g26_A           84 PGLSRGFDIFKQMIVDKVVPNEAT----------FTNGARLAVAKDDPEMAFDMVKQM-KAFGIQPRLRSYGPALFGFCR  152 (501)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCHHH----------HHHHHHHHHHHTCHHHHHHHHHHH-HHTTCCCCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhCCCCCHHH----------HHHHHHHHHhcCCHHHHHHHHHHH-HHcCCCCccceehHHHHHHHH
Confidence              6789999999974    89888          999999999999999999999999 889999999999999999999


Q ss_pred             CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcC
Q 042593          149 NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMH  218 (352)
Q Consensus       149 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~  218 (352)
                      .|++++|.+++++|.+.|+.| +..+|++||++|++.|++++|.++|++|...  .|+..||++++..|+..
T Consensus       153 ~g~~~~A~~l~~~M~~~G~~P-d~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          153 KGDADKAYEVDAHMVESEVVP-EEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             CCCHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            999999999999999999999 9999999999999999999999999999765  79999999999999864

>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=4e-32  Score=247.54  Aligned_cols=214  Identities=11%  Similarity=-0.008  Sum_probs=179.9

Q ss_pred             hHHHHHhccCCCCCchh-HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC---
Q 042593           76 KDSSKLFDELPERNLVT-WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGE---  151 (352)
Q Consensus        76 ~~a~~~~~~m~~~~~~~-~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~---  151 (352)
                      ..++.+.+++.+..... ...+      ++.+|++|++.|++++|+++|++| ...|+.||..||+++|.+|++.+.   
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~------l~~~id~c~k~G~~~~A~~lf~~M-~~~Gv~pd~~tyn~Li~~c~~~~~~~~   79 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEAL------LKQKLDMCSKKGDVLEALRLYDEA-RRNGVQLSQYHYNVLLYVCSLAEAATE   79 (501)
T ss_dssp             -----------------CHHHH------HHHHHHHTTTSCCHHHHHHHHHHH-HHHTCCCCHHHHHHHHHHHTTCCCCSS
T ss_pred             chHHHHHHHHHHhcccCCCHHH------HHHHHHHHHhCCCHHHHHHHHHHH-HHcCCCCCHhHHHHHHHHHHhCCchhh
Confidence            34556666666432211 1111      888999999999999999999999 889999999999999999998765   


Q ss_pred             ------hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCCHHH
Q 042593          152 ------VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGMGKE  223 (352)
Q Consensus       152 ------~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~  223 (352)
                            ++.|.++|++|.+.|+.| |..+|+++|.+|++.|++++|.++|++|...  .||..|||++|.+|++.|++++
T Consensus        80 ~~~~~~l~~A~~lf~~M~~~G~~P-d~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~  158 (501)
T 4g26_A           80 SSPNPGLSRGFDIFKQMIVDKVVP-NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADK  158 (501)
T ss_dssp             SSCCHHHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             hhhcchHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHH
Confidence                  578999999999999999 9999999999999999999999999999876  7999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhh
Q 042593          224 AVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVW  301 (352)
Q Consensus       224 a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~  301 (352)
                      |.++|++|.+.                         |+.||..||++||.+|++.|++++|.+++++|++.  .|+..||
T Consensus       159 A~~l~~~M~~~-------------------------G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~  213 (501)
T 4g26_A          159 AYEVDAHMVES-------------------------EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTF  213 (501)
T ss_dssp             HHHHHHHHHHT-------------------------TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHH
T ss_pred             HHHHHHHHHhc-------------------------CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHH
Confidence            99999999987                         77789999999999999999999999999999877  8999999


Q ss_pred             HHHHHHHHhcccccCcccccc
Q 042593          302 RTGFLRLLINSYFFSPITLNS  322 (352)
Q Consensus       302 ~~li~~~~~~g~~~~a~~~~~  322 (352)
                      +.++..+...+....+.....
T Consensus       214 ~~l~~~F~s~~a~~~g~~~~d  234 (501)
T 4g26_A          214 DMIEEWFKSEVATKTGVKKWD  234 (501)
T ss_dssp             HHHHHHHHSHHHHTCCBSCCC
T ss_pred             HHHHHHHhcCcchhhhhhhhh
Confidence            999999988776655544443

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.95  E-value=3.4e-26  Score=214.66  Aligned_cols=299  Identities=10%  Similarity=-0.012  Sum_probs=236.4

Q ss_pred             hhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593            2 LVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus         2 ~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      .+|++|..       ..|   |..++..++.+|.+.|++++|..+|+.+...  ++++.+++.++.+|.+.|++++|.++
T Consensus       105 ~~~~~~~~-------~~p---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~  172 (597)
T 2xpi_A          105 FVGEKVLD-------ITG---NPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAFCLVKLYDWQGALNL  172 (597)
T ss_dssp             HHHHHHHH-------HHC---CHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHh-------hCC---CchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHHHHHHHhhHHHHHHH
Confidence            34556654       346   7778888888888888888888888877543  67888899999999999999999999


Q ss_pred             hccCCCCC-------------------chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC-----------
Q 042593           82 FDELPERN-------------------LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY-----------  131 (352)
Q Consensus        82 ~~~m~~~~-------------------~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----------  131 (352)
                      |+++...+                   ..+          |+.++.+|.+.|++++|.++|++|.+...           
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~  242 (597)
T 2xpi_A          173 LGETNPFRKDEKNANKLLMQDGGIKLEASM----------CYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVS  242 (597)
T ss_dssp             HCSSCTTC----------CCCSSCCHHHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HhccCCccccccccccccccccccchhHHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHH
Confidence            99644322                   344          77788888888888888888877733211           


Q ss_pred             ----------------------------------------------------------CCCChhhHHHHHHHHHhCCChh
Q 042593          132 ----------------------------------------------------------TEPSEITILAVLPAIWKNGEVR  153 (352)
Q Consensus       132 ----------------------------------------------------------~~p~~~t~~~ll~~~~~~~~~~  153 (352)
                                                                                .+++..+++.++.++.+.|+++
T Consensus       243 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  322 (597)
T 2xpi_A          243 NHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFI  322 (597)
T ss_dssp             TTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHH
T ss_pred             hhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHH
Confidence                                                                      0256677888888888888888


Q ss_pred             hHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          154 NCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       154 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      +|..+++++.+.+..  +..+++.++.+|.+.|++++|.++++++... +.+..+|+.++..|.+.|++++|.++|+++.
T Consensus       323 ~A~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  400 (597)
T 2xpi_A          323 DVLAITTKILEIDPY--NLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSKSS  400 (597)
T ss_dssp             HHHHHHHHHHHHCTT--CCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcc--cHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            888888888877643  6778888888888888888888888887654 4468889999999999999999999999988


Q ss_pred             hcCCCCCcc-hhh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCch
Q 042593          233 KVGLKPNRS-WRI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVV  299 (352)
Q Consensus       233 ~~~~~p~~~-~~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~  299 (352)
                      +..  |+.. ++.           .++|.++|+++.+.  .+.+..+|..++.+|.+.|++++|.++|+++... +.+..
T Consensus       401 ~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  476 (597)
T 2xpi_A          401 TMD--PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARL--FQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPL  476 (597)
T ss_dssp             HHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT--TTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHH
T ss_pred             HhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChH
Confidence            743  3322 222           88999999998874  3457889999999999999999999999988765 66788


Q ss_pred             hhHHHHHHHHhcccccCcccccccchhhh
Q 042593          300 VWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       300 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      +|+.++..|.+.|++++|++++.+++...
T Consensus       477 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  505 (597)
T 2xpi_A          477 LLNELGVVAFNKSDMQTAINHFQNALLLV  505 (597)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhh
Confidence            99999999999999999999999887653

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.95  E-value=3.1e-26  Score=214.97  Aligned_cols=294  Identities=10%  Similarity=-0.080  Sum_probs=177.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHH--------------------------------------H
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNT--------------------------------------A   64 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~--------------------------------------~   64 (352)
                      +..+|+.++.++.+.|++++|.++|+.|.+.+ +.+...+.                                      .
T Consensus       199 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  277 (597)
T 2xpi_A          199 EASMCYLRGQVYTNLSNFDRAKECYKEALMVD-AKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYML  277 (597)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-chhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHH
Confidence            68899999999999999999999999998765 22223222                                      2


Q ss_pred             HHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc------------
Q 042593           65 LGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE------------  130 (352)
Q Consensus        65 li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------------  130 (352)
                      ++..|.+.|++++|.++|+++.+  ++..+          |+.++.+|.+.|++++|.++|+++....            
T Consensus       278 ~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~----------~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~  347 (597)
T 2xpi_A          278 KLNKTSHEDELRRAEDYLSSINGLEKSSDL----------LLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLA  347 (597)
T ss_dssp             TSCTTTTHHHHHHHHHHHHTSTTGGGCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHH
T ss_pred             HHHHHcCcchHHHHHHHHHHhhcCCchHHH----------HHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHH
Confidence            24455567777778888877776  55566          4555555555555555555555552211            


Q ss_pred             --------------------CCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH
Q 042593          131 --------------------YTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS  190 (352)
Q Consensus       131 --------------------~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  190 (352)
                                          ..+.+..+++.++.+|.+.|++++|..+++++.+....  +..+|+.++.+|.+.|++++
T Consensus       348 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~  425 (597)
T 2xpi_A          348 SLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQ--FGPAWIGFAHSFAIEGEHDQ  425 (597)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHH
Confidence                                01223445555566666666666666666665554322  45556666666666666666


Q ss_pred             HHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHhHHHHHHHHHHh
Q 042593          191 ASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEEGLKFFDKMVEE  258 (352)
Q Consensus       191 a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~a~~~~~~m~~~  258 (352)
                      |.++|+++.... .+..+|+.++.+|.+.|++++|.++|+++.+.... +..++.           .++|..+|+++.+.
T Consensus       426 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  504 (597)
T 2xpi_A          426 AISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQY-DPLLLNELGVVAFNKSDMQTAINHFQNALLL  504 (597)
T ss_dssp             HHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            666666554442 35556666666666666666666666666553211 222222           66666666666543


Q ss_pred             c---CCCCC--hhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhh
Q 042593          259 C---EVLPD--IKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPA  330 (352)
Q Consensus       259 ~---~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  330 (352)
                      .   +..|+  ..+|..++.+|.+.|++++|.+.++++... +.+..+|..+...|...|++++|.+.+.+.+...|.
T Consensus       505 ~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~p~  582 (597)
T 2xpi_A          505 VKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAISPN  582 (597)
T ss_dssp             HHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             hhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC
Confidence            1   33454  456666666666666666666666665544 445666666666666666666666666666554443

>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=99.91  E-value=2e-22  Score=179.09  Aligned_cols=293  Identities=11%  Similarity=0.019  Sum_probs=230.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      +..+|..+..++.+.|++++|.+.|+.+.+.. +.+..+|..+..++.+.|++++|.+.|+++.+  |+...  .     
T Consensus        66 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~--~-----  137 (388)
T 1w3b_A           66 LAEAYSNLGNVYKERGQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYC--V-----  137 (388)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTH--H-----
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHH--H-----
Confidence            55667777777777777777777777776654 33455677777777777777777777777654  43322  1     


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                        +..+...+...|++++|.+.|+++...   .| +..+|..+...+.+.|++++|...++++.+.+..  +...+..+.
T Consensus       138 --~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg  210 (388)
T 1w3b_A          138 --RSDLGNLLKALGRLEEAKACYLKAIET---QPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPN--FLDAYINLG  210 (388)
T ss_dssp             --HHHHHHHHHTTSCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT--CHHHHHHHH
T ss_pred             --HHHHHHHHHHccCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC--cHHHHHHHH
Confidence              667777888888999999998888442   24 3567888888889999999999999988887543  677888888


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc-hhh-----------hH
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS-WRI-----------GE  246 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~~-----------~~  246 (352)
                      .++...|++++|...|++.....| +..++..+..++.+.|++++|...|+++.+..  |+.. .+.           .+
T Consensus       211 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~  288 (388)
T 1w3b_A          211 NVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKEKGSVA  288 (388)
T ss_dssp             HHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHHHSCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHH
Confidence            999999999999999988765555 57889999999999999999999999998854  4322 222           89


Q ss_pred             hHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          247 EGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       247 ~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      +|...++++.+.  .+.+..++..+...+.+.|++++|.+.++++... +.+..+|..+...|...|++++|+..+.+++
T Consensus       289 ~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~  366 (388)
T 1w3b_A          289 EAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAI  366 (388)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999999885  3457889999999999999999999999998877 6677899999999999999999999999988


Q ss_pred             hhhhhHHHH
Q 042593          326 FFFPAALYA  334 (352)
Q Consensus       326 ~~~~~~~~~  334 (352)
                      ...|....+
T Consensus       367 ~~~p~~~~a  375 (388)
T 1w3b_A          367 RISPTFADA  375 (388)
T ss_dssp             TTCTTCHHH
T ss_pred             hhCCCCHHH
Confidence            766654333

>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=99.88  E-value=4.5e-21  Score=170.32  Aligned_cols=288  Identities=12%  Similarity=0.059  Sum_probs=243.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~   99 (352)
                      +...+..+...+...|++++|...++...+.. +.+..+|..+..+|.+.|++++|.+.|+++.+  |+. .+       
T Consensus        32 ~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------  103 (388)
T 1w3b_A           32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDG-------  103 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHH-------
Confidence            44566666777888999999999999888765 66888999999999999999999999999864  443 34       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                         |..+..++.+.|++++|.+.|+++.+.   .|+. ..+..+...+...|++++|...++++.+....  +..+|..+
T Consensus       104 ---~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~l  175 (388)
T 1w3b_A          104 ---YINLAAALVAAGDMEGAVQAYVSALQY---NPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPN--FAVAWSNL  175 (388)
T ss_dssp             ---HHHHHHHHHHHSCSSHHHHHHHHHHHH---CTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTT--CHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC--CHHHHHHH
Confidence               888999999999999999999999442   3554 46777888899999999999999999987543  78899999


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------h
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------G  245 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~  245 (352)
                      ..++.+.|++++|.+.|+++....| +...|..+...+...|++++|...+++..+.  .|+.....            .
T Consensus       176 ~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~  253 (388)
T 1w3b_A          176 GCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLI  253 (388)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHHHHHHHHHHcCCH
Confidence            9999999999999999999876655 5788999999999999999999999998875  35432222            8


Q ss_pred             HhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          246 EEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       246 ~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      ++|...++++.+.  .+.+..+|..+..++.+.|++++|.+.++++... +.+..+|+.+...+...|++++|+..+.++
T Consensus       254 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  331 (388)
T 1w3b_A          254 DLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKA  331 (388)
T ss_dssp             HHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            8999999999874  2235678999999999999999999999998776 678889999999999999999999999998


Q ss_pred             hhhhhh
Q 042593          325 LFFFPA  330 (352)
Q Consensus       325 ~~~~~~  330 (352)
                      +...|.
T Consensus       332 l~~~p~  337 (388)
T 1w3b_A          332 LEVFPE  337 (388)
T ss_dssp             TTSCTT
T ss_pred             HhcCCC
Confidence            766554

>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=99.87  E-value=6.5e-21  Score=172.45  Aligned_cols=288  Identities=10%  Similarity=0.021  Sum_probs=244.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|..+|+.+.+.. +.+..++..+..+|...|++++|...|+++.+  |+ ...       
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------   96 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAA-------   96 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHH-------
Confidence            67789999999999999999999999999875 56788999999999999999999999999875  33 333       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh----hhHHHH------------HHHHHhCCChhhHHHHHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE----ITILAV------------LPAIWKNGEVRNCQLIHGYGE  163 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~t~~~l------------l~~~~~~~~~~~a~~~~~~~~  163 (352)
                         |..+...|.+.|++++|...|+++.. .  .|+.    ..+..+            ...+.+.|++++|...++.+.
T Consensus        97 ---~~~l~~~~~~~g~~~~A~~~~~~~~~-~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  170 (450)
T 2y4t_A           97 ---RLQRGHLLLKQGKLDEAEDDFKKVLK-S--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKIL  170 (450)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHT-S--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHh-c--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence               88899999999999999999999943 2  3443    444444            445889999999999999999


Q ss_pred             hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          164 KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       164 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      +....  +..++..+..+|.+.|++++|.+.|+++... +.+..+|..+...|...|++++|...|+++.+.  .|+...
T Consensus       171 ~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~  246 (450)
T 2y4t_A          171 EVCVW--DAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKR  246 (450)
T ss_dssp             HHCTT--CHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHH
T ss_pred             HhCCC--ChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHH
Confidence            87544  7889999999999999999999999998765 557899999999999999999999999999875  344433


Q ss_pred             h----------------h--------hHhHHHHHHHHHHhcCCCCC-----hhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          243 R----------------I--------GEEGLKFFDKMVEECEVLPD-----IKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       243 ~----------------~--------~~~a~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      .                .        .++|...++++.+.   .|+     ...+..+..++.+.|++++|...++++..
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  323 (450)
T 2y4t_A          247 CFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT---EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQ  323 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2                1        88999999999875   343     45788999999999999999999998865


Q ss_pred             C-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          294 Q-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       294 ~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      . +.+..+|..+...|...|++++|+..+.+.+...|..
T Consensus       324 ~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~  362 (450)
T 2y4t_A          324 MEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNEND  362 (450)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSC
T ss_pred             hCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcch
Confidence            5 5578999999999999999999999999987765543

>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=99.82  E-value=4.7e-18  Score=153.62  Aligned_cols=276  Identities=8%  Similarity=-0.003  Sum_probs=223.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCc------hhHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNL------VTWNVI   96 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~------~~~~~~   96 (352)
                      +..++..+..++...|++++|...++.+.+.+ +.+..++..+..+|.+.|++++|.+.|+++.+.++      ..+..+
T Consensus        59 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l  137 (450)
T 2y4t_A           59 NYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSENEEKEAQSQL  137 (450)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChhhHHHHHHH
Confidence            68889999999999999999999999999886 55688999999999999999999999999876332      343332


Q ss_pred             HHHHH--hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593           97 ITGLV--KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus        97 i~~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                      ...+.  .+..+...+...|++++|...|+++....  +.+..++..+..++.+.|++++|...++.+.+....  +..+
T Consensus       138 ~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~  213 (450)
T 2y4t_A          138 IKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLKND--NTEA  213 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCS--CHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHH
Confidence            22111  13344566899999999999999994422  246678999999999999999999999999887543  7889


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHH------------HHHHHcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTI------------ISGFAMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~l------------i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      +..+..+|...|++++|.+.|+++....| +...+..+            ...|...|++++|...|+++.+.  .|+..
T Consensus       214 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~  291 (450)
T 2y4t_A          214 FYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIA  291 (450)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcch
Confidence            99999999999999999999999876655 44555544            78899999999999999999884  35532


Q ss_pred             h-----hh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHH
Q 042593          242 W-----RI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTG  304 (352)
Q Consensus       242 ~-----~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~l  304 (352)
                      .     +.           .++|...++++.+.  .+.+...|..+..+|...|++++|...++++... +.+...+..+
T Consensus       292 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l  369 (450)
T 2y4t_A          292 EYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM--EPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNENDQQIREGL  369 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHH
Confidence            2     11           89999999998875  2336789999999999999999999999998777 4456667666


Q ss_pred             HHH
Q 042593          305 FLR  307 (352)
Q Consensus       305 i~~  307 (352)
                      ...
T Consensus       370 ~~~  372 (450)
T 2y4t_A          370 EKA  372 (450)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>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=99.82  E-value=2.8e-18  Score=148.33  Aligned_cols=269  Identities=11%  Similarity=-0.057  Sum_probs=200.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +...+......+...|++++|.++++.+.+.. +.+...+..++.++...|++++|..+++++.+  | +...       
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-------   92 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVS-------   92 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHH-------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHH-------
Confidence            78889999999999999999999999999876 55677788889999999999999999999865  3 3444       


Q ss_pred             HHhHHHHHHHHHhcC-CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          100 LVKWTGIIDGYSRMN-RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       100 ~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                         |..+...+...| ++++|...|++.....  +.+...+..+...+...|++++|...++...+....  +...+..+
T Consensus        93 ---~~~l~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~l  165 (330)
T 3hym_B           93 ---WFAVGCYYLMVGHKNEHARRYLSKATTLE--KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG--CHLPMLYI  165 (330)
T ss_dssp             ---HHHHHHHHHHSCSCHHHHHHHHHHHHTTC--TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT--CSHHHHHH
T ss_pred             ---HHHHHHHHHHhhhhHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc--cHHHHHHH
Confidence               888889999999 9999999999994322  234568999999999999999999999999988654  56777789


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCC-------CCc-chhh-----
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLK-------PNR-SWRI-----  244 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-------p~~-~~~~-----  244 (352)
                      ..+|...|++++|.+.+++..... .+...+..+...+...|++++|...+++..+....       |+. ..+.     
T Consensus       166 ~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~  245 (330)
T 3hym_B          166 GLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHV  245 (330)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHH
Confidence            999999999999999999987764 46788999999999999999999999998774211       110 1111     


Q ss_pred             ------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHH
Q 042593          245 ------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRL  308 (352)
Q Consensus       245 ------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~  308 (352)
                            .++|...+++..+. . +.+...+..+..++.+.|++++|.+.+++.... +.+...+..+...+
T Consensus       246 ~~~~g~~~~A~~~~~~a~~~-~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~  314 (330)
T 3hym_B          246 CRKLKKYAEALDYHRQALVL-I-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCI  314 (330)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH-S-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSCCHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhh-C-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence                  44455555544443 1 113344444555555555555555555554444 33334444444444

>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=99.82  E-value=8.7e-19  Score=154.14  Aligned_cols=267  Identities=13%  Similarity=0.004  Sum_probs=217.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|...++.+.+.. +.+..++..+..++...|++++|.+.|+++.+  | +..+       
T Consensus        63 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~-------  134 (368)
T 1fch_A           63 DHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTA-------  134 (368)
T ss_dssp             TCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHH-------
Confidence            46678889999999999999999999999875 55778899999999999999999999998764  3 3334       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHH---------------HHHHHHhCCChhhHHHHHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILA---------------VLPAIWKNGEVRNCQLIHGYGE  163 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~---------------ll~~~~~~~~~~~a~~~~~~~~  163 (352)
                         |..+...+...|++++|...++++....   |+.. .+..               .+..+...|++++|...++++.
T Consensus       135 ---~~~l~~~~~~~g~~~~A~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~  208 (368)
T 1fch_A          135 ---LMALAVSFTNESLQRQACEILRDWLRYT---PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAV  208 (368)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHTS---TTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHhC---cCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHH
Confidence               8888899999999999999999984432   3222 2211               2333448899999999999998


Q ss_pred             hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          164 KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       164 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      +......+..++..+..+|.+.|++++|.+.|++.....| +..+|..+...+...|++++|...+++..+..       
T Consensus       209 ~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------  281 (368)
T 1fch_A          209 RLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-------  281 (368)
T ss_dssp             HHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------
T ss_pred             HhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------
Confidence            8754422577888999999999999999999998766544 67889999999999999999999999988631       


Q ss_pred             hhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCC-----------chhhHHHHHHHHh
Q 042593          243 RIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITN-----------VVVWRTGFLRLLI  310 (352)
Q Consensus       243 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~-----------~~~~~~li~~~~~  310 (352)
                                         +.+...+..+..+|.+.|++++|...++++... +.+           ..+|..+...|..
T Consensus       282 -------------------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  342 (368)
T 1fch_A          282 -------------------PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSM  342 (368)
T ss_dssp             -------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHH
T ss_pred             -------------------CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHH
Confidence                               235678899999999999999999999887655 223           6889999999999


Q ss_pred             cccccCcccccccchhhhh
Q 042593          311 NSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       311 ~g~~~~a~~~~~~~~~~~~  329 (352)
                      .|++++|..+..+.+..+.
T Consensus       343 ~g~~~~A~~~~~~~l~~~~  361 (368)
T 1fch_A          343 LGQSDAYGAADARDLSTLL  361 (368)
T ss_dssp             HTCGGGHHHHHTTCHHHHH
T ss_pred             hCChHhHHHhHHHHHHHHH
Confidence            9999999999998775554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.82  E-value=2.2e-18  Score=150.61  Aligned_cols=288  Identities=9%  Similarity=0.018  Sum_probs=239.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      |+..+..+...+.+.|++++|...++.+.+.. +.+..++..+..++...|++++|...|+++.+  |+ ...       
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-------   73 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAA-------   73 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchH-------
Confidence            45678888899999999999999999999876 55788999999999999999999999999865  43 333       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC---C-hhhHHHH------------HHHHHhCCChhhHHHHHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP---S-EITILAV------------LPAIWKNGEVRNCQLIHGYGE  163 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p---~-~~t~~~l------------l~~~~~~~~~~~a~~~~~~~~  163 (352)
                         |..+...+...|++++|...|++...   ..|   + ...+..+            ...+...|++++|...++.+.
T Consensus        74 ---~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  147 (359)
T 3ieg_A           74 ---RLQRGHLLLKQGKLDEAEDDFKKVLK---SNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKIL  147 (359)
T ss_dssp             ---HHHHHHHHHHHTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHcCChHHHHHHHHHHHh---cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence               88899999999999999999999943   235   3 3344444            578889999999999999999


Q ss_pred             hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          164 KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       164 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      +....  +...+..+..++...|++++|.+.+++..... .+..++..+...+...|++++|...+++..+..  |+...
T Consensus       148 ~~~~~--~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~  223 (359)
T 3ieg_A          148 EVCVW--DAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD--QDHKR  223 (359)
T ss_dssp             HHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHH
T ss_pred             HhCCC--chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--ccchH
Confidence            87654  78899999999999999999999999987664 478889999999999999999999999998754  33222


Q ss_pred             --------------------hh----hHhHHHHHHHHHHhcCCCCC-h----hhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          243 --------------------RI----GEEGLKFFDKMVEECEVLPD-I----KHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       243 --------------------~~----~~~a~~~~~~m~~~~~~~p~-~----~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                                          +.    .++|...+++..+. .  |+ .    ..+..+..++.+.|++++|...+++...
T Consensus       224 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~--~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  300 (359)
T 3ieg_A          224 CFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT-E--PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQ  300 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C--CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-C--CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence                                11    88999999998876 2  33 2    3355678899999999999999998876


Q ss_pred             C-CCCchhhHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          294 Q-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       294 ~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      . +.+..+|..+...+...|++++|+..+.+.+...|..
T Consensus       301 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~  339 (359)
T 3ieg_A          301 MEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNEND  339 (359)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTC
T ss_pred             hCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC
Confidence            5 5578899999999999999999999999988766654

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.80  E-value=6.1e-19  Score=155.21  Aligned_cols=266  Identities=12%  Similarity=-0.029  Sum_probs=214.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|..+|+.+.+.. +.+..++..+..+|...|++++|++.|++..+  |+ ..+       
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------  135 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKA-------  135 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHH-------
Confidence            56679999999999999999999999999876 56788999999999999999999999999875  33 344       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC--------ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP--------SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD  171 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p--------~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  171 (352)
                         |..+...|...|++++|...|+++.+...-.+        ....+..+...+.+.|++++|...++++.+......+
T Consensus       136 ---~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~  212 (365)
T 4eqf_A          136 ---LMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMID  212 (365)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCC
T ss_pred             ---HHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccC
Confidence               88999999999999999999999844221001        1123344578899999999999999999988654226


Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHH
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLK  250 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~  250 (352)
                      ..++..+..+|.+.|++++|.+.|++..... .+..+|+.+..+|...|++++|...|++..+..  |            
T Consensus       213 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p------------  278 (365)
T 4eqf_A          213 PDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ--P------------  278 (365)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T------------
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--C------------
Confidence            7889999999999999999999999987654 468899999999999999999999999988741  2            


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCC-------------CchhhHHHHHHHHhcccccCc
Q 042593          251 FFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQIT-------------NVVVWRTGFLRLLINSYFFSP  317 (352)
Q Consensus       251 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~-------------~~~~~~~li~~~~~~g~~~~a  317 (352)
                                  .+..++..+..+|.+.|++++|...++++....|             +...|..+...+...|+.+.+
T Consensus       279 ------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  346 (365)
T 4eqf_A          279 ------------GFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELF  346 (365)
T ss_dssp             ------------TCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHH
T ss_pred             ------------CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHH
Confidence                        2577889999999999999999999987755411             367899999999999999888


Q ss_pred             ccccccch
Q 042593          318 ITLNSQRL  325 (352)
Q Consensus       318 ~~~~~~~~  325 (352)
                      .....+.+
T Consensus       347 ~~~~~~~l  354 (365)
T 4eqf_A          347 QAANLGDL  354 (365)
T ss_dssp             HHHHTTCC
T ss_pred             HHHHHhhH
Confidence            77766654

>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=99.80  E-value=1.5e-18  Score=149.88  Aligned_cols=267  Identities=11%  Similarity=-0.018  Sum_probs=222.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +...+......+...|++++|..+++.+.+.. +.+...+..+..++...|++++|.+.|+++.+  | +...       
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~-------   91 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAV-------   91 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHH-------
Confidence            56678888899999999999999999999876 55778899999999999999999999998865  3 3334       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHH--------------HH-HHHhCCChhhHHHHHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAV--------------LP-AIWKNGEVRNCQLIHGYGE  163 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~l--------------l~-~~~~~~~~~~a~~~~~~~~  163 (352)
                         |..+...+...|++++|.+.++++....   |+.. .+..+              .. .+...|++++|...++++.
T Consensus        92 ---~~~la~~~~~~~~~~~A~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  165 (327)
T 3cv0_A           92 ---HAALAVSHTNEHNANAALASLRAWLLSQ---PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAAL  165 (327)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHTS---TTTTTC--------------------CCTTSHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHhC---CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHH
Confidence               8888899999999999999999994432   3322 33222              22 3677899999999999999


Q ss_pred             hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch
Q 042593          164 KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       164 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      +....  +...+..+..+|.+.|++++|.+.+++.....| +..++..+...+...|++++|...+++..+..       
T Consensus       166 ~~~~~--~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-------  236 (327)
T 3cv0_A          166 EMNPN--DAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-------  236 (327)
T ss_dssp             HHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------
T ss_pred             hhCCC--CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------
Confidence            87644  788999999999999999999999999866544 67889999999999999999999999988742       


Q ss_pred             hhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CC------------CchhhHHHHHHHH
Q 042593          243 RIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-IT------------NVVVWRTGFLRLL  309 (352)
Q Consensus       243 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~------------~~~~~~~li~~~~  309 (352)
                                         +.+...+..+..+|.+.|++++|.+.++++... +.            +..+|..+...+.
T Consensus       237 -------------------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  297 (327)
T 3cv0_A          237 -------------------PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLN  297 (327)
T ss_dssp             -------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHH
T ss_pred             -------------------CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHH
Confidence                               225678889999999999999999999887655 33            5779999999999


Q ss_pred             hcccccCcccccccchhhhhhH
Q 042593          310 INSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       310 ~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      ..|++++|..++.+.+..+|..
T Consensus       298 ~~g~~~~A~~~~~~~l~~~~~~  319 (327)
T 3cv0_A          298 VMNRPDLVELTYAQNVEPFAKE  319 (327)
T ss_dssp             HTTCHHHHHHHTTCCSHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHhcchh
Confidence            9999999999999988776654

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.80  E-value=9.3e-18  Score=154.09  Aligned_cols=312  Identities=11%  Similarity=-0.056  Sum_probs=222.9

Q ss_pred             hhhHHHHHHhhccCCCCCCCCCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHH
Q 042593            2 LVYKQLQQIYIHSHSPLPPLFDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKL   81 (352)
Q Consensus         2 ~~~~~M~~~~~~~~g~~P~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~   81 (352)
                      ..|+++..       ..|   |..+|..+..++.+.|++++|...++.+.+.+ +.+..++..+..+|.+.|++++|...
T Consensus        27 ~~~~~al~-------~~p---~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~   95 (514)
T 2gw1_A           27 KYYNWALE-------LKE---DPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFD   95 (514)
T ss_dssp             HHHHHHHH-------HCC---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHh-------cCc---cHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            34566665       237   88999999999999999999999999999876 55678899999999999999999988


Q ss_pred             hccCCCCCc---h-------------------------------------------------------------------
Q 042593           82 FDELPERNL---V-------------------------------------------------------------------   91 (352)
Q Consensus        82 ~~~m~~~~~---~-------------------------------------------------------------------   91 (352)
                      |+++.+.+.   .                                                                   
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  175 (514)
T 2gw1_A           96 LSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPEL  175 (514)
T ss_dssp             HHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCC
T ss_pred             HHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHH
Confidence            876532100   0                                                                   


Q ss_pred             -----------------------------------hHHHHHH------------------HHHhHHHHHHHHHhcCCHHH
Q 042593           92 -----------------------------------TWNVIIT------------------GLVKWTGIIDGYSRMNRSNE  118 (352)
Q Consensus        92 -----------------------------------~~~~~i~------------------~~~~~~~li~~~~~~~~~~~  118 (352)
                                                         .+...+.                  ....|..+...+...|++++
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (514)
T 2gw1_A          176 TFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLG  255 (514)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHH
T ss_pred             HHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHH
Confidence                                               0000000                  00125556666777788888


Q ss_pred             HHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          119 ALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       119 a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      |...|+++.. ..  |+..++..+..++...|++++|...++.+.+....  +..++..+..++...|++++|.+.|++.
T Consensus       256 A~~~~~~~l~-~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~  330 (514)
T 2gw1_A          256 AHEDIKKAIE-LF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSN--NSSVYYHRGQMNFILQNYDQAGKDFDKA  330 (514)
T ss_dssp             HHHHHHHHHH-HC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTT--CTHHHHHHHHHHHHTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHh-hC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcC--CHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            8888887733 22  33667777788888888888888888887776543  6677788888888888888888888877


Q ss_pred             ccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----------hHhHHHHHHHHHHhcCCCCC--
Q 042593          199 SVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----------GEEGLKFFDKMVEECEVLPD--  264 (352)
Q Consensus       199 ~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----------~~~a~~~~~~m~~~~~~~p~--  264 (352)
                      ....| +...+..+...+...|++++|...++++.+.... +...+.           .++|...++++.....-.++  
T Consensus       331 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~  409 (514)
T 2gw1_A          331 KELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPE-APEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIY  409 (514)
T ss_dssp             HHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCS
T ss_pred             HHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccc-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHH
Confidence            65543 5677778888888888888888888887765321 111221           77888888877764122222  


Q ss_pred             --hhhHHHHHHHHHH---cCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhh
Q 042593          265 --IKHYGCLIDILER---AGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPA  330 (352)
Q Consensus       265 --~~~~~~li~~~~~---~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  330 (352)
                        ...+..+..++.+   .|++++|...++.+... +.+..+|..+...|...|++++|...+.+.+...|.
T Consensus       410 ~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  481 (514)
T 2gw1_A          410 VGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESADLART  481 (514)
T ss_dssp             SCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhccc
Confidence              3377788888888   88888888888876655 456677888888888888888888888887665544

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.78  E-value=9.7e-20  Score=171.84  Aligned_cols=149  Identities=11%  Similarity=0.050  Sum_probs=123.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCC-------CCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELP-------ERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY  131 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~-------~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  131 (352)
                      ..|||+||++||+.|++++|.++|++|.       .||++|          ||+||++||+.|++++|.++|++| +..|
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvT----------YNtLI~Glck~G~~~eA~~Lf~eM-~~~G  195 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDM----------YNAVMLGWARQGAFKELVYVLFMV-KDAG  195 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHH----------HHHHHHHHHHHTCHHHHHHHHHHH-HHTT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhH----------HHHHHHHHHhCCCHHHHHHHHHHH-HHcC
Confidence            4589999999999999999999997764       489999          999999999999999999999999 9999


Q ss_pred             CCCChhhHHHHHHHHHhCCCh-hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCCHhh
Q 042593          132 TEPSEITILAVLPAIWKNGEV-RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKNLVS  207 (352)
Q Consensus       132 ~~p~~~t~~~ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~~~~  207 (352)
                      +.||..||+++|.++++.|+. ++|.+++++|.+.|+.| |..+|++++....+.+-++.+.++..++...   .|.+.+
T Consensus       196 ~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~P-D~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~~~~~~~~t  274 (1134)
T 3spa_A          196 LTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKL-QALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNT  274 (1134)
T ss_dssp             CCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCS-HHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCCCCCCCC
T ss_pred             CCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCC-ChhhcccccChhhHHHHHHHHHHhCcccCCCCCCcccccc
Confidence            999999999999999999985 78999999999999999 9999999998777665444444443333221   122445


Q ss_pred             HHHHHHHHHcCC
Q 042593          208 WTTIISGFAMHG  219 (352)
Q Consensus       208 ~~~li~~~~~~~  219 (352)
                      ...|.+.|.+.+
T Consensus       275 ~~LL~dl~s~d~  286 (1134)
T 3spa_A          275 SKLLRDVYAKDG  286 (1134)
T ss_dssp             CTTTHHHHCCCS
T ss_pred             hHHHHHHHccCC
Confidence            556666777655

>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=99.78  E-value=2.3e-16  Score=136.26  Aligned_cols=240  Identities=14%  Similarity=0.038  Sum_probs=195.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC-ChhHHHHHhccCCC--C-CchhHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG-FLKDSSKLFDELPE--R-NLVTWNVIIT   98 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~--~-~~~~~~~~i~   98 (352)
                      +...+..++..+...|++++|..+++.+.+.. +.+...+..+...+...| ++++|.+.|++..+  | +...      
T Consensus        55 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~------  127 (330)
T 3hym_B           55 HASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPA------  127 (330)
T ss_dssp             CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTTCTHH------
T ss_pred             ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCccHHH------
Confidence            56677888899999999999999999999875 557888999999999999 99999999999765  3 3344      


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                          |..+...+...|++++|...|+++....  +.+...+..+...+...|++++|...+++..+....  +...+..+
T Consensus       128 ----~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~--~~~~~~~l  199 (330)
T 3hym_B          128 ----WIAYGHSFAVESEHDQAMAAYFTAAQLM--KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPE--DPFVMHEV  199 (330)
T ss_dssp             ----HHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT--CHHHHHHH
T ss_pred             ----HHHHHHHHHHccCHHHHHHHHHHHHHhc--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCC--ChHHHHHH
Confidence                8889999999999999999999994432  234567778999999999999999999999887644  78899999


Q ss_pred             HHHHHhhCChHHHHHHHHHhccC----------CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch-hh---
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVD----------RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW-RI---  244 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~----------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~-~~---  244 (352)
                      ...+...|++++|.+.+++....          +.+..++..+...+...|++++|...+++..+..  |+... +.   
T Consensus       200 ~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~la  277 (330)
T 3hym_B          200 GVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI--PQNASTYSAIG  277 (330)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCSHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC--ccchHHHHHHH
Confidence            99999999999999999986543          2345789999999999999999999999998864  33222 22   


Q ss_pred             --------hHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHH-HHcCChh
Q 042593          245 --------GEEGLKFFDKMVEECEVLP-DIKHYGCLIDIL-ERAGRLE  282 (352)
Q Consensus       245 --------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~-~~~g~~~  282 (352)
                              .++|...+++..+.   .| +...+..+..++ ...|+.+
T Consensus       278 ~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          278 YIHSLMGNFENAVDYFHTALGL---RRDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHHHHTCHHHHHHHHHTTTTT---CSCCHHHHHHHHHHHHTTTTC--
T ss_pred             HHHHHhccHHHHHHHHHHHHcc---CCCchHHHHHHHHHHHHHhCchh
Confidence                    88888888887753   44 567777787777 4555543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.76  E-value=2e-17  Score=151.91  Aligned_cols=293  Identities=11%  Similarity=-0.082  Sum_probs=236.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+......+.+.|++++|...|+.+.+..  |+..++..+..+|.+.|++++|...|+++.+  |+ ...       
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------   75 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKV-------   75 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHH-------
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHH-------
Confidence            34567788899999999999999999999877  7999999999999999999999999999875  43 334       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCC----------------------------------------------
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTE----------------------------------------------  133 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~----------------------------------------------  133 (352)
                         |..+..++.+.|++++|...|+++....+..                                              
T Consensus        76 ---~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  152 (514)
T 2gw1_A           76 ---LLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERK  152 (514)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC-----------------------
T ss_pred             ---HHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHH
Confidence               8889999999999999999999984433200                                              


Q ss_pred             ------------------------------CC-hhhHHHHHHHHH---hCCChhhHHHHHHHHHh-----cCCC------
Q 042593          134 ------------------------------PS-EITILAVLPAIW---KNGEVRNCQLIHGYGEK-----RGFN------  168 (352)
Q Consensus       134 ------------------------------p~-~~t~~~ll~~~~---~~~~~~~a~~~~~~~~~-----~~~~------  168 (352)
                                                    |+ ...+......+.   +.|++++|...++++.+     ....      
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  232 (514)
T 2gw1_A          153 DKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKL  232 (514)
T ss_dssp             ----CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHH
T ss_pred             hhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCcccccc
Confidence                                          00 122223333333   38999999999999988     3111      


Q ss_pred             -CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---
Q 042593          169 -AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---  244 (352)
Q Consensus       169 -~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---  244 (352)
                       |.+..++..+..++...|++++|.+.|++.....|+...+..+...+...|++++|...++++.+..... ...+.   
T Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~-~~~~~~l~  311 (514)
T 2gw1_A          233 KEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNN-SSVYYHRG  311 (514)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTC-THHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCC-HHHHHHHH
Confidence             2256788899999999999999999999987666668889999999999999999999999998854322 22222   


Q ss_pred             --------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhccccc
Q 042593          245 --------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFF  315 (352)
Q Consensus       245 --------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~  315 (352)
                              .++|...+++..+.  .+.+...+..+...+...|++++|...++++... +.+..+|..+...+...|+++
T Consensus       312 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~  389 (514)
T 2gw1_A          312 QMNFILQNYDQAGKDFDKAKEL--DPENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFD  389 (514)
T ss_dssp             HHHHHTTCTTHHHHHHHHHHHT--CSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHh--ChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHH
Confidence                    88999999998875  2336778889999999999999999999988766 557789999999999999999


Q ss_pred             Ccccccccchhhhhh
Q 042593          316 SPITLNSQRLFFFPA  330 (352)
Q Consensus       316 ~a~~~~~~~~~~~~~  330 (352)
                      +|+..+.+.+...|.
T Consensus       390 ~A~~~~~~a~~~~~~  404 (514)
T 2gw1_A          390 KALKQYDLAIELENK  404 (514)
T ss_dssp             HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhhc
Confidence            999999988765554

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.76  E-value=7.1e-19  Score=166.00  Aligned_cols=97  Identities=9%  Similarity=0.091  Sum_probs=70.0

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHH---hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGE---KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTI  211 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~l  211 (352)
                      .||+++|++|++.|++++|..++++|.   +.|+.| |..+||+||++||+.|++++|.++|++|...  .||+.|||+|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~P-dvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL-TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTC-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCC-CHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            467777777777777777777776654   346666 7777777777777777777777777777655  5777777777


Q ss_pred             HHHHHcCCCH-HHHHHHHHHHHhc
Q 042593          212 ISGFAMHGMG-KEAVENFERMQKV  234 (352)
Q Consensus       212 i~~~~~~~~~-~~a~~~~~~m~~~  234 (352)
                      |.++|+.|+. ++|.++|++|.+.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~k  230 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQE  230 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHc
Confidence            7777777764 6677777777766

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.75  E-value=9.1e-16  Score=133.90  Aligned_cols=281  Identities=7%  Similarity=-0.021  Sum_probs=221.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCc---hhHHHHHH-
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNL---VTWNVIIT-   98 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~~~i~-   98 (352)
                      +..++..+...+...|++++|...++.+.+.. +.+...+..+..++...|++++|...|++..+.++   ........ 
T Consensus        36 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l  114 (359)
T 3ieg_A           36 NYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQL  114 (359)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHH
Confidence            57789999999999999999999999999875 44678899999999999999999999999876333   22111100 


Q ss_pred             --H--HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593           99 --G--LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus        99 --~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                        .  ...+..+...+...|++++|...++++....  +.+...+..+...+...|++++|...++...+....  +..+
T Consensus       115 ~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~  190 (359)
T 3ieg_A          115 VKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLKSD--NTEA  190 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSC--CHHH
T ss_pred             HHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHH
Confidence              0  0012233678899999999999999994432  245678999999999999999999999999887543  7889


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCCCC-HhhHH------------HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDRKN-LVSWT------------TIISGFAMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~------------~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      +..+..++...|++++|.+.|++.....|+ ...+.            .+...+.+.|++++|...+++..+..  |+..
T Consensus       191 ~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~  268 (359)
T 3ieg_A          191 FYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVA  268 (359)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCch
Confidence            999999999999999999999998665443 34333            23667899999999999999998854  4432


Q ss_pred             hhh----------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHH
Q 042593          242 WRI----------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTG  304 (352)
Q Consensus       242 ~~~----------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~l  304 (352)
                      ...                .++|...+++..+.  .+.+..++..+..++.+.|++++|.+.+++.... +.+...+..+
T Consensus       269 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l  346 (359)
T 3ieg_A          269 EYTVRSKERICHCFSKDEKPVEAIRICSEVLQM--EPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGL  346 (359)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChHHHHHH
Confidence            211                89999999999875  2336789999999999999999999999998877 5556677777


Q ss_pred             HHHHHhcc
Q 042593          305 FLRLLINS  312 (352)
Q Consensus       305 i~~~~~~g  312 (352)
                      .......+
T Consensus       347 ~~~~~~~~  354 (359)
T 3ieg_A          347 EKAQRLLK  354 (359)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66655443

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.75  E-value=4.4e-17  Score=138.72  Aligned_cols=253  Identities=10%  Similarity=-0.050  Sum_probs=195.7

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCc--hhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSH--VYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIID  108 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~  108 (352)
                      ++.....|+++.|+...+.....  .|+  ....-.+..+|...|+++.|...++....|+..+          +..+..
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~--~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~~~~~~~a----------~~~la~   73 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPS--SPERDVERDVFLYRAYLAQRKYGVVLDEIKPSSAPELQA----------VRMFAE   73 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCC--SHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTTSCHHHHH----------HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccC--CchhhHHHHHHHHHHHHHCCCHHHHHHHhcccCChhHHH----------HHHHHH
Confidence            44556788999888887765433  343  3455667889999999999999887753334334          778888


Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      .+...++.++|++.++++ -..+..|+. ..+..+..++...|++++|...++.      .. +...+..+..+|.+.|+
T Consensus        74 ~~~~~~~~~~A~~~l~~l-l~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~-~~~~~~~l~~~~~~~g~  145 (291)
T 3mkr_A           74 YLASHSRRDAIVAELDRE-MSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GD-SLECMAMTVQILLKLDR  145 (291)
T ss_dssp             HHHCSTTHHHHHHHHHHH-HHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CC-SHHHHHHHHHHHHHTTC
T ss_pred             HHcCCCcHHHHHHHHHHH-HhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CC-CHHHHHHHHHHHHHCCC
Confidence            899999999999999998 444444654 4566777889999999999999987      23 78889999999999999


Q ss_pred             hHHHHHHHHHhccCCCCHhhH---HHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCC
Q 042593          188 IFSASKLFEDTSVDRKNLVSW---TTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPD  264 (352)
Q Consensus       188 ~~~a~~~~~~~~~~~~~~~~~---~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~  264 (352)
                      .++|.+.|+++....|+....   ...+..+...|++++|..+|+++.+.                          .+.+
T Consensus       146 ~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~--------------------------~p~~  199 (291)
T 3mkr_A          146 LDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK--------------------------CSPT  199 (291)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--------------------------SCCC
T ss_pred             HHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh--------------------------CCCc
Confidence            999999999987666664322   22334455668999999999998874                          2347


Q ss_pred             hhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccC-cccccccchhhhh
Q 042593          265 IKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFS-PITLNSQRLFFFP  329 (352)
Q Consensus       265 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~~~  329 (352)
                      ...++.+..++.+.|++++|...+++.... +.+..++..++..+...|+..+ +.+++++.+...|
T Consensus       200 ~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P  266 (291)
T 3mkr_A          200 LLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHR  266 (291)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence            888999999999999999999999987766 6677899999999999999876 4567777665444

>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=99.72  E-value=9e-16  Score=141.76  Aligned_cols=300  Identities=11%  Similarity=-0.052  Sum_probs=235.6

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCch----------
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLV----------   91 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~----------   91 (352)
                      +..++..+..++.+.|++++|.+.++.+.+.. +.+..++..+..++...|++++|.+.|+.+.. |+..          
T Consensus        58 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  136 (537)
T 3fp2_A           58 EPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLER  136 (537)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHC-----------CHHHH
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHH
Confidence            67889999999999999999999999999876 55788899999999999999999988854421 1100          


Q ss_pred             -----------------------------------------------------------hHHHHHH--------------
Q 042593           92 -----------------------------------------------------------TWNVIIT--------------   98 (352)
Q Consensus        92 -----------------------------------------------------------~~~~~i~--------------   98 (352)
                                                                                 ....+..              
T Consensus       137 ~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~  216 (537)
T 3fp2_A          137 NLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVAND  216 (537)
T ss_dssp             HHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence                                                                       0000000              


Q ss_pred             -------H------------------HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChh
Q 042593           99 -------G------------------LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVR  153 (352)
Q Consensus        99 -------~------------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~  153 (352)
                             .                  ...|..+...+...|++++|...|++...   ..|+..++..+...+...|+++
T Consensus       217 ~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~  293 (537)
T 3fp2_A          217 LLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESIN---LHPTPNSYIFLALTLADKENSQ  293 (537)
T ss_dssp             HHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCCCHHHHHHHHHHTCCSSCCH
T ss_pred             HHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHh---cCCCchHHHHHHHHHHHhcCHH
Confidence                   0                  00256666788889999999999999944   2466778999999999999999


Q ss_pred             hHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          154 NCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       154 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      +|...++.+.+....  +..++..+..++...|++++|.+.|++.....| +...|..+...+...|++++|...++++.
T Consensus       294 ~A~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  371 (537)
T 3fp2_A          294 EFFKFFQKAVDLNPE--YPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETK  371 (537)
T ss_dssp             HHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999999987644  788899999999999999999999999876544 57889999999999999999999999998


Q ss_pred             hcCCCCCcch-hh-----------hHhHHHHHHHHHHhcCCCC----ChhhHHHHHHHHHHc----------CChhHHHH
Q 042593          233 KVGLKPNRSW-RI-----------GEEGLKFFDKMVEECEVLP----DIKHYGCLIDILERA----------GRLEQAEE  286 (352)
Q Consensus       233 ~~~~~p~~~~-~~-----------~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~----------g~~~~A~~  286 (352)
                      +..  |+... +.           .++|...+++..+...-.+    ....+..+..++.+.          |++++|..
T Consensus       372 ~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~  449 (537)
T 3fp2_A          372 LKF--PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIK  449 (537)
T ss_dssp             HHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHH
T ss_pred             HhC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHH
Confidence            864  33322 22           8899999998876511111    122244556778888          99999999


Q ss_pred             HHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhhhh
Q 042593          287 VASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPA  330 (352)
Q Consensus       287 ~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  330 (352)
                      .+++.... +.+..+|..+...|...|++++|+..+.+.+...|.
T Consensus       450 ~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~  494 (537)
T 3fp2_A          450 LLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILART  494 (537)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            99988766 567789999999999999999999999998765443

>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=99.71  E-value=3.2e-16  Score=144.77  Aligned_cols=291  Identities=11%  Similarity=-0.030  Sum_probs=225.5

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGL  100 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~  100 (352)
                      ...+..+...+.+.|++++|...|+.+.+.. +.++.++..+..+|.+.|++++|++.|+++.+  |+ ...        
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~--------   95 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKA--------   95 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHH--------
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHH--------
Confidence            4677888899999999999999999999876 56789999999999999999999999999875  43 334        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCC------------------------------------CChhhHH----
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTE------------------------------------PSEITIL----  140 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~------------------------------------p~~~t~~----  140 (352)
                        |..+..++...|++++|...|+.+ ...+-.                                    |+.....    
T Consensus        96 --~~~la~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  172 (537)
T 3fp2_A           96 --LLRRASANESLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFG  172 (537)
T ss_dssp             --HHHHHHHHHHHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHH
T ss_pred             --HHHHHHHHHHcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHH
Confidence              888889999999999999999644 221110                                    1111100    


Q ss_pred             ----------------------HHHHHHHh------------CCChhhHHHHHHHHHhcCCCCCc-----hhhHHHHHHH
Q 042593          141 ----------------------AVLPAIWK------------NGEVRNCQLIHGYGEKRGFNAFD-----IHVSNCLIDT  181 (352)
Q Consensus       141 ----------------------~ll~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~~li~~  181 (352)
                                            .+..++..            .|++++|..+++.+.+.....+.     ..++..+...
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~  252 (537)
T 3fp2_A          173 IFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIF  252 (537)
T ss_dssp             TSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHH
T ss_pred             hcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHH
Confidence                                  01122211            14788899999988876544201     2356677788


Q ss_pred             HHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc-chhh-----------hHhHH
Q 042593          182 YAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR-SWRI-----------GEEGL  249 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~-----------~~~a~  249 (352)
                      +...|++++|.+.|++.....|+...+..+...+...|++++|...+++..+..  |+. ..+.           .++|.
T Consensus       253 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~  330 (537)
T 3fp2_A          253 HFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN--PEYPPTYYHRGQMYFILQDYKNAK  330 (537)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC--CCCHHHHHHHHHHHHhcCCHHHHH
Confidence            889999999999999987777888889999999999999999999999998854  332 2222           89999


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhh
Q 042593          250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       250 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      ..+++..+. . +.+...+..+..++...|++++|...++++... +.+...|..+...+...|++++|+..+.+.+...
T Consensus       331 ~~~~~a~~~-~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  408 (537)
T 3fp2_A          331 EDFQKAQSL-N-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLE  408 (537)
T ss_dssp             HHHHHHHHH-C-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC
Confidence            999999875 2 235678899999999999999999999988766 5677899999999999999999999999987655


Q ss_pred             hh
Q 042593          329 PA  330 (352)
Q Consensus       329 ~~  330 (352)
                      |.
T Consensus       409 ~~  410 (537)
T 3fp2_A          409 EV  410 (537)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.69  E-value=5.6e-16  Score=136.18  Aligned_cols=253  Identities=12%  Similarity=-0.061  Sum_probs=192.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +..++..+...+.+.|++++|...|+.+.+.. +.+..++..+..+|...|++++|...|+++.+  |+ ...+..+...
T Consensus        98 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~  176 (365)
T 4eqf_A           98 DAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGS  176 (365)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccc
Confidence            67889999999999999999999999999876 55688999999999999999999999999865  21 1111100000


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                      ...+..+...+...|++++|...|+++.....-.++..++..+...+.+.|++++|...+++..+....  +..++..+.
T Consensus       177 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~l~  254 (365)
T 4eqf_A          177 PGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPE--DYSLWNRLG  254 (365)
T ss_dssp             ------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHH
T ss_pred             hHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CHHHHHHHH
Confidence            001455688899999999999999999554433236779999999999999999999999999987644  788999999


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHh
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEE  258 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~  258 (352)
                      .+|.+.|++++|.+.|++.....| +..+|..+..+|...|++++|...|++..+.........             ...
T Consensus       255 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~-------------~~~  321 (365)
T 4eqf_A          255 ATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQ-------------QVP  321 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC--------------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCc-------------ccc
Confidence            999999999999999999876655 588899999999999999999999999887421100000             000


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                       ....+...|..+..++...|+.+.+.++.++-.
T Consensus       322 -~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~l  354 (365)
T 4eqf_A          322 -HPAISGNIWAALRIALSLMDQPELFQAANLGDL  354 (365)
T ss_dssp             ------CHHHHHHHHHHHHHTCHHHHHHHHTTCC
T ss_pred             -hhhhHHHHHHHHHHHHHHcCcHHHHHHHHHhhH
Confidence             011246789999999999999999999887643

>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=99.68  E-value=1.9e-15  Score=132.78  Aligned_cols=250  Identities=12%  Similarity=-0.044  Sum_probs=193.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHH---
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVI---   96 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~---   96 (352)
                      +..++..+..++.+.|++++|.+.++.+.+.. +.+..++..+..+|...|++++|.+.|+++.+  |+. ..+...   
T Consensus        97 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  175 (368)
T 1fch_A           97 HMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEG  175 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC-----
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH
Confidence            67789999999999999999999999999876 56788999999999999999999999998764  221 110000   


Q ss_pred             ---HHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchh
Q 042593           97 ---ITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus        97 ---i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                         ...-..+. .+..+...|++++|...|+++.....-.++..++..+...+.+.|++++|...++++.+....  +..
T Consensus       176 ~~~~~~~~~~~-~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~--~~~  252 (368)
T 1fch_A          176 AGGAGLGPSKR-ILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPN--DYL  252 (368)
T ss_dssp             ----------C-TTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHH
T ss_pred             hhhhcccHHHH-HHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC--CHH
Confidence               00000011 233344889999999999999554332235778999999999999999999999999887543  788


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHH
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFF  252 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~  252 (352)
                      ++..+..++.+.|++++|.+.|++..... .+...+..+..+|.+.|++++|...|++..+........           
T Consensus       253 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~-----------  321 (368)
T 1fch_A          253 LWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGP-----------  321 (368)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC--------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCc-----------
Confidence            99999999999999999999999976654 468889999999999999999999999988742110000           


Q ss_pred             HHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcC
Q 042593          253 DKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGI  291 (352)
Q Consensus       253 ~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  291 (352)
                         ... .......+|..+..+|.+.|+.++|..++++.
T Consensus       322 ---~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          322 ---RGE-GGAMSENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             ---ccc-ccchhhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence               000 01123678999999999999999999998753

>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=99.67  E-value=5.1e-17  Score=142.41  Aligned_cols=235  Identities=11%  Similarity=0.022  Sum_probs=79.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      ++.+|..+..++.+.|++++|.+.|..      .+|..+|..++.++...|++++|++.++...+  +++.+        
T Consensus        31 ~~~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~~~~~~i--------   96 (449)
T 1b89_A           31 EPAVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYV--------   96 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCccchh--------
Confidence            444666666666666666666666643      24555666666666666666666665555543  23333        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        .+.++.+|.+.|+++++.++++        .|+..+|..+...|...|.+++|...|..+          ..|..++.
T Consensus        97 --~~~Li~~Y~Klg~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a----------~n~~~LA~  156 (449)
T 1b89_A           97 --ETELIFALAKTNRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV----------SNFGRLAS  156 (449)
T ss_dssp             --------------CHHHHTTTTT--------CC----------------CTTTHHHHHHHT----------TCHHHHHH
T ss_pred             --HHHHHHHHHHhCCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh----------hhHHHHHH
Confidence              5566666666666666555442        245556666666666666666666666643          24666666


Q ss_pred             HHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          181 TYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      ++.+.|++++|.+.++++    .++.+|..++.+|+..|+++.|......+                            .
T Consensus       157 ~L~~Lg~yq~AVea~~KA----~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L----------------------------~  204 (449)
T 1b89_A          157 TLVHLGEYQAAVDGARKA----NSTRTWKEVCFACVDGKEFRLAQMCGLHI----------------------------V  204 (449)
T ss_dssp             HHHTTTCHHHHHHHHHHH----TCHHHHHHHHHHHHHTTCHHHHHHTTTTT----------------------------T
T ss_pred             HHHHhccHHHHHHHHHHc----CCchhHHHHHHHHHHcCcHHHHHHHHHHH----------------------------H
Confidence            666666666666666666    25666666666666666666663322211                            1


Q ss_pred             CCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHh--cccccCcccccccch
Q 042593          261 VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLI--NSYFFSPITLNSQRL  325 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~--~g~~~~a~~~~~~~~  325 (352)
                      .  ++.-...++..|.+.|++++|..+++..... +-....|+-|...|++  -++..+.++.+..++
T Consensus       205 ~--~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~i  270 (449)
T 1b89_A          205 V--HADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRV  270 (449)
T ss_dssp             T--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTS
T ss_pred             h--CHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            1  2222334666677777777777666665544 4455555555555543  344445555555443

>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=99.64  E-value=1.2e-14  Score=125.30  Aligned_cols=253  Identities=9%  Similarity=-0.089  Sum_probs=193.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|.+.++.+.+.. +.+..++..+...+...|++++|.+.++++.+  |+ ...+..+...
T Consensus        54 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  132 (327)
T 3cv0_A           54 REEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQA  132 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTTTC-------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHH
Confidence            66788889999999999999999999999875 55788899999999999999999999998764  22 2221110000


Q ss_pred             HH---hHHHH-HH-HHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593          100 LV---KWTGI-ID-GYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus       100 ~~---~~~~l-i~-~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                      ..   ....+ .. .+...|++++|...++++.. .. +.+..++..+...+.+.|++++|...++++.+....  +..+
T Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~  208 (327)
T 3cv0_A          133 DVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALE-MN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPD--DAQL  208 (327)
T ss_dssp             -------------CCTTSHHHHHHHHHHHHHHHH-HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHH
T ss_pred             HHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHh-hC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--cHHH
Confidence            00   00001 22 37788999999999999944 32 236678999999999999999999999999887543  7888


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHH
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFD  253 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~  253 (352)
                      +..+..++...|++++|.+.|++..... .+...+..+...+...|++++|...+++..+.........           
T Consensus       209 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~-----------  277 (327)
T 3cv0_A          209 WNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPT-----------  277 (327)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-------------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCcccccc-----------
Confidence            9999999999999999999999976654 4688899999999999999999999999887432211000           


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                         .......+...+..+..++.+.|+.++|..++++....
T Consensus       278 ---~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  315 (327)
T 3cv0_A          278 ---GEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEP  315 (327)
T ss_dssp             ------CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHH
T ss_pred             ---ccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence               00000114678899999999999999999999876543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.63  E-value=6.9e-14  Score=118.94  Aligned_cols=194  Identities=7%  Similarity=-0.032  Sum_probs=104.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCC-chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLV  101 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~  101 (352)
                      +..++..+...+...++.++|.+.++.+...+..| +...+..+..++...|++++|++.+++  ..+...         
T Consensus        64 ~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~---------  132 (291)
T 3mkr_A           64 ELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLEC---------  132 (291)
T ss_dssp             HHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHH---------
T ss_pred             hHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHH---------
Confidence            44555555566666666666666666665554333 334445555566666666666666665  223333         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhH---HHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITI---LAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~---~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                       +..+...+.+.|++++|.+.|+++...   .|+....   ..++..+...|++++|..+++++.+...  .+...++.+
T Consensus       133 -~~~l~~~~~~~g~~~~A~~~l~~~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p--~~~~~~~~l  206 (291)
T 3mkr_A          133 -MAMTVQILLKLDRLDLARKELKKMQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCS--PTLLLLNGQ  206 (291)
T ss_dssp             -HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSC--CCHHHHHHH
T ss_pred             -HHHHHHHHHHCCCHHHHHHHHHHHHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCC--CcHHHHHHH
Confidence             555555666666666666666666322   2332211   1122223334566666666666665522  255566666


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHH-HHHHHHHHHh
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKE-AVENFERMQK  233 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~-a~~~~~~m~~  233 (352)
                      ..++.+.|++++|.+.|++.....| +..++..++..+...|+.++ +.++++++.+
T Consensus       207 a~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          207 AACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            6666666666666666666444333 45556666666666666543 4455555554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.63  E-value=2.4e-14  Score=118.95  Aligned_cols=229  Identities=7%  Similarity=-0.024  Sum_probs=189.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~   99 (352)
                      ....+..+...+...|++++|...++...+..  .+...+..+..++...|++++|.+.+++..+  |+. ..+......
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            34578889999999999999999999999988  7889999999999999999999999998765  211 011100111


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                         |..+...+...|++++|...|++....   .|+.       ..+.+.|++++|...++.+.+....  +...+..+.
T Consensus        82 ---~~~l~~~~~~~~~~~~A~~~~~~a~~~---~~~~-------~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~  146 (258)
T 3uq3_A           82 ---FARIGNAYHKLGDLKKTIEYYQKSLTE---HRTA-------DILTKLRNAEKELKKAEAEAYVNPE--KAEEARLEG  146 (258)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHH---CCCH-------HHHHHHHHHHHHHHHHHHHHHCCHH--HHHHHHHHH
T ss_pred             ---HHHHHHHHHHcccHHHHHHHHHHHHhc---Cchh-------HHHHHHhHHHHHHHHHHHHHHcCcc--hHHHHHHHH
Confidence               889999999999999999999999442   3442       4566778899999999999886433  778899999


Q ss_pred             HHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHh
Q 042593          180 DTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEE  258 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~  258 (352)
                      .++...|++++|.+.|++.... +.+...|..+..++...|++++|...+++..+..                       
T Consensus       147 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-----------------------  203 (258)
T 3uq3_A          147 KEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-----------------------  203 (258)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----------------------
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-----------------------
Confidence            9999999999999999998665 4468889999999999999999999999988742                       


Q ss_pred             cCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          259 CEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       259 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                         +.+...+..+..++.+.|++++|.+.+++....
T Consensus       204 ---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          204 ---PNFVRAYIRKATAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             ---TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence               225778889999999999999999999887654

>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=99.62  E-value=1e-14  Score=127.89  Aligned_cols=261  Identities=10%  Similarity=0.007  Sum_probs=145.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      |...|..++.++...|++++|...++..++.  .+++.+.+.|+.+|.+.|++++++++++.   |+..+          
T Consensus        60 D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~---pn~~a----------  124 (449)
T 1b89_A           60 DPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFING---PNNAH----------  124 (449)
T ss_dssp             ---------------------------------------------------CHHHHTTTTTC---C--------------
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHcC---CcHHH----------
Confidence            8889999999999999999999987777664  45688899999999999999999988864   66666          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+.+...|...|++++|...|..+          ..|..+..++.+.|++++|.+.+..+      . ++.+|..++.+|
T Consensus       125 ~~~IGd~~~~~g~yeeA~~~Y~~a----------~n~~~LA~~L~~Lg~yq~AVea~~KA------~-~~~~Wk~v~~aC  187 (449)
T 1b89_A          125 IQQVGDRCYDEKMYDAAKLLYNNV----------SNFGRLASTLVHLGEYQAAVDGARKA------N-STRTWKEVCFAC  187 (449)
T ss_dssp             ------------CTTTHHHHHHHT----------TCHHHHHHHHHTTTCHHHHHHHHHHH------T-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHh----------hhHHHHHHHHHHhccHHHHHHHHHHc------C-CchhHHHHHHHH
Confidence            999999999999999999999988          27999999999999999999999987      2 789999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh----------hHhHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI----------GEEGLKFF  252 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~----------~~~a~~~~  252 (352)
                      ...|+++.|..+...+. ..|+  -...++..|.+.|++++|..+++...... +.....|.          ++...+.+
T Consensus       188 v~~~ef~lA~~~~l~L~-~~ad--~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl  263 (449)
T 1b89_A          188 VDGKEFRLAQMCGLHIV-VHAD--ELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHL  263 (449)
T ss_dssp             HHTTCHHHHHHTTTTTT-TCHH--HHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHcCcHHHHHHHHHHHH-hCHh--hHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            99999999988777653 3343  34468899999999999999999987543 22222232          55555555


Q ss_pred             HHHHHhcCCCC------ChhhHHHHHHHHHHcCChhHHHHHHhcC-CC------------CCCCchhhHHHHHHHHhccc
Q 042593          253 DKMVEECEVLP------DIKHYGCLIDILERAGRLEQAEEVASGI-PS------------QITNVVVWRTGFLRLLINSY  313 (352)
Q Consensus       253 ~~m~~~~~~~p------~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~------------~~~~~~~~~~li~~~~~~g~  313 (352)
                      +....+-+++|      +...|.-++-.|...|+++.|....-+- ..            +..|...|-..+.-|+  +.
T Consensus       264 ~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl--~~  341 (449)
T 1b89_A          264 ELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL--EF  341 (449)
T ss_dssp             HHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH--HH
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHH--hc
Confidence            54444434555      5678999999999999999887765433 22            1345666666666666  34


Q ss_pred             ccCccccc
Q 042593          314 FFSPITLN  321 (352)
Q Consensus       314 ~~~a~~~~  321 (352)
                      ...++.-+
T Consensus       342 ~p~~l~~l  349 (449)
T 1b89_A          342 KPLLLNDL  349 (449)
T ss_dssp             CGGGHHHH
T ss_pred             CHHHHHHH
Confidence            44444333

>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=99.61  E-value=1.7e-13  Score=113.71  Aligned_cols=197  Identities=10%  Similarity=-0.066  Sum_probs=170.2

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGL  100 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~  100 (352)
                      ...+..+...+...|++++|.+.++.+.+.. +.+...+..+...|...|++++|.+.|+++.+  | +...        
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~--------  107 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARV--------  107 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH--------
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHH--------
Confidence            5678888889999999999999999999875 55788899999999999999999999998764  3 3333        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                        |..+...+...|++++|.+.++++ ...+..|+ ...+..+...+...|++++|...+++..+....  +...+..+.
T Consensus       108 --~~~la~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~la  182 (252)
T 2ho1_A          108 --LNNYGGFLYEQKRYEEAYQRLLEA-SQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRN--QPSVALEMA  182 (252)
T ss_dssp             --HHHHHHHHHHTTCHHHHHHHHHHH-TTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC--CHHHHHHHH
T ss_pred             --HHHHHHHHHHHhHHHHHHHHHHHH-HhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcc--cHHHHHHHH
Confidence              888889999999999999999999 43334454 457888999999999999999999999887643  688899999


Q ss_pred             HHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          180 DTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .++...|++++|.+.++..... +.+...+..+...+...|+.++|.+.++++.+.
T Consensus       183 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          183 DLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            9999999999999999998766 456778888999999999999999999999875

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.60  E-value=3.7e-14  Score=115.29  Aligned_cols=193  Identities=13%  Similarity=0.040  Sum_probs=157.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|...++...+.. +.+...+..+..++.+.|++++|+..|++..+  |+ ...       
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a-------   75 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGG-------   75 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHH-------
Confidence            78889999999999999999999999998876 56788999999999999999999999999875  43 334       


Q ss_pred             HHhHHHHHHHHHhc-----------CCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCC
Q 042593          100 LVKWTGIIDGYSRM-----------NRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGF  167 (352)
Q Consensus       100 ~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  167 (352)
                         |..+...+...           |++++|+..|++..+.   .|+ ...+..+..++...|++++|...+++..+.. 
T Consensus        76 ---~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~---~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-  148 (217)
T 2pl2_A           76 ---YMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV---NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE-  148 (217)
T ss_dssp             ---HHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             ---HHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc-
Confidence               77888888888           9999999999999442   344 5688899999999999999999999999988 


Q ss_pred             CCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          168 NAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       168 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                       . +...+..+..+|...|++++|...|++.....| +...+..+...+...|++++|...+++..
T Consensus       149 -~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          149 -D-TPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             -C-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             -c-chHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence             4 889999999999999999999999999876655 67889999999999999999999998754

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.59  E-value=1.4e-13  Score=111.71  Aligned_cols=198  Identities=14%  Similarity=-0.053  Sum_probs=170.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      +...+..+...+...|++++|.+.++.+.+.. +.+...+..+...+...|++++|.+.+++..+  | +...       
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~-------   78 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEI-------   78 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHH-------
Confidence            56788889999999999999999999999876 55678899999999999999999999998864  3 3334       


Q ss_pred             HHhHHHHHHHHHhc-CCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593          100 LVKWTGIIDGYSRM-NRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus       100 ~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                         |..+...+... |++++|...++++.. .+..|+ ...+..+..++...|++++|...++++.+....  +...+..
T Consensus        79 ---~~~l~~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~  152 (225)
T 2vq2_A           79 ---NNNYGWFLCGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQ--FPPAFKE  152 (225)
T ss_dssp             ---HHHHHHHHHTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHH
T ss_pred             ---HHHHHHHHHHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CchHHHH
Confidence               88888999999 999999999999944 333344 467889999999999999999999999887543  6888999


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccC-C-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVD-R-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~-~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +..++.+.|++++|.+.+++.... + .+...+..+...+...|+.++|..+++.+.+.
T Consensus       153 la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          153 LARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            999999999999999999997655 4 57788888888899999999999999998764

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.58  E-value=9.7e-14  Score=112.78  Aligned_cols=199  Identities=15%  Similarity=0.038  Sum_probs=99.9

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP-  134 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-  134 (352)
                      |+++..+..+...+.+.|++++|...|++..+.++.....       |..+...+.+.|++++|+..|++....   .| 
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a-------~~~lg~~~~~~g~~~~A~~~~~~al~~---~P~   71 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEA-------LYWLARTQLKLGLVNPALENGKTLVAR---TPR   71 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTT
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCC
Confidence            4455566666666666666666666666654422211111       555666666666666666666666332   23 


Q ss_pred             ChhhHHHHHHHHHhC-----------CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          135 SEITILAVLPAIWKN-----------GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      +...+..+..++...           |++++|...++...+....  +...+..+..+|...|++++|...|++......
T Consensus        72 ~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~  149 (217)
T 2pl2_A           72 YLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPR--YAPLHLQRGLVYALLGERDKAEASLKQALALED  149 (217)
T ss_dssp             CHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcc--cHHHHHHHHHHHHHcCChHHHHHHHHHHHhccc
Confidence            234555556666665           6666666666665555332  455555555666666666666666655432224


Q ss_pred             CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhH
Q 042593          204 NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQ  283 (352)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  283 (352)
                      +...+..+..+|...|++++|...|++..+..  |                        -+...+..+..++.+.|+.++
T Consensus       150 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--P------------------------~~~~~~~~la~~~~~~g~~~~  203 (217)
T 2pl2_A          150 TPEIRSALAELYLSMGRLDEALAQYAKALEQA--P------------------------KDLDLRVRYASALLLKGKAEE  203 (217)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--T------------------------TCHHHHHHHHHHHTC------
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C------------------------CChHHHHHHHHHHHHccCHHH
Confidence            45555555556666666666666666555421  1                        134455555555666666666


Q ss_pred             HHHHHhcCC
Q 042593          284 AEEVASGIP  292 (352)
Q Consensus       284 A~~~~~~m~  292 (352)
                      |...+++..
T Consensus       204 A~~~~~~~~  212 (217)
T 2pl2_A          204 AARAAALEH  212 (217)
T ss_dssp             ---------
T ss_pred             HHHHHHHHh
Confidence            665555443

>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=2e-13  Score=113.17  Aligned_cols=203  Identities=8%  Similarity=-0.067  Sum_probs=161.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      ...+..+...+...|++++|.+.|+++.+  | +...          |..+...+...|++++|.+.|+++....  +.+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~----------~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~  104 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADA----------HAALAVVFQTEMEPKLADEEYRKALASD--SRN  104 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTC
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCc
Confidence            56788888899999999999999998764  3 3333          7888888999999999999999984432  235


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISG  214 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~  214 (352)
                      ...+..+...+...|++++|...++++.+.+..|.+...+..+..++...|++++|.+.|++.....| +...+..+...
T Consensus       105 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~  184 (252)
T 2ho1_A          105 ARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADL  184 (252)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHH
Confidence            66788888899999999999999999887333443677888888999999999999999988765544 57888888999


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      +...|++++|...+++..+.                          .+.+...+..+...+.+.|+.++|.+.++++...
T Consensus       185 ~~~~g~~~~A~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          185 LYKEREYVPARQYYDLFAQG--------------------------GGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHHTT--------------------------SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh--------------------------CcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            99999999999999988763                          2235667788888899999999999998887655


Q ss_pred             CCCch
Q 042593          295 ITNVV  299 (352)
Q Consensus       295 ~~~~~  299 (352)
                      .|+..
T Consensus       239 ~p~~~  243 (252)
T 2ho1_A          239 YPGSL  243 (252)
T ss_dssp             CTTSH
T ss_pred             CCCCH
Confidence            34433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.57  E-value=1.6e-13  Score=115.11  Aligned_cols=249  Identities=8%  Similarity=-0.078  Sum_probs=187.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchh-HHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVT-WNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~~i~~   99 (352)
                      |...+......+...|++++|...++...+.. +.+...+..+..+|...|++++|.+.|++..+  ++... ..+    
T Consensus         2 n~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~----   76 (272)
T 3u4t_A            2 NDDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSAD----   76 (272)
T ss_dssp             ---CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHH----
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHH----
Confidence            45567778888999999999999999998865 44666888899999999999999999998765  22211 111    


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                         |..+...+...|++++|...|++.....  +.+..++..+...+...|++++|...+++..+....  +...+..+.
T Consensus        77 ---~~~lg~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~--~~~~~~~l~  149 (272)
T 3u4t_A           77 ---FEYYGKILMKKGQDSLAIQQYQAAVDRD--TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTT--DPKVFYELG  149 (272)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCC--CHHHHHHHH
T ss_pred             ---HHHHHHHHHHcccHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCC--cHHHHHHHH
Confidence               7788889999999999999999984432  234568889999999999999999999998877433  677777777


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCC---HHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHH
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGM---GKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKM  255 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m  255 (352)
                      ..+...+++++|.+.|++.....| +...+..+..++...|+   +++|...+++..+..                    
T Consensus       150 ~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--------------------  209 (272)
T 3u4t_A          150 QAYYYNKEYVKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVC--------------------  209 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHH--------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHH--------------------
Confidence            344445599999999998876655 46777778888887787   788888888877631                    


Q ss_pred             HHhcCCCCC------hhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHH
Q 042593          256 VEECEVLPD------IKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLR  307 (352)
Q Consensus       256 ~~~~~~~p~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~  307 (352)
                          .-.|+      ...|..+...|.+.|++++|.+.+++.... +.+...+..+...
T Consensus       210 ----~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~  264 (272)
T 3u4t_A          210 ----APGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNKKAIDGLKMK  264 (272)
T ss_dssp             ----GGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHC--
T ss_pred             ----hcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHHHHHHHhhhh
Confidence                11122      257888999999999999999999988766 4455555555443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.57  E-value=3.2e-14  Score=119.47  Aligned_cols=247  Identities=11%  Similarity=-0.063  Sum_probs=189.0

Q ss_pred             HHhcCCcchHHHHHHHHHHhCC---CCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHH
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGF---QSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li  107 (352)
                      ....|++++|+..++.+.+...   +.+..++..+..++...|++++|...|++..+  | +...          |..+.
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~----------~~~la   84 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEV----------FNYLG   84 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHH----------HHHHH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHH----------HHHHH
Confidence            3456889999999999988642   22567899999999999999999999999865  3 3344          88899


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC  187 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  187 (352)
                      ..+...|++++|...|++.....  +.+..++..+..++.+.|++++|...++.+.+....   .......+..+...|+
T Consensus        85 ~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~---~~~~~~~~~~~~~~~~  159 (275)
T 1xnf_A           85 IYLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPN---DPFRSLWLYLAEQKLD  159 (275)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT---CHHHHHHHHHHHHHHC
T ss_pred             HHHHHccCHHHHHHHHHHHHhcC--ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC---ChHHHHHHHHHHHhcC
Confidence            99999999999999999994432  235678999999999999999999999999887543   3334445556677899


Q ss_pred             hHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCC-Ch
Q 042593          188 IFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLP-DI  265 (352)
Q Consensus       188 ~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p-~~  265 (352)
                      +++|...+++.... +++...+ .+...+...++.++|...+++..+...                       ...| +.
T Consensus       160 ~~~A~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~-----------------------~~~~~~~  215 (275)
T 1xnf_A          160 EKQAKEVLKQHFEKSDKEQWGW-NIVEFYLGNISEQTLMERLKADATDNT-----------------------SLAEHLS  215 (275)
T ss_dssp             HHHHHHHHHHHHHHSCCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHH-----------------------HHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccc-----------------------ccccccc
Confidence            99999999776544 3444444 477778888889999999988765310                       0111 25


Q ss_pred             hhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCccccc
Q 042593          266 KHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLN  321 (352)
Q Consensus       266 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  321 (352)
                      ..+..+..+|.+.|++++|...+++....  ++..+.....++...|++++|++.+
T Consensus       216 ~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          216 ETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHNFVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTTCHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CchhHHHHHHHHHHHHHHHhhHHHH
Confidence            78889999999999999999999998877  3334555577788999999988765

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.57  E-value=5.8e-14  Score=116.61  Aligned_cols=225  Identities=9%  Similarity=-0.024  Sum_probs=189.1

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC-CCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY-TEP  134 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p  134 (352)
                      ....+..+...+...|++++|...|++..+  .+...          |..+..++...|++++|...+++...... ..|
T Consensus         4 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~----------~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~   73 (258)
T 3uq3_A            4 MADKEKAEGNKFYKARQFDEAIEHYNKAWELHKDITY----------LNNRAAAEYEKGEYETAISTLNDAVEQGREMRA   73 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCTHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhccHHH----------HHHHHHHHHHcccHHHHHHHHHHHHHhCccccc
Confidence            356788899999999999999999998754  34444          88899999999999999999999844221 122


Q ss_pred             C----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHH
Q 042593          135 S----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWT  209 (352)
Q Consensus       135 ~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~  209 (352)
                      +    ..++..+...+...|++++|...++...+...   +       ...+.+.|++++|.+.++......| +...+.
T Consensus        74 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~---~-------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  143 (258)
T 3uq3_A           74 DYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHR---T-------ADILTKLRNAEKELKKAEAEAYVNPEKAEEAR  143 (258)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC---C-------HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCc---h-------hHHHHHHhHHHHHHHHHHHHHHcCcchHHHHH
Confidence            3    46888999999999999999999999988643   3       2457778899999999999876655 567788


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHh
Q 042593          210 TIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVAS  289 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~  289 (352)
                      .+...+...|++++|...+++..+..                          +.+...+..+..+|.+.|++++|...++
T Consensus       144 ~~~~~~~~~~~~~~A~~~~~~a~~~~--------------------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~  197 (258)
T 3uq3_A          144 LEGKEYFTKSDWPNAVKAYTEMIKRA--------------------------PEDARGYSNRAAALAKLMSFPEAIADCN  197 (258)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--------------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHhcC--------------------------cccHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            99999999999999999999988742                          2367789999999999999999999999


Q ss_pred             cCCCC-CCCchhhHHHHHHHHhcccccCcccccccchhhh
Q 042593          290 GIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       290 ~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      +.... +.+...|..+...+...|++++|+..+.+.+...
T Consensus       198 ~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          198 KAIEKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            88766 5678899999999999999999999999998776

>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=1.8e-13  Score=111.10  Aligned_cols=209  Identities=10%  Similarity=-0.015  Sum_probs=160.6

Q ss_pred             CchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCC
Q 042593           57 SHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTE  133 (352)
Q Consensus        57 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~  133 (352)
                      .+...+..+...+...|++++|.+.|++..+  |+ ...          |..+...+...|++++|...++++....  +
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~----------~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~   73 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELA----------WLVRAEIYQYLKVNDKAQESFRQALSIK--P   73 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--T
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHH----------HHHHHHHHHHcCChHHHHHHHHHHHHhC--C
Confidence            3567788888899999999999999988764  32 333          7788888899999999999999884432  2


Q ss_pred             CChhhHHHHHHHHHhC-CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHH
Q 042593          134 PSEITILAVLPAIWKN-GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTI  211 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~l  211 (352)
                      .+..++..+...+... |++++|...++.+.+.+..|.+...+..+..++...|++++|.+.|++.....| +...+..+
T Consensus        74 ~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l  153 (225)
T 2vq2_A           74 DSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKEL  153 (225)
T ss_dssp             TCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             CChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHH
Confidence            3566788888889999 999999999998888433343567888888999999999999999988765544 57888888


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcC
Q 042593          212 ISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGI  291 (352)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  291 (352)
                      ...+...|++++|...+++..+..  |                       ..+...+..+...+...|+.+.|...++.+
T Consensus       154 a~~~~~~~~~~~A~~~~~~~~~~~--~-----------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  208 (225)
T 2vq2_A          154 ARTKMLAGQLGDADYYFKKYQSRV--E-----------------------VLQADDLLLGWKIAKALGNAQAAYEYEAQL  208 (225)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHH--C-----------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC--C-----------------------CCCHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            889999999999999998887631  1                       135566777788888899999998888877


Q ss_pred             CCCCCCchhhH
Q 042593          292 PSQITNVVVWR  302 (352)
Q Consensus       292 ~~~~~~~~~~~  302 (352)
                      ....|+.....
T Consensus       209 ~~~~p~~~~~~  219 (225)
T 2vq2_A          209 QANFPYSEELQ  219 (225)
T ss_dssp             HHHCTTCHHHH
T ss_pred             HHhCCCCHHHH
Confidence            54434444433

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.56  E-value=1.1e-13  Score=114.02  Aligned_cols=198  Identities=11%  Similarity=0.037  Sum_probs=153.4

Q ss_pred             CCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHH
Q 042593           22 FDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIIT   98 (352)
Q Consensus        22 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~   98 (352)
                      .+...|..+...+...|++++|...++.+.+.. +.+...+..+...+...|++++|.+.|++..+  | +...      
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~------   93 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATA------   93 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH------
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHH------
Confidence            467888889999999999999999999998865 55788899999999999999999999998764  3 3334      


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                          |..+...+...|++++|.+.++++.+..  +.+...+..+...+.+.|++++|...++++.+....  +...+..+
T Consensus        94 ----~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~l  165 (243)
T 2q7f_A           94 ----YYGAGNVYVVKEMYKEAKDMFEKALRAG--MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNEN--DTEARFQF  165 (243)
T ss_dssp             ----HHHHHHHHHHTTCHHHHHHHHHHHHHHT--CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTT--CHHHHHHH
T ss_pred             ----HHHHHHHHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCc--cHHHHHHH
Confidence                8888899999999999999999984432  245678889999999999999999999999887544  78889999


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..++.+.|++++|.+.|++..... .+..++..+..+|...|++++|...+++..+.
T Consensus       166 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          166 GMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc
Confidence            999999999999999999976654 46788999999999999999999999999874

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.55  E-value=2.5e-13  Score=113.93  Aligned_cols=241  Identities=9%  Similarity=-0.054  Sum_probs=189.7

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      |+..+......+...|++++|+..|++..+  | +...          |..+...+...|++++|+..+++... .+..|
T Consensus         2 n~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~----------~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~   70 (272)
T 3u4t_A            2 NDDVEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYI----------YNRRAVCYYELAKYDLAQKDIETYFS-KVNAT   70 (272)
T ss_dssp             ---CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTT----------HHHHHHHHHHTTCHHHHHHHHHHHHT-TSCTT
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHH----------HHHHHHHHHHHhhHHHHHHHHHHHHh-ccCch
Confidence            344556678888999999999999999764  3 3445          88888899999999999999999944 33223


Q ss_pred             Ch--hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHH
Q 042593          135 SE--ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTI  211 (352)
Q Consensus       135 ~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~l  211 (352)
                      +.  ..|..+...+...|++++|...++...+....  +..++..+..+|...|++++|.+.|++.....| +...|..+
T Consensus        71 ~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l  148 (272)
T 3u4t_A           71 KAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTT--RLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYEL  148 (272)
T ss_dssp             TCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcc--cHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHH
Confidence            32  24889999999999999999999999987654  778999999999999999999999999877654 56777777


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCC---hhHHHHHH
Q 042593          212 ISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGR---LEQAEEVA  288 (352)
Q Consensus       212 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~---~~~A~~~~  288 (352)
                      ...+...+++++|...|++..+..                          +.+...+..+..++...|+   .++|...+
T Consensus       149 ~~~~~~~~~~~~A~~~~~~a~~~~--------------------------p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~  202 (272)
T 3u4t_A          149 GQAYYYNKEYVKADSSFVKVLELK--------------------------PNIYIGYLWRARANAAQDPDTKQGLAKPYY  202 (272)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS--------------------------TTCHHHHHHHHHHHHHHSTTCSSCTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhC--------------------------ccchHHHHHHHHHHHHcCcchhhHHHHHHH
Confidence            734444569999999999988732                          1246677778888888888   77788777


Q ss_pred             hcCCCC---CCCc------hhhHHHHHHHHhcccccCcccccccchhhhhhHHHHhhh
Q 042593          289 SGIPSQ---ITNV------VVWRTGFLRLLINSYFFSPITLNSQRLFFFPAALYALTQ  337 (352)
Q Consensus       289 ~~m~~~---~~~~------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  337 (352)
                      ++....   .|+.      .+|..+...|...|++++|+..+.+.+...|..-.+...
T Consensus       203 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~  260 (272)
T 3u4t_A          203 EKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNKKAIDG  260 (272)
T ss_dssp             HHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHHHHHHH
Confidence            766544   2332      578889999999999999999999999888877555443

>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=99.55  E-value=1.9e-13  Score=120.29  Aligned_cols=249  Identities=12%  Similarity=0.003  Sum_probs=199.9

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC-hhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF-LKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      ...|+.+..++.+.|++++|++.++..++.. +-+...|+.+..++...|+ +++|+..|++..+-++..+.+       
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a-------  168 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQV-------  168 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHH-------
Confidence            4578888889999999999999999999876 5567889999999999997 999999999987633222222       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+.+..++...|++++|+..|+++....  +-+...|..+..++.+.|++++|...++++.+....  +...|+.+..++
T Consensus       169 ~~~~g~~~~~~g~~~eAl~~~~kal~ld--P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~--~~~a~~~lg~~l  244 (382)
T 2h6f_A          169 WHHRRVLVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR--NNSVWNQRYFVI  244 (382)
T ss_dssp             HHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence            8889999999999999999999995532  235668999999999999999999999999998765  889999999999


Q ss_pred             Hh-hCChHHH-----HHHHHHhccCCC-CHhhHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHH
Q 042593          183 AK-CGCIFSA-----SKLFEDTSVDRK-NLVSWTTIISGFAMHG--MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFD  253 (352)
Q Consensus       183 ~~-~g~~~~a-----~~~~~~~~~~~~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~  253 (352)
                      .+ .|..++|     ++.|++.....| +...|+.+...+...|  ++++|.+.+.++ +                    
T Consensus       245 ~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~--------------------  303 (382)
T 2h6f_A          245 SNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-Q--------------------  303 (382)
T ss_dssp             HHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-T--------------------
T ss_pred             HHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-c--------------------
Confidence            99 6665777     477877655544 6788999998899888  688998888876 3                    


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcC--------C-hhHHHHHHhcC-CCC-CCCchhhHHHHHHHHhc
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAG--------R-LEQAEEVASGI-PSQ-ITNVVVWRTGFLRLLIN  311 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g--------~-~~~A~~~~~~m-~~~-~~~~~~~~~li~~~~~~  311 (352)
                            ..+.+...+..+..+|.+.|        + .++|.++++++ ... +.....|..+...+...
T Consensus       304 ------~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~~~  366 (382)
T 2h6f_A          304 ------PSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSK  366 (382)
T ss_dssp             ------TTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHH
T ss_pred             ------cCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHH
Confidence                  22236778888999998874        2 58999999998 555 44556777777666543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.55  E-value=1.3e-13  Score=115.80  Aligned_cols=221  Identities=10%  Similarity=-0.085  Sum_probs=174.4

Q ss_pred             CCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHH
Q 042593           22 FDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIIT   98 (352)
Q Consensus        22 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~   98 (352)
                      .+..++..+...+...|++++|...++.+.+.. +.+..++..+..+|...|++++|.+.|++..+  | +...      
T Consensus        41 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~------  113 (275)
T 1xnf_A           41 ERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYA------  113 (275)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHH------
T ss_pred             hhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHH------
Confidence            357789999999999999999999999999876 55788999999999999999999999999875  4 3444      


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                          |..+...+...|++++|...|+++..   ..|+.......+..+...|+.++|...++........  +...+ .+
T Consensus       114 ----~~~la~~~~~~g~~~~A~~~~~~a~~---~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~-~~  183 (275)
T 1xnf_A          114 ----HLNRGIALYYGGRDKLAQDDLLAFYQ---DDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDK--EQWGW-NI  183 (275)
T ss_dssp             ----HHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCC--CSTHH-HH
T ss_pred             ----HHHHHHHHHHhccHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc--chHHH-HH
Confidence                88899999999999999999999944   2355555555556667789999999999888776433  44444 47


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCCC-----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHH
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRKN-----LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFD  253 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~  253 (352)
                      +..+...++.++|.+.++......|+     ...+..+...|...|++++|...|++..+..  |+              
T Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~--------------  247 (275)
T 1xnf_A          184 VEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN--VH--------------  247 (275)
T ss_dssp             HHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--CT--------------
T ss_pred             HHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC--ch--------------
Confidence            77888888999999999998766442     5788999999999999999999999988642  21              


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHH
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA  288 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~  288 (352)
                                +   +.....++...|++++|.+.+
T Consensus       248 ----------~---~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          248 ----------N---FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             ----------T---CHHHHHHHHHHHHHHHC----
T ss_pred             ----------h---HHHHHHHHHHHHHHHhhHHHH
Confidence                      2   223355667778888877665

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.53  E-value=1e-13  Score=114.15  Aligned_cols=210  Identities=10%  Similarity=0.006  Sum_probs=142.3

Q ss_pred             CchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh
Q 042593           57 SHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE  136 (352)
Q Consensus        57 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  136 (352)
                      .+..+|..+...+...|++++|...|++..+.++.....       +..+...+...|++++|...+++.....  +.+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~-------~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~   91 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIP-------YINFANLLSSVNELERALAFYDKALELD--SSAA   91 (243)
T ss_dssp             ---------------------CCTTHHHHHTTCTTCHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHcC--Ccch
Confidence            355677778888888899999988888876522211111       7778888888999999999998884432  2356


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~  215 (352)
                      .++..+...+...|++++|...++++.+....  +...+..+..++.+.|++++|.+.+++.... +.+...+..+...+
T Consensus        92 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  169 (243)
T 2q7f_A           92 TAYYGAGNVYVVKEMYKEAKDMFEKALRAGME--NGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCL  169 (243)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCC--SHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            67888888888899999999999888877543  6777888888889999999999999887655 34677888888888


Q ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-
Q 042593          216 AMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-  294 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-  294 (352)
                      ...|++++|...+++..+..                          +.+..++..+..+|.+.|++++|.+.++++... 
T Consensus       170 ~~~~~~~~A~~~~~~~~~~~--------------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          170 ANEGMLDEALSQFAAVTEQD--------------------------PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHTCCHHHHHHHHHHHHHC--------------------------TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHcCCHHHHHHHHHHHHHhC--------------------------cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            88999999998888877631                          225667888888888999999998888877655 


Q ss_pred             CCCchhhHH
Q 042593          295 ITNVVVWRT  303 (352)
Q Consensus       295 ~~~~~~~~~  303 (352)
                      +.+...+..
T Consensus       224 p~~~~~~~~  232 (243)
T 2q7f_A          224 PDHMLALHA  232 (243)
T ss_dssp             TTCHHHHHH
T ss_pred             cchHHHHHH
Confidence            333344433

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.52  E-value=2.9e-13  Score=120.12  Aligned_cols=276  Identities=9%  Similarity=-0.016  Sum_probs=199.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCc----hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSH----VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTW   93 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~   93 (352)
                      ....+......+...|++++|...++...+.+ +.+    ...+..+...|...|++++|...+++..+     .+... 
T Consensus         8 ~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-   85 (406)
T 3sf4_A            8 SCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG-   85 (406)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH-
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH-
Confidence            56667778888999999999999999999875 223    35788899999999999999999988643     11111 


Q ss_pred             HHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCC------------------
Q 042593           94 NVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGE------------------  151 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~------------------  151 (352)
                      ....     |..+...+...|++++|...+++......-.++    ..++..+...+...|+                  
T Consensus        86 ~~~~-----~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~  160 (406)
T 3sf4_A           86 EAKA-----SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVR  160 (406)
T ss_dssp             HHHH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHH
T ss_pred             HHHH-----HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHH
Confidence            1111     888889999999999999999987433221122    3478888889999999                  


Q ss_pred             --hhhHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHHHHHHHHcC
Q 042593          152 --VRNCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTTIISGFAMH  218 (352)
Q Consensus       152 --~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~li~~~~~~  218 (352)
                        +++|...+++..+.    +..+....++..+..+|...|++++|.+.+++....   .++    ..++..+...|...
T Consensus       161 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  240 (406)
T 3sf4_A          161 DALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFL  240 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHc
Confidence              99999888876543    222213567888999999999999999999986543   222    34788889999999


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ---  294 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---  294 (352)
                      |++++|...+++..+.....                     +..+ ...++..+...|...|++++|...+++....   
T Consensus       241 g~~~~A~~~~~~al~~~~~~---------------------~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  299 (406)
T 3sf4_A          241 GEFETASEYYKKTLLLARQL---------------------KDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQE  299 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHT---------------------TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHhC---------------------cCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHh
Confidence            99999999999977531100                     1111 1445666777777777777777776655433   


Q ss_pred             CCC----chhhHHHHHHHHhcccccCcccccccchh
Q 042593          295 ITN----VVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       295 ~~~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      .++    ..++..+...|...|++++|+..+.+.+.
T Consensus       300 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          300 LNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            111    44666667777777777777777776654

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.50  E-value=8.5e-12  Score=115.26  Aligned_cols=71  Identities=14%  Similarity=0.025  Sum_probs=57.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNV   95 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~   95 (352)
                      |...|..++. +.+.|+++.|..+|+.+.+.. |.+...|..++..+.+.|++++|..+|++..+  |+...|..
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~   84 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKC   84 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHH
Confidence            6677888887 477899999999999998764 55777899999999999999999999999875  65544443

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.50  E-value=6e-14  Score=120.92  Aligned_cols=276  Identities=9%  Similarity=-0.017  Sum_probs=206.9

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCc----hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSH----VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWN   94 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~   94 (352)
                      ...+......+...|++++|...++.+.+.. +.+    ...+..+...+...|++++|.+.+++..+     ++... .
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~   82 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG-E   82 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH-H
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHH-H
Confidence            3455666778889999999999999999875 223    36788999999999999999999988653     22111 1


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCC-------------------
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGE-------------------  151 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~-------------------  151 (352)
                      ..+     +..+...+...|++++|...+++......-.++    ..++..+...+...|+                   
T Consensus        83 ~~~-----~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~  157 (338)
T 3ro2_A           83 AKA-----SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRN  157 (338)
T ss_dssp             HHH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHH
T ss_pred             HHH-----HHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHH
Confidence            111     888889999999999999999987433221223    3378888888999999                   


Q ss_pred             -hhhHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHHHHHHHHcCC
Q 042593          152 -VRNCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTTIISGFAMHG  219 (352)
Q Consensus       152 -~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~li~~~~~~~  219 (352)
                       +++|...+++..+.    +..+....++..+...+...|++++|.+.+++....   .++    ..++..+...+...|
T Consensus       158 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g  237 (338)
T 3ro2_A          158 ALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLG  237 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcC
Confidence             99999888876543    222213567888999999999999999999986543   122    347888889999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCC-CChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---C
Q 042593          220 MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVL-PDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---I  295 (352)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~-p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~  295 (352)
                      ++++|...+++..+...                    .. +.. ....++..+...|...|++++|...+++....   .
T Consensus       238 ~~~~A~~~~~~al~~~~--------------------~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  296 (338)
T 3ro2_A          238 EFETASEYYKKTLLLAR--------------------QL-KDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQEL  296 (338)
T ss_dssp             CHHHHHHHHHHHHHHHH--------------------HT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHH--------------------hh-cchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence            99999999998775310                    00 111 12557788899999999999999998876543   1


Q ss_pred             CC----chhhHHHHHHHHhcccccCcccccccchhh
Q 042593          296 TN----VVVWRTGFLRLLINSYFFSPITLNSQRLFF  327 (352)
Q Consensus       296 ~~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  327 (352)
                      .+    ..++..+...|...|++++|...+.+.+..
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            11    447788899999999999999988887643

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.48  E-value=1.1e-13  Score=123.34  Aligned_cols=278  Identities=11%  Similarity=0.008  Sum_probs=208.3

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCch----hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV----YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWN   94 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~   94 (352)
                      ...+..+...+...|++++|...++.+.+.+ +.+.    ..+..+...|...|++++|...|++..+     .+.. ..
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~-~~  125 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRL-GE  125 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHH-HH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCch-HH
Confidence            3445566678889999999999999999875 2233    4788999999999999999999988753     1111 11


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc---CCCC-ChhhHHHHHHHHHhCCC-----------------hh
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE---YTEP-SEITILAVLPAIWKNGE-----------------VR  153 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~~p-~~~t~~~ll~~~~~~~~-----------------~~  153 (352)
                      ...     +..+...|...|++++|...+++.....   +-.| ...++..+...+...|+                 ++
T Consensus       126 ~~~-----~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~  200 (411)
T 4a1s_A          126 AKS-----SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALT  200 (411)
T ss_dssp             HHH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHH
T ss_pred             HHH-----HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHH
Confidence            111     8889999999999999999999874321   1112 23478888899999999                 99


Q ss_pred             hHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC---CC----HhhHHHHHHHHHcCCCHH
Q 042593          154 NCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR---KN----LVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       154 ~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~---~~----~~~~~~li~~~~~~~~~~  222 (352)
                      +|...+++..+.    +..+....++..+..+|...|++++|.+.+++.....   ++    ...+..+...|...|+++
T Consensus       201 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  280 (411)
T 4a1s_A          201 RAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFE  280 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHH
Confidence            999888876543    2222144688889999999999999999999875442   22    247888999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CC---
Q 042593          223 EAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---IT---  296 (352)
Q Consensus       223 ~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~---  296 (352)
                      +|...+++..+...                    ..........++..+...|...|++++|...+++....   .+   
T Consensus       281 ~A~~~~~~al~~~~--------------------~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  340 (411)
T 4a1s_A          281 DAAEHYKRTLALAV--------------------ELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRI  340 (411)
T ss_dssp             HHHHHHHHHHHHHH--------------------HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHH--------------------HcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChH
Confidence            99999998776310                    00011113567888999999999999999999876544   11   


Q ss_pred             -CchhhHHHHHHHHhcccccCcccccccchhhh
Q 042593          297 -NVVVWRTGFLRLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       297 -~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                       ...++..+...|...|++++|...+.+.+..+
T Consensus       341 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  373 (411)
T 4a1s_A          341 GEARACWSLGNAHSAIGGHERALKYAEQHLQLA  373 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence             23478888999999999999999999886543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.47  E-value=4.1e-12  Score=115.34  Aligned_cols=290  Identities=11%  Similarity=-0.061  Sum_probs=202.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh-----C---CCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-------
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV-----G---FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------   87 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------   87 (352)
                      ....||.+..++...|+.++|++.|++..+.     +   .+....+|+.+..+|...|++++|...+++..+       
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            6778999999999999999999999987652     1   122456899999999999999999998887642       


Q ss_pred             C-CchhHHHHHHHHHhHHHHHHHHHh--cCCHHHHHHHHHHhHhccCCCCCh-hhHHHHHHH---HHhCCChhhHHHHHH
Q 042593           88 R-NLVTWNVIITGLVKWTGIIDGYSR--MNRSNEALALFRRMAACEYTEPSE-ITILAVLPA---IWKNGEVRNCQLIHG  160 (352)
Q Consensus        88 ~-~~~~~~~~i~~~~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~~p~~-~t~~~ll~~---~~~~~~~~~a~~~~~  160 (352)
                      + +...-.+       ++.+..++..  .+++++|...|++....   .|+. ..+..+..+   +...++.++|...++
T Consensus       130 ~~~~~~~~~-------~~~~g~~~~~~~~~~y~~A~~~~~kal~~---~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~  199 (472)
T 4g1t_A          130 PYRIESPEL-------DCEEGWTRLKCGGNQNERAKVCFEKALEK---KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLR  199 (472)
T ss_dssp             SSCCCCHHH-------HHHHHHHHHHHCTTHHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHH
T ss_pred             ccchhhHHH-------HHHHHHHHHHHccccHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHH
Confidence            1 1111111       4444444444  45799999999998553   3443 344444433   456688889999999


Q ss_pred             HHHhcCCCCCchhhHHHHHHHHHh----hCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          161 YGEKRGFNAFDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       161 ~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      +..+....  +..++..+...+..    .|+.++|.+.+++.... +.+...+..+...|...|++++|...+++..+. 
T Consensus       200 ~al~l~p~--~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~-  276 (472)
T 4g1t_A          200 QAIRLNPD--NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEY-  276 (472)
T ss_dssp             HHHHHCSS--CHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHhhcCCc--chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh-
Confidence            88877544  66666666655554    46788999999887655 456788999999999999999999999998875 


Q ss_pred             CCCCcchhh-------------------------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHH
Q 042593          236 LKPNRSWRI-------------------------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQA  284 (352)
Q Consensus       236 ~~p~~~~~~-------------------------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  284 (352)
                       .|+.....                               .+.|...+++..+.  -+.+...+..+...|...|++++|
T Consensus       277 -~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~lg~~~~~~~~~~~A  353 (472)
T 4g1t_A          277 -IPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEA--NDNLFRVCSILASLHALADQYEEA  353 (472)
T ss_dssp             -STTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHH--CTTTCCCHHHHHHHHHHTTCHHHH
T ss_pred             -CCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhc--CCchhhhhhhHHHHHHHhccHHHH
Confidence             35433221                               45667777776654  223566788899999999999999


Q ss_pred             HHHHhcCCCCCCCch----hhHHHHH-HHHhcccccCcccccccchhhh
Q 042593          285 EEVASGIPSQITNVV----VWRTGFL-RLLINSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       285 ~~~~~~m~~~~~~~~----~~~~li~-~~~~~g~~~~a~~~~~~~~~~~  328 (352)
                      .+.|++.....|+..    .+..+.. .+...|++++|+..+.+.+...
T Consensus       354 ~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~  402 (472)
T 4g1t_A          354 EYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKIN  402 (472)
T ss_dssp             HHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            999988765422222    1222222 2346788889988887776533

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.47  E-value=3e-11  Score=101.42  Aligned_cols=222  Identities=10%  Similarity=-0.065  Sum_probs=184.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh----cCChhHHHHHhccCCCC-CchhHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS----LGFLKDSSKLFDELPER-NLVTWNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~~i   97 (352)
                      ++.++..+...+...|++++|.+.|+...+.+   +...+..+...|..    .+++++|.+.|++..+. +...     
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a-----   76 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNG-----   76 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH-----
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHH-----
Confidence            66788888999999999999999999998843   55778889999999    99999999999987654 3344     


Q ss_pred             HHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCC
Q 042593           98 TGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus        98 ~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~  169 (352)
                           +..+...|..    .+++++|+..|++... .+   +...+..+...+..    .++.++|...+++..+.+   
T Consensus        77 -----~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---  144 (273)
T 1ouv_A           77 -----CHLLGNLYYSGQGVSQNTNKALQYYSKACD-LK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---  144 (273)
T ss_dssp             -----HHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---
T ss_pred             -----HHHHHHHHhCCCCcccCHHHHHHHHHHHHH-cC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---
Confidence                 7788888888    9999999999999943 33   67788889999998    999999999999999875   


Q ss_pred             CchhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCCHhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          170 FDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKNLVSWTTIISGFAM----HGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       170 ~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                       +...+..+...|..    .+++++|.+.|++..+. .+...+..+...|..    .+++++|...+++..+.+      
T Consensus       145 -~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~-~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~------  216 (273)
T 1ouv_A          145 -DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDL-KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE------  216 (273)
T ss_dssp             -CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT------
T ss_pred             -cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC------
Confidence             45667788888888    89999999999987644 356778888888988    999999999999988752      


Q ss_pred             hhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH----cCChhHHHHHHhcCCCC
Q 042593          242 WRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILER----AGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       242 ~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~  294 (352)
                                            +...+..+..+|.+    .|+.++|.+.+++....
T Consensus       217 ----------------------~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          217 ----------------------NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             ----------------------CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHH
T ss_pred             ----------------------CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHc
Confidence                                  24566677778887    88888888888776544

>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=99.45  E-value=2e-11  Score=102.51  Aligned_cols=225  Identities=8%  Similarity=-0.110  Sum_probs=188.3

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCCCCc-hhHHHHHHHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPERNL-VTWNVIITGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYT  132 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~~~~~~i~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~  132 (352)
                      ++.++..+...|...|++++|.+.|++..+++. ..          +..+...|..    .+++++|...|++. ...+ 
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~a----------~~~lg~~~~~g~~~~~~~~~A~~~~~~a-~~~~-   72 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSG----------CFNLGVLYYQGQGVEKNLKKAASFYAKA-CDLN-   72 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHH----------HHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHTT-
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHH----------HHHHHHHHHcCCCcCCCHHHHHHHHHHH-HHCC-
Confidence            567788889999999999999999998876543 33          7778888888    99999999999999 4333 


Q ss_pred             CCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCC
Q 042593          133 EPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~  204 (352)
                        +...+..+...+..    .++.++|...+++..+.+    +...+..+...|..    .+++++|.+.|++..... +
T Consensus        73 --~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~----~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~-~  145 (273)
T 1ouv_A           73 --YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK----YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN-D  145 (273)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT-C
T ss_pred             --CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC----CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC-c
Confidence              67788889999999    999999999999998874    66788889999999    999999999999876544 6


Q ss_pred             HhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH---
Q 042593          205 LVSWTTIISGFAM----HGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILER---  277 (352)
Q Consensus       205 ~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~---  277 (352)
                      ...+..+...|..    .+++++|...|++..+.+                            +...+..+...|..   
T Consensus       146 ~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~----------------------------~~~a~~~lg~~~~~g~~  197 (273)
T 1ouv_A          146 GDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK----------------------------DSPGCFNAGNMYHHGEG  197 (273)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----------------------------CHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----------------------------CHHHHHHHHHHHHcCCC
Confidence            6777888888887    899999999999987742                            45677788899999   


Q ss_pred             -cCChhHHHHHHhcCCCCCCCchhhHHHHHHHHh----cccccCcccccccchhhhhh
Q 042593          278 -AGRLEQAEEVASGIPSQITNVVVWRTGFLRLLI----NSYFFSPITLNSQRLFFFPA  330 (352)
Q Consensus       278 -~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~  330 (352)
                       .++.++|...+++.... .+...+..+...|..    .+++++|++.+.+.+..-|.
T Consensus       198 ~~~~~~~A~~~~~~a~~~-~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~~  254 (273)
T 1ouv_A          198 ATKNFKEALARYSKACEL-ENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAK  254 (273)
T ss_dssp             SCCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             CCccHHHHHHHHHHHHhC-CCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcCCH
Confidence             99999999999887665 346778888888888    99999999999998764443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.44  E-value=1.5e-13  Score=117.32  Aligned_cols=245  Identities=11%  Similarity=-0.027  Sum_probs=164.9

Q ss_pred             CchhhHHHHHHHHHhcCChhHHHHHhccCCC--------CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHh
Q 042593           57 SHVYVNTALGDMYVSLGFLKDSSKLFDELPE--------RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAA  128 (352)
Q Consensus        57 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--------~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  128 (352)
                      .+..++..+...+...|++++|..+|+++.+        .+.....+       +..+...+...|++++|...+++...
T Consensus        25 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~-------~~~la~~~~~~g~~~~A~~~~~~al~   97 (311)
T 3nf1_A           25 ARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATM-------LNILALVYRDQNKYKDAANLLNDALA   97 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHH-------HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3456788888888899999999998888764        12222111       88889999999999999999999844


Q ss_pred             cc-----CCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhc------CCCCCchhhHHHHHHHHHhhCChHHHHHHHH
Q 042593          129 CE-----YTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKR------GFNAFDIHVSNCLIDTYAKCGCIFSASKLFE  196 (352)
Q Consensus       129 ~~-----~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  196 (352)
                      ..     +-.| ...++..+...+...|++++|...+++..+.      +..+.....+..+..++...|++++|.+.|+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  177 (311)
T 3nf1_A           98 IREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQ  177 (311)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            31     2123 3457889999999999999999999998865      3333256778899999999999999999999


Q ss_pred             HhccC--------CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC-------CCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          197 DTSVD--------RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG-------LKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       197 ~~~~~--------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-------~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      +....        .| ...++..+...|...|++++|...++++.+..       ..+....                  
T Consensus       178 ~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~------------------  239 (311)
T 3nf1_A          178 RALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKP------------------  239 (311)
T ss_dssp             HHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CC------------------
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHH------------------
Confidence            87543        22 34678889999999999999999999987631       1110000                  


Q ss_pred             CCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          261 VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      .......+..+...+...+.+.+|...++..... +.+..+|..+...|...|++++|+..+.+.+.
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          240 IWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0001122333344444555566666666665544 44556777788888888888888877777653

>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=99.44  E-value=2.4e-12  Score=113.34  Aligned_cols=227  Identities=10%  Similarity=-0.033  Sum_probs=183.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCC-HHHHHHHHHHhHhccCCCC-Ch
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNR-SNEALALFRRMAACEYTEP-SE  136 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~~p-~~  136 (352)
                      ...|..+..++.+.|++++|++.|++..+-++..+.+       |+.+...+...|+ +++|+..|++....   .| +.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a-------~~~~g~~l~~~g~d~~eAl~~~~~al~l---~P~~~  166 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTV-------WHFRRVLLKSLQKDLHEEMNYITAIIEE---QPKNY  166 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHH-------HHHHHHHHHHTTCCHHHHHHHHHHHHHH---CTTCH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHH-------HHHHHHHHHHcccCHHHHHHHHHHHHHH---CCCCH
Confidence            4678888999999999999999999987533222222       8889999999996 99999999999542   34 45


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      ..|..+..++...|++++|...++.+.+....  +...|..+..++.+.|++++|+..|+++....| +...|+.+..++
T Consensus       167 ~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~--~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l  244 (382)
T 2h6f_A          167 QVWHHRRVLVEWLRDPSQELEFIADILNQDAK--NYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVI  244 (382)
T ss_dssp             HHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCcc--CHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            68999999999999999999999999998655  889999999999999999999999999876654 688999999999


Q ss_pred             Hc-CCCHHHH-----HHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcC--ChhHHHHH
Q 042593          216 AM-HGMGKEA-----VENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAG--RLEQAEEV  287 (352)
Q Consensus       216 ~~-~~~~~~a-----~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g--~~~~A~~~  287 (352)
                      .. .|..++|     +..+++.++..  |                        -+...|..+..++.+.|  +.++|.+.
T Consensus       245 ~~l~~~~~eA~~~~el~~~~~Al~l~--P------------------------~~~~a~~~l~~ll~~~g~~~~~~a~~~  298 (382)
T 2h6f_A          245 SNTTGYNDRAVLEREVQYTLEMIKLV--P------------------------HNESAWNYLKGILQDRGLSKYPNLLNQ  298 (382)
T ss_dssp             HHTTCSCSHHHHHHHHHHHHHHHHHS--T------------------------TCHHHHHHHHHHHTTTCGGGCHHHHHH
T ss_pred             HHhcCcchHHHHHHHHHHHHHHHHHC--C------------------------CCHHHHHHHHHHHHccCccchHHHHHH
Confidence            98 6665777     46676666521  2                        25678888888898888  68999999


Q ss_pred             HhcCCCC-CCCchhhHHHHHHHHhcc---------cccCcccccccc
Q 042593          288 ASGIPSQ-ITNVVVWRTGFLRLLINS---------YFFSPITLNSQR  324 (352)
Q Consensus       288 ~~~m~~~-~~~~~~~~~li~~~~~~g---------~~~~a~~~~~~~  324 (352)
                      ++++ .. +.+...+..+...|...|         ..++|++++.+.
T Consensus       299 ~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          299 LLDL-QPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEIL  344 (382)
T ss_dssp             HHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             HHHh-ccCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHH
Confidence            9888 44 666778889999998875         246777777665

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.43  E-value=3.1e-12  Score=116.41  Aligned_cols=211  Identities=11%  Similarity=0.012  Sum_probs=170.4

Q ss_pred             chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCCh-hHHHHHhccCCC--CC-chhHHHHHHHHHhHHHHHHHHHhcCCH
Q 042593           41 NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFL-KDSSKLFDELPE--RN-LVTWNVIITGLVKWTGIIDGYSRMNRS  116 (352)
Q Consensus        41 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~~li~~~~~~~~~  116 (352)
                      +.++..++...... +.+...+..+..++...|++ ++|++.|++..+  |+ ...          |..+...|...|++
T Consensus        85 ~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a----------~~~lg~~~~~~g~~  153 (474)
T 4abn_A           85 EKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEA----------WNQLGEVYWKKGDV  153 (474)
T ss_dssp             HHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHH----------HHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHH----------HHHHHHHHHHcCCH
Confidence            34444555443332 34678888999999999999 999999998765  43 334          88889999999999


Q ss_pred             HHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC---------CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh--
Q 042593          117 NEALALFRRMAACEYTEPSEITILAVLPAIWKN---------GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC--  185 (352)
Q Consensus       117 ~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~--  185 (352)
                      ++|.+.|++...   ..|+...+..+...+...         |++++|...+++..+....  +...|..+..+|...  
T Consensus       154 ~~A~~~~~~al~---~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~~~  228 (474)
T 4abn_A          154 TSAHTCFSGALT---HCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL--DGRSWYILGNAYLSLYF  228 (474)
T ss_dssp             HHHHHHHHHHHT---TCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh---hCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHH
Confidence            999999999844   347778888899999999         9999999999999887644  788899999999998  


Q ss_pred             ------CChHHHHHHHHHhccCCC----CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHH
Q 042593          186 ------GCIFSASKLFEDTSVDRK----NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKM  255 (352)
Q Consensus       186 ------g~~~~a~~~~~~~~~~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m  255 (352)
                            |++++|.+.|++.....|    +...|..+..+|...|++++|...|++..+..  |                 
T Consensus       229 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p-----------------  289 (474)
T 4abn_A          229 NTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD--P-----------------  289 (474)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-----------------
T ss_pred             hhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-----------------
Confidence                  999999999998876555    78889999999999999999999999988742  2                 


Q ss_pred             HHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          256 VEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       256 ~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                             -+...+..+..++...|+.++|.+.+.++..
T Consensus       290 -------~~~~a~~~l~~~~~~lg~~~eAi~~~~~~~~  320 (474)
T 4abn_A          290 -------AWPEPQQREQQLLEFLSRLTSLLESKGKTKP  320 (474)
T ss_dssp             -------TCHHHHHHHHHHHHHHHHHHHHHHHTTTCCH
T ss_pred             -------CCHHHHHHHHHHHHHHHHHHHHHHHhccccC
Confidence                   2556778888888899999999888777643

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.43  E-value=2.8e-12  Score=109.41  Aligned_cols=205  Identities=12%  Similarity=0.059  Sum_probs=163.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHh-------CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-------C
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKV-------GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------R   88 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-------~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~   88 (352)
                      +..++..+...+...|++++|..+++.+.+.       ..+.....+..+...|...|++++|...+++..+       +
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            5677888999999999999999999998874       3344567889999999999999999999998753       1


Q ss_pred             CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc-----CCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHH
Q 042593           89 NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE-----YTEPS-EITILAVLPAIWKNGEVRNCQLIHGYG  162 (352)
Q Consensus        89 ~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~  162 (352)
                      +... ....     |..+...+...|++++|...+++.....     +-.|+ ...+..+...+...|++++|...+++.
T Consensus       106 ~~~~-~~~~-----~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  179 (311)
T 3nf1_A          106 DHPA-VAAT-----LNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRA  179 (311)
T ss_dssp             TCHH-HHHH-----HHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CChH-HHHH-----HHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            1111 1111     8889999999999999999999984432     22233 347888999999999999999999998


Q ss_pred             Hhc------CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-----------------------------------
Q 042593          163 EKR------GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-----------------------------------  201 (352)
Q Consensus       163 ~~~------~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-----------------------------------  201 (352)
                      .+.      +..+....++..+..+|...|++++|.+.+++....                                   
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (311)
T 3nf1_A          180 LEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTS  259 (311)
T ss_dssp             HHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CC
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHH
Confidence            775      323325678889999999999999999999886531                                   


Q ss_pred             ---------------CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          202 ---------------RKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       202 ---------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                                     +.+..++..+..+|.+.|++++|...+++..+
T Consensus       260 ~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          260 FGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             SCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                           12356788899999999999999999998776

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.41  E-value=7.4e-12  Score=98.56  Aligned_cols=166  Identities=12%  Similarity=0.000  Sum_probs=94.0

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      ++..|..+...+.+.|++++|++.|+...+.. |-+..++..+..+|.+.|++++|...++....  |+ ...       
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------   75 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEA-------   75 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHH-------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHH-------
Confidence            44566666666666666666666666666554 33555666666666666666666666665543  21 122       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                         +..+...+...++++.|...+.+.....  +-+...+..+..++.+.|++++|...+++..+....  +..+|..+.
T Consensus        76 ---~~~~~~~~~~~~~~~~a~~~~~~a~~~~--~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~--~~~~~~~lg  148 (184)
T 3vtx_A           76 ---YYILGSANFMIDEKQAAIDALQRAIALN--TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPG--FIRAYQSIG  148 (184)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcch--hhhHHHHHH
Confidence               4445555556666666666666552211  123345555555566666666666666665555332  455555666


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCC
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      .+|.+.|++++|.+.|++..+..|
T Consensus       149 ~~~~~~g~~~~A~~~~~~al~~~p  172 (184)
T 3vtx_A          149 LAYEGKGLRDEAVKYFKKALEKEE  172 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhCCc
Confidence            666666666666666665544444

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.40  E-value=6.9e-11  Score=101.25  Aligned_cols=214  Identities=11%  Similarity=0.034  Sum_probs=171.1

Q ss_pred             chHHHHHHHHHHhCCCCchhhHHHHHHHHH-------hcCCh-------hHHHHHhccCCC---CCc-hhHHHHHHHHHh
Q 042593           41 NLGTQLHAVFSKVGFQSHVYVNTALGDMYV-------SLGFL-------KDSSKLFDELPE---RNL-VTWNVIITGLVK  102 (352)
Q Consensus        41 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~-------~~g~~-------~~a~~~~~~m~~---~~~-~~~~~~i~~~~~  102 (352)
                      +.|..+|+...... +.++..|..++..+.       +.|++       ++|..+|++..+   |+. ..          
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~----------  101 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL----------  101 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHH----------
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHH----------
Confidence            57788999998865 567788888888776       35886       899999998765   332 23          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-h-hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-I-TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      |..+...+.+.|++++|..+|++..+   +.|+. . .|..+...+.+.|++++|..++++..+....  +...|.....
T Consensus       102 ~~~~~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~--~~~~~~~~a~  176 (308)
T 2ond_A          102 YFAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART--RHHVYVTAAL  176 (308)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHT---SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTC--CTHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh---ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCC--CHHHHHHHHH
Confidence            88889999999999999999999944   34543 3 7999999999999999999999999887543  5566654443


Q ss_pred             HHH-hhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHh
Q 042593          181 TYA-KCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEE  258 (352)
Q Consensus       181 ~~~-~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~  258 (352)
                      ... ..|+.++|.++|+...+. +.+...|..++..+.+.|+.++|..+|++..+..                       
T Consensus       177 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-----------------------  233 (308)
T 2ond_A          177 MEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG-----------------------  233 (308)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSS-----------------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcc-----------------------
Confidence            322 369999999999988665 4468889999999999999999999999998752                       


Q ss_pred             cCCCC--ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          259 CEVLP--DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       259 ~~~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                       .+.|  ....|..++..+.+.|+.+.|..+++++...
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             1233  4568888899999999999999999887655

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.38  E-value=3e-10  Score=103.77  Aligned_cols=274  Identities=10%  Similarity=0.005  Sum_probs=171.4

Q ss_pred             cHHHHHHHHHh----cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh----cCChhHHHHHhccCCCC-CchhHHHH
Q 042593           26 TYSFLIRTCVT----LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS----LGFLKDSSKLFDELPER-NLVTWNVI   96 (352)
Q Consensus        26 ~~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~~   96 (352)
                      .+..+...+..    .+++++|...|+...+.|   ++..+..|...|..    .++.++|.+.|++..+. +...    
T Consensus       113 a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a----  185 (490)
T 2xm6_A          113 AQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWS----  185 (490)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH----
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHH----
Confidence            34444444444    445555555555544443   23344444444444    44555555555544322 2222    


Q ss_pred             HHHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCC
Q 042593           97 ITGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus        97 i~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~  168 (352)
                            +..+...|..    .++.++|...|++. ...+   +...+..+...+..    .++.++|...++...+.|  
T Consensus       186 ------~~~Lg~~y~~g~g~~~~~~~A~~~~~~a-~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~--  253 (490)
T 2xm6_A          186 ------CNQLGYMYSRGLGVERNDAISAQWYRKS-ATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG--  253 (490)
T ss_dssp             ------HHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT--
T ss_pred             ------HHHHHHHHhcCCCCCcCHHHHHHHHHHH-HHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC--
Confidence                  4455555555    56677777777666 3222   34455555555554    567777777777766653  


Q ss_pred             CCchhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcC-----CCHHHHHHHHHHHHhcCCCCC
Q 042593          169 AFDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMH-----GMGKEAVENFERMQKVGLKPN  239 (352)
Q Consensus       169 ~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~  239 (352)
                        +...+..+...|..    .++.++|.+.|+..... -+...+..+...|...     ++.++|...|++..+.|..  
T Consensus       254 --~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~-~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~~~--  328 (490)
T 2xm6_A          254 --NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQ-GNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGDA--  328 (490)
T ss_dssp             --CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTTCH--
T ss_pred             --CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcCCH--
Confidence              34455566666666    67788888888776433 3455666666667666     7888888888887776421  


Q ss_pred             cchhh-------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH----cCChhHHHHHHhcCCCCCCCchhhH
Q 042593          240 RSWRI-------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILER----AGRLEQAEEVASGIPSQITNVVVWR  302 (352)
Q Consensus       240 ~~~~~-------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~~~~~~~~~  302 (352)
                      ...+.             .++|..+|++..+. +   +...+..|...|..    .++.++|.+.|++.... .+...+.
T Consensus       329 ~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~-~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~-~~~~a~~  403 (490)
T 2xm6_A          329 TAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK-G---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQ-GLSAAQV  403 (490)
T ss_dssp             HHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-TCHHHHH
T ss_pred             HHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhC-CCHHHHH
Confidence            11111             56788888887775 3   56778888888888    88999999999887654 4667888


Q ss_pred             HHHHHHHh----cccccCcccccccchhhh
Q 042593          303 TGFLRLLI----NSYFFSPITLNSQRLFFF  328 (352)
Q Consensus       303 ~li~~~~~----~g~~~~a~~~~~~~~~~~  328 (352)
                      .|...|..    .+++++|...+.+.+..-
T Consensus       404 ~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          404 QLGEIYYYGLGVERDYVQAWAWFDTASTND  433 (490)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHCC
Confidence            88888887    788999998888887654

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.38  E-value=5.9e-12  Score=99.15  Aligned_cols=161  Identities=11%  Similarity=0.016  Sum_probs=99.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |..+...|.+.|++++|++.|++..+.   .| +..++..+..++.+.|++++|...+.........  +...+..+...
T Consensus         8 y~~lG~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~~~   82 (184)
T 3vtx_A            8 YMDIGDKKRTKGDFDGAIRAYKKVLKA---DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT--SAEAYYILGSA   82 (184)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC--CHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch--hHHHHHHHHHH
Confidence            666666666677777777777666332   23 3345666666666667777766666666655433  45556666666


Q ss_pred             HHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          182 YAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      +...++++.|.+.+.+..... .+...+..+...|.+.|++++|.+.|++..+..                         
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-------------------------  137 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-------------------------  137 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-------------------------
Confidence            666666666666666654433 345566666666666666666666666665521                         


Q ss_pred             CCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          261 VLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                       +-+..+|..+..+|.+.|++++|.+.|++..+.
T Consensus       138 -p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          138 -PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             -chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence             124556666666666666666666666655443

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.36  E-value=2.1e-10  Score=104.88  Aligned_cols=190  Identities=8%  Similarity=-0.007  Sum_probs=114.3

Q ss_pred             CcccHHHHHHHHHh----cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh----cCChhHHHHHhccCCCC-CchhH
Q 042593           23 DSFTYSFLIRTCVT----LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS----LGFLKDSSKLFDELPER-NLVTW   93 (352)
Q Consensus        23 ~~~~~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~-~~~~~   93 (352)
                      ++..+..+...+..    .++++.|.+.|+...+.|   ++..+..|...|..    .++.++|.+.|++..+. +... 
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a-  113 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQA-  113 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH-
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHH-
Confidence            55566666666666    677777777777777654   45566667777777    77777777777776543 2333 


Q ss_pred             HHHHHHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhc
Q 042593           94 NVIITGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKR  165 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~  165 (352)
                               +..|...|..    .+++++|...|++. ...+   +...+..+...|..    .++.++|...++...+.
T Consensus       114 ---------~~~Lg~~y~~g~g~~~~~~~A~~~~~~a-~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~  180 (490)
T 2xm6_A          114 ---------QQNLGVMYHEGNGVKVDKAESVKWFRLA-AEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ  180 (490)
T ss_dssp             ---------HHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             ---------HHHHHHHHHcCCCCCCCHHHHHHHHHHH-HHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence                     4455555555    56777777777766 3332   34455555555555    56666666666666654


Q ss_pred             CCCCCchhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCCHhhHHHHHHHHHc----CCCHHHHHHHHHHHHhc
Q 042593          166 GFNAFDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKNLVSWTTIISGFAM----HGMGKEAVENFERMQKV  234 (352)
Q Consensus       166 ~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~  234 (352)
                      |    +...+..+...|..    .++.++|.+.|++.... .+...+..+...|..    .++.++|...|++..+.
T Consensus       181 ~----~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~-~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~  252 (490)
T 2xm6_A          181 G----NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATS-GDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQ  252 (490)
T ss_dssp             T----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTT
T ss_pred             C----CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence            3    44555566666665    56666666666654322 234445555555543    55666666666655544

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.33  E-value=4.3e-12  Score=112.56  Aligned_cols=274  Identities=13%  Similarity=0.030  Sum_probs=198.5

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHh----CCCC-chhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKV----GFQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTW   93 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~   93 (352)
                      ..++..+...+...|++++|...++.....    +-.| ...++..+...|...|++++|...+++..+     ++... 
T Consensus        47 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-  125 (406)
T 3sf4_A           47 SAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVG-  125 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH-
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccc-
Confidence            357888899999999999999999987653    2122 356788899999999999999999998764     22111 


Q ss_pred             HHHHHHHHhHHHHHHHHHhcCC--------------------HHHHHHHHHHhHhc---cCCCCC-hhhHHHHHHHHHhC
Q 042593           94 NVIITGLVKWTGIIDGYSRMNR--------------------SNEALALFRRMAAC---EYTEPS-EITILAVLPAIWKN  149 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~~~~--------------------~~~a~~~~~~m~~~---~~~~p~-~~t~~~ll~~~~~~  149 (352)
                        ...   .+..+...+...|+                    +++|...+++....   .+-.|. ..++..+...+...
T Consensus       126 --~~~---~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  200 (406)
T 3sf4_A          126 --EAR---ALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLL  200 (406)
T ss_dssp             --HHH---HHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             --hHH---HHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHc
Confidence              011   18888899999999                    99999999886332   111121 34688888999999


Q ss_pred             CChhhHHHHHHHHHhcCCC----CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHHHHHHHHcC
Q 042593          150 GEVRNCQLIHGYGEKRGFN----AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTTIISGFAMH  218 (352)
Q Consensus       150 ~~~~~a~~~~~~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~li~~~~~~  218 (352)
                      |++++|...+++..+....    +....++..+..+|...|++++|.+.+++....   .++    ..++..+...|...
T Consensus       201 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  280 (406)
T 3sf4_A          201 GNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  280 (406)
T ss_dssp             TBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHh
Confidence            9999999999988754211    112347888999999999999999999986543   122    56788899999999


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCC-CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEV-LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---  294 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~-~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---  294 (352)
                      |++++|...+++..+...                    .. +. .....++..+..+|.+.|++++|.+.+++....   
T Consensus       281 g~~~~A~~~~~~a~~~~~--------------------~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~  339 (406)
T 3sf4_A          281 QDYEKAIDYHLKHLAIAQ--------------------EL-NDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISRE  339 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHH--------------------HT-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHH--------------------hc-CCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            999999999999776310                    00 11 112567888999999999999999998875443   


Q ss_pred             ----CCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          295 ----ITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       295 ----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                          .....++..+...+...|+...+..-..+.
T Consensus       340 ~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~  373 (406)
T 3sf4_A          340 VGDKSGELTARLNLSDLQMVLGLSYSTNNSIMSE  373 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTTSCC-------
T ss_pred             hcCCcchhHHHHHHHHHHHHhhHhHHHHHHHHHH
Confidence                123457777888888888886554444333

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.32  E-value=1.2e-11  Score=112.49  Aligned_cols=196  Identities=8%  Similarity=-0.076  Sum_probs=167.4

Q ss_pred             CcccHHHHHHHHHhcCCc-chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYP-NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~   99 (352)
                      +...+..+...+...|++ ++|.+.|+...+.. +.+...|..+..+|...|++++|.+.|++..+  |+...       
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~-------  172 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHCKNKVS-------  172 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCCCHHH-------
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCHHH-------
Confidence            677888889999999999 99999999999876 45688999999999999999999999999876  55333       


Q ss_pred             HHhHHHHHHHHHhc---------CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC--------CChhhHHHHHHHH
Q 042593          100 LVKWTGIIDGYSRM---------NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN--------GEVRNCQLIHGYG  162 (352)
Q Consensus       100 ~~~~~~li~~~~~~---------~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~--------~~~~~a~~~~~~~  162 (352)
                         |..+...+...         |++++|...|++.....  +-+...|..+..++...        |++++|...+++.
T Consensus       173 ---~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~a  247 (474)
T 4abn_A          173 ---LQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD--VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQA  247 (474)
T ss_dssp             ---HHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHH
Confidence               88888999999         99999999999985432  23466889999999988        9999999999999


Q ss_pred             HhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 042593          163 EKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERM  231 (352)
Q Consensus       163 ~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (352)
                      .+.... +.+...|..+..+|...|++++|.+.|++.....| +...+..+...+...|++++|.+.+.++
T Consensus       248 l~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          248 EKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             HHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            987541 02889999999999999999999999999866554 5678889999999999999998876554

>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=99.32  E-value=2.8e-10  Score=88.99  Aligned_cols=165  Identities=12%  Similarity=0.006  Sum_probs=136.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhh
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEIT  138 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t  138 (352)
                      ...+..+...+...|++++|.+.++++.+.++.....       |..+...+...|++++|...++++....  +.+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~   78 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDV-------ALHLGIAYVKTGAVDRGTELLERSLADA--PDNVKV   78 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHH-------HHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCCHHH
Confidence            4567778888999999999999999987632222111       7888889999999999999999984432  235668


Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHc
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAM  217 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~  217 (352)
                      +..+...+...|++++|...++.+.+....  +...+..+..++...|++++|.+.+++..... .+...+..+...+..
T Consensus        79 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~  156 (186)
T 3as5_A           79 ATVLGLTYVQVQKYDLAVPLLIKVAEANPI--NFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQ  156 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcCcH--hHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHH
Confidence            888899999999999999999999887543  77888899999999999999999999876554 467889999999999


Q ss_pred             CCCHHHHHHHHHHHHhc
Q 042593          218 HGMGKEAVENFERMQKV  234 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~~  234 (352)
                      .|++++|...+++..+.
T Consensus       157 ~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          157 MGRHEEALPHFKKANEL  173 (186)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHc
Confidence            99999999999998764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.31  E-value=2.8e-10  Score=97.39  Aligned_cols=198  Identities=9%  Similarity=-0.028  Sum_probs=158.3

Q ss_pred             CcccHHHHHHHHH-------hcCCc-------chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-
Q 042593           23 DSFTYSFLIRTCV-------TLSYP-------NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-   87 (352)
Q Consensus        23 ~~~~~~~ll~~~~-------~~g~~-------~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-   87 (352)
                      ++..|......+.       +.|++       ++|..+|+...+.-.+-+...|..++..+.+.|++++|.++|++..+ 
T Consensus        49 ~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~  128 (308)
T 2ond_A           49 HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI  128 (308)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Confidence            6667777777765       35887       89999999998842144567899999999999999999999999876 


Q ss_pred             -CC-ch-hHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHH-HhCCChhhHHHHHHHHH
Q 042593           88 -RN-LV-TWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAI-WKNGEVRNCQLIHGYGE  163 (352)
Q Consensus        88 -~~-~~-~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~-~~~~~~~~a~~~~~~~~  163 (352)
                       |+ .. .          |..+...+.+.|++++|..+|++..+ .. +++...|....... ...|+.++|..+|+...
T Consensus       129 ~p~~~~~~----------~~~~~~~~~~~~~~~~A~~~~~~a~~-~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al  196 (308)
T 2ond_A          129 EDIDPTLV----------YIQYMKFARRAEGIKSGRMIFKKARE-DA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGL  196 (308)
T ss_dssp             SSSCTHHH----------HHHHHHHHHHHHCHHHHHHHHHHHHT-ST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHH
T ss_pred             cccCccHH----------HHHHHHHHHHhcCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             33 22 3          88888889999999999999999944 22 23344454433332 23799999999999998


Q ss_pred             hcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CC--CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          164 KRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RK--NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       164 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +....  +...|..++..+.+.|+.++|..+|++....   .|  ....|..++....+.|+.++|..+++++.+.
T Consensus       197 ~~~p~--~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          197 KKYGD--IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHTT--CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HhCCC--cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            87433  7889999999999999999999999998764   44  4678999999999999999999999998875

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.31  E-value=4.2e-10  Score=110.38  Aligned_cols=255  Identities=11%  Similarity=0.068  Sum_probs=150.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGL  100 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~  100 (352)
                      +..+|..+.+++.+.|++++|.+.|...      -|...|..++.++.+.|++++|.+.+....+  ++...        
T Consensus      1104 ~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~I-------- 1169 (1630)
T 1xi4_A         1104 EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYV-------- 1169 (1630)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccc--------
Confidence            3456666777777777777777666442      3455666677777777777777777665433  22222        


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          101 VKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       101 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                        .+.++.+|++.+++++.....    .    .|+...|..+...|...|++++|..+|..          ...|..+..
T Consensus      1170 --dt~LafaYAKl~rleele~fI----~----~~n~ad~~~iGd~le~eg~YeeA~~~Y~k----------A~ny~rLA~ 1229 (1630)
T 1xi4_A         1170 --ETELIFALAKTNRLAELEEFI----N----GPNNAHIQQVGDRCYDEKMYDAAKLLYNN----------VSNFGRLAS 1229 (1630)
T ss_pred             --cHHHHHHHHhhcCHHHHHHHH----h----CCCHHHHHHHHHHHHhcCCHHHHHHHHHh----------hhHHHHHHH
Confidence              223444455555544322221    0    23334444555666666666666666654          235666677


Q ss_pred             HHHhhCChHHHHHHHHHhccCC--------------------------CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          181 TYAKCGCIFSASKLFEDTSVDR--------------------------KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~~~~~--------------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +|++.|+++.|.+.+++.....                          .+...+..++..|-+.|.+++|..+++.-...
T Consensus      1230 tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~L 1309 (1630)
T 1xi4_A         1230 TLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL 1309 (1630)
T ss_pred             HHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc
Confidence            7777777777776666543221                          23445667888888999999999999776643


Q ss_pred             CCCCCcchhh----------hHhHHHHHHHHHHhcCCCC------ChhhHHHHHHHHHHcCChhHHHHHH----------
Q 042593          235 GLKPNRSWRI----------GEEGLKFFDKMVEECEVLP------DIKHYGCLIDILERAGRLEQAEEVA----------  288 (352)
Q Consensus       235 ~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p------~~~~~~~li~~~~~~g~~~~A~~~~----------  288 (352)
                      . +.....+.          .+...+.++....+..++|      +...|.-++-.|.+.|+++.|....          
T Consensus      1310 e-raH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~ 1388 (1630)
T 1xi4_A         1310 E-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKE 1388 (1630)
T ss_pred             C-hhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhh
Confidence            3 12222222          4444444444444424433      4567889999999999999888332          


Q ss_pred             ---hcCCCCCCCchhhHHHHHHHHhcc
Q 042593          289 ---SGIPSQITNVVVWRTGFLRLLINS  312 (352)
Q Consensus       289 ---~~m~~~~~~~~~~~~li~~~~~~g  312 (352)
                         .+...+..|...|-..+.-|....
T Consensus      1389 ~~Fk~~i~kv~n~elyykai~Fyl~~~ 1415 (1630)
T 1xi4_A         1389 GQFKDIITKVANVELYYRAIQFYLEFK 1415 (1630)
T ss_pred             HHHHHHhcccccHHHHHHHHHHHHhhC
Confidence               222222457777777788887666

>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=99.28  E-value=1.1e-10  Score=91.19  Aligned_cols=162  Identities=15%  Similarity=0.028  Sum_probs=136.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...++++ .... +.+..++..+...+...|++++|...++.+.+....  +...+..+...+
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~   86 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLLEQV-YDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPD--NVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTTT-CCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHH-HHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC--CHHHHHHHHHHH
Confidence            777888899999999999999998 3322 235668888999999999999999999999887543  778888999999


Q ss_pred             HhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCC
Q 042593          183 AKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEV  261 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~  261 (352)
                      ...|++++|.+.+++.... +.+...+..+...+...|++++|...+++..+..                          
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--------------------------  140 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR--------------------------  140 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------------------
T ss_pred             HHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC--------------------------
Confidence            9999999999999987655 4567888889999999999999999999988742                          


Q ss_pred             CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          262 LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       262 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      +.+...+..+...+.+.|++++|.+.+++....
T Consensus       141 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          141 PNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            225678888999999999999999999876544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.28  E-value=2.5e-10  Score=100.86  Aligned_cols=254  Identities=7%  Similarity=-0.100  Sum_probs=185.1

Q ss_pred             HHHHHHHHhCCCCch----hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhcCC
Q 042593           45 QLHAVFSKVGFQSHV----YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRMNR  115 (352)
Q Consensus        45 ~~~~~m~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~~~  115 (352)
                      +.++.+.....+.+.    ..+-.....+...|++++|...|++..+     ++... .+..     |..+...|...|+
T Consensus        85 ~~~~~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~a~~-----~~~lg~~~~~~~~  158 (383)
T 3ulq_A           85 DLLLEIDKKQARLTGLLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIE-KAEF-----FFKMSESYYYMKQ  158 (383)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHH-HHHH-----HHHHHHHHHHTTC
T ss_pred             hHHHHHHhcCCCchhHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHH-HHHH-----HHHHHHHHHHcCC
Confidence            777776543311111    1222366677889999999999998754     33221 1111     8889999999999


Q ss_pred             HHHHHHHHHHhHhccCCCCC-----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCC----CCCchhhHHHHHHHHHhhC
Q 042593          116 SNEALALFRRMAACEYTEPS-----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGF----NAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       116 ~~~a~~~~~~m~~~~~~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~~li~~~~~~g  186 (352)
                      +++|...+++......-.++     ..+++.+..++...|++++|...+++..+...    .+....++..+..+|...|
T Consensus       159 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g  238 (383)
T 3ulq_A          159 TYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQS  238 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCC
Confidence            99999999998443222222     34788889999999999999999998875421    1112357889999999999


Q ss_pred             ChHHHHHHHHHhcc-----CC-C-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhc
Q 042593          187 CIFSASKLFEDTSV-----DR-K-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEEC  259 (352)
Q Consensus       187 ~~~~a~~~~~~~~~-----~~-~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~  259 (352)
                      ++++|.+.|++...     .. | ...++..+...|.+.|++++|...+++..+..                 .   .. 
T Consensus       239 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-----------------~---~~-  297 (383)
T 3ulq_A          239 QYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYS-----------------Q---KA-  297 (383)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----------------H---HH-
T ss_pred             CHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-----------------H---Hc-
Confidence            99999999998765     22 4 35678899999999999999999999977631                 0   11 


Q ss_pred             CCCCChhhHHHHHHHHHHcCC---hhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          260 EVLPDIKHYGCLIDILERAGR---LEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       260 ~~~p~~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      +.+.....+..+...|...|+   .++|..++++....+.....+..+...|...|++++|...+.+.+
T Consensus       298 ~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          298 GDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             TCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            212223346678888888998   889999998885433344577888999999999999999988876

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.28  E-value=2.1e-11  Score=104.90  Aligned_cols=244  Identities=14%  Similarity=0.062  Sum_probs=181.8

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHh----CCCC-chhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhH
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKV----GFQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTW   93 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~   93 (352)
                      ...+..+...+...|++++|.+.++...+.    +-.| ...++..+...+...|++++|...+++..+     ++....
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  122 (338)
T 3ro2_A           43 SAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGE  122 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHH
Confidence            467888999999999999999999987643    2122 356788999999999999999999988753     221111


Q ss_pred             HHHHHHHHhHHHHHHHHHhcCC--------------------HHHHHHHHHHhHhc---cCCCCC-hhhHHHHHHHHHhC
Q 042593           94 NVIITGLVKWTGIIDGYSRMNR--------------------SNEALALFRRMAAC---EYTEPS-EITILAVLPAIWKN  149 (352)
Q Consensus        94 ~~~i~~~~~~~~li~~~~~~~~--------------------~~~a~~~~~~m~~~---~~~~p~-~~t~~~ll~~~~~~  149 (352)
                       .  .   .+..+...+...|+                    +++|...+++....   .+..|. ..++..+...+...
T Consensus       123 -~--~---~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~  196 (338)
T 3ro2_A          123 -A--R---ALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLL  196 (338)
T ss_dssp             -H--H---HHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             -H--H---HHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh
Confidence             1  1   18888899999999                    99999999886322   111111 34688888899999


Q ss_pred             CChhhHHHHHHHHHhcCC----CCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHHHHHHHHcC
Q 042593          150 GEVRNCQLIHGYGEKRGF----NAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTTIISGFAMH  218 (352)
Q Consensus       150 ~~~~~a~~~~~~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~li~~~~~~  218 (352)
                      |++++|...+++..+...    .+....++..+..++...|++++|.+.+++....   ..+    ..++..+...+...
T Consensus       197 ~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  276 (338)
T 3ro2_A          197 GNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  276 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHh
Confidence            999999999998875421    1112347888999999999999999999986543   122    56788889999999


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      |++++|...+++..+..                    ...........++..+...|.+.|++++|...+++...
T Consensus       277 g~~~~A~~~~~~a~~~~--------------------~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  331 (338)
T 3ro2_A          277 QDYEKAIDYHLKHLAIA--------------------QELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  331 (338)
T ss_dssp             TCHHHHHHHHHHHHHHH--------------------HHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHH--------------------HhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            99999999999877631                    01101112345778899999999999999999987654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.27  E-value=1.3e-11  Score=109.98  Aligned_cols=244  Identities=11%  Similarity=0.023  Sum_probs=183.3

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHh----C-CCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKV----G-FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWN   94 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~   94 (352)
                      ..+..+...+...|++++|...++...+.    + .+.....+..+...|...|++++|...+++..+     .+... .
T Consensus        87 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~  165 (411)
T 4a1s_A           87 AIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLS-E  165 (411)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH-H
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHH-H
Confidence            47888999999999999999999988764    1 123457788999999999999999999998754     11111 1


Q ss_pred             HHHHHHHhHHHHHHHHHhcCC-----------------HHHHHHHHHHhHhcc---CCCCC-hhhHHHHHHHHHhCCChh
Q 042593           95 VIITGLVKWTGIIDGYSRMNR-----------------SNEALALFRRMAACE---YTEPS-EITILAVLPAIWKNGEVR  153 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~-----------------~~~a~~~~~~m~~~~---~~~p~-~~t~~~ll~~~~~~~~~~  153 (352)
                      ..     .+..+...|...|+                 +++|...+++.....   +-.+. ..++..+...+...|+++
T Consensus       166 ~~-----~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  240 (411)
T 4a1s_A          166 GR-----ALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQ  240 (411)
T ss_dssp             HH-----HHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HH-----HHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChH
Confidence            11     18888899999999                 999999988863221   11121 247888889999999999


Q ss_pred             hHHHHHHHHHhcCCCC----CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-------CHhhHHHHHHHHHcCCCHH
Q 042593          154 NCQLIHGYGEKRGFNA----FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-------NLVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       154 ~a~~~~~~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~~~~li~~~~~~~~~~  222 (352)
                      +|...+++..+.....    .....+..+..+|...|++++|.+.+++.....+       ...++..+...|...|+++
T Consensus       241 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  320 (411)
T 4a1s_A          241 AAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFN  320 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            9999999887643211    0133788899999999999999999998654311       2567888999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          223 EAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       223 ~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      +|...+++..+..                 ....   .......++..+..+|.+.|+.++|.+.+++....
T Consensus       321 ~A~~~~~~al~~~-----------------~~~~---~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          321 TAIEYHNRHLAIA-----------------QELG---DRIGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHHHHHHHHHHHH-----------------HHHT---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-----------------HHCC---ChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            9999999977631                 1100   11113457888999999999999999999876543

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.26  E-value=7.9e-10  Score=108.48  Aligned_cols=169  Identities=12%  Similarity=0.087  Sum_probs=75.8

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      ..-+...+...|.+++|..+|+...     -.....+.++.   ..+++++|.++.++...  ..+          |..+
T Consensus      1052 ~~eIA~Iai~lglyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aervn~--p~v----------WsqL 1111 (1630)
T 1xi4_A         1052 APDIANIAISNELFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERCNE--PAV----------WSQL 1111 (1630)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhcCC--HHH----------HHHH
Confidence            4445666777777777777777641     11111222221   34445555555544422  112          4444


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      ..++.+.|++++|.+-|.+.       -|...|..++.++.+.|++++|.+.+....+...   ++...+.++.+|++.+
T Consensus      1112 AKAql~~G~~kEAIdsYiKA-------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~---e~~Idt~LafaYAKl~ 1181 (1630)
T 1xi4_A         1112 AKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR---ESYVETELIFALAKTN 1181 (1630)
T ss_pred             HHHHHhCCCHHHHHHHHHhc-------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcc---cccccHHHHHHHHhhc
Confidence            55555555555555554333       2333444455555555555555555544443321   1122223444444444


Q ss_pred             ChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          187 CIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      ++++...+.     ..++...|..+...|...|++++|..+|..
T Consensus      1182 rleele~fI-----~~~n~ad~~~iGd~le~eg~YeeA~~~Y~k 1220 (1630)
T 1xi4_A         1182 RLAELEEFI-----NGPNNAHIQQVGDRCYDEKMYDAAKLLYNN 1220 (1630)
T ss_pred             CHHHHHHHH-----hCCCHHHHHHHHHHHHhcCCHHHHHHHHHh
Confidence            444322221     123333344444444444444444444444

>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=99.26  E-value=1.4e-10  Score=97.26  Aligned_cols=194  Identities=11%  Similarity=0.047  Sum_probs=149.1

Q ss_pred             HHhcCCcchHHHHHHHHHHh-------CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-------C-CchhHHHHHH
Q 042593           34 CVTLSYPNLGTQLHAVFSKV-------GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------R-NLVTWNVIIT   98 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~-------~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~-~~~~~~~~i~   98 (352)
                      ....|++++|...++...+.       ..+....++..+...|...|++++|+..+++..+       + +.....+   
T Consensus        11 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~---   87 (283)
T 3edt_B           11 SSGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAAT---   87 (283)
T ss_dssp             --CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHH---
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHH---
Confidence            34678899999988887752       2133567899999999999999999999998753       1 1222111   


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc-----CCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhc------C
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACE-----YTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKR------G  166 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~  166 (352)
                          |..+...+...|++++|...|++.....     .-.|+ ..++..+...+...|++++|...+++..+.      +
T Consensus        88 ----~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  163 (283)
T 3edt_B           88 ----LNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGP  163 (283)
T ss_dssp             ----HHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCT
T ss_pred             ----HHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCC
Confidence                8899999999999999999999984331     11232 457889999999999999999999998876      2


Q ss_pred             CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---------------------------------------------
Q 042593          167 FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---------------------------------------------  201 (352)
Q Consensus       167 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---------------------------------------------  201 (352)
                      ..|....++..+..+|.+.|++++|.+.+++....                                             
T Consensus       164 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (283)
T 3edt_B          164 DDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKA  243 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------C
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHh
Confidence            23325678889999999999999999999876431                                             


Q ss_pred             ----CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          202 ----RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       202 ----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                          .| ...++..+...|...|++++|...+++..+.
T Consensus       244 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          244 CKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                11 2356778889999999999999999987753

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.26  E-value=6.2e-10  Score=100.91  Aligned_cols=280  Identities=8%  Similarity=-0.111  Sum_probs=176.5

Q ss_pred             cccHHHHHHHHHhc--CCcchHHHHHHHHHHhCCCCchhhHHHHHHH---HHhcCChhHHHHHhccCCC--CC-chhHHH
Q 042593           24 SFTYSFLIRTCVTL--SYPNLGTQLHAVFSKVGFQSHVYVNTALGDM---YVSLGFLKDSSKLFDELPE--RN-LVTWNV   95 (352)
Q Consensus        24 ~~~~~~ll~~~~~~--g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~---~~~~g~~~~a~~~~~~m~~--~~-~~~~~~   95 (352)
                      ..+++....++...  +++++|.+.|+...+.. |-++..+..+..+   +...++.++|++.+++..+  |+ ...   
T Consensus       136 ~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~---  211 (472)
T 4g1t_A          136 PELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYL---  211 (472)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHH---
T ss_pred             HHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHH---
Confidence            45666666666654  56899999999998875 3355555555554   4456778888888877653  33 333   


Q ss_pred             HHHHHHhHHHHHHHH----HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc
Q 042593           96 IITGLVKWTGIIDGY----SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD  171 (352)
Q Consensus        96 ~i~~~~~~~~li~~~----~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  171 (352)
                             +..+...+    ...++.++|.+.+++.....  +.+..++..+...+...|++++|...+++..+....  +
T Consensus       212 -------~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~--~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~--~  280 (472)
T 4g1t_A          212 -------KVLLALKLHKMREEGEEEGEGEKLVEEALEKA--PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPN--N  280 (472)
T ss_dssp             -------HHHHHHHHHHCC------CHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--C
T ss_pred             -------HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC--ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCC--h
Confidence                   33333333    34567888999998874322  234567888899999999999999999998887544  6


Q ss_pred             hhhHHHHHHHHHhh-------------------CChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 042593          172 IHVSNCLIDTYAKC-------------------GCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERM  231 (352)
Q Consensus       172 ~~~~~~li~~~~~~-------------------g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (352)
                      ..++..+..+|...                   +..+.|...|+..... +.+..++..+...|...|++++|.+.|++.
T Consensus       281 ~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~ka  360 (472)
T 4g1t_A          281 AYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKE  360 (472)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHH
Confidence            77777776666432                   3467788888876554 445677888889999999999999999998


Q ss_pred             HhcCCCCCcch---hh-----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CC
Q 042593          232 QKVGLKPNRSW---RI-----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-IT  296 (352)
Q Consensus       232 ~~~~~~p~~~~---~~-----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~  296 (352)
                      .+....+....   +.           .++|...|++..+.   .|+.......+         ..+.++++..... +.
T Consensus       361 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i---~~~~~~~~~~~---------~~l~~~~~~~l~~~p~  428 (472)
T 4g1t_A          361 FSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI---NQKSREKEKMK---------DKLQKIAKMRLSKNGA  428 (472)
T ss_dssp             HHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS---CCCCHHHHHHH---------HHHHHHHHHHHHHCC-
T ss_pred             HhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CcccHHHHHHH---------HHHHHHHHHHHHhCCC
Confidence            87654443221   00           67788888887753   45543332222         2334444433333 55


Q ss_pred             CchhhHHHHHHHHhcccccCcccccccchhhhhh
Q 042593          297 NVVVWRTGFLRLLINSYFFSPITLNSQRLFFFPA  330 (352)
Q Consensus       297 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  330 (352)
                      +..+|..+...|...|++++|++.+.+++..-|.
T Consensus       429 ~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~  462 (472)
T 4g1t_A          429 DSEALHVLAFLQELNEKMQQADEDSERGLESGSL  462 (472)
T ss_dssp             CTTHHHHHHHHHHHHHHCC---------------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            7789999999999999999999999999864443

>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=99.23  E-value=1.3e-10  Score=110.42  Aligned_cols=160  Identities=9%  Similarity=0.048  Sum_probs=92.3

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      ..+++.|..+|.+.|++++|++.|++..+  |+ ..+          |+.+..+|.+.|++++|++.|++..+.   .|+
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a----------~~nLg~~l~~~g~~~eA~~~~~~Al~l---~P~   75 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAA----------HSNLASVLQQQGKLQEALMHYKEAIRI---SPT   75 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCC
Confidence            45555566666666666666666655543  22 222          555556666666666666666665331   233


Q ss_pred             -hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHH
Q 042593          136 -EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIIS  213 (352)
Q Consensus       136 -~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~  213 (352)
                       ...|..+..++.+.|++++|...+++..+....  +...|+.+..+|.+.|++++|++.|++..+..| +...|..+..
T Consensus        76 ~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l~P~--~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~  153 (723)
T 4gyw_A           76 FADAYSNMGNTLKEMQDVQGALQCYTRAIQINPA--FADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAH  153 (723)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhh
Confidence             345666666666666666666666666555432  556666666666666666666666666544433 3556666666


Q ss_pred             HHHcCCCHHHHHHHHHHHHh
Q 042593          214 GFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ++...|++++|.+.+++..+
T Consensus       154 ~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          154 CLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHHHTTCCTTHHHHHHHHHH
T ss_pred             HHHhcccHHHHHHHHHHHHH
Confidence            66666666666666655443

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.23  E-value=4.7e-10  Score=99.04  Aligned_cols=231  Identities=6%  Similarity=-0.115  Sum_probs=171.7

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHh----CCCC-chhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKV----GFQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITG   99 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~   99 (352)
                      ....+...|++++|...++...+.    +-++ ...++..+..+|...|++++|...+++..+     ++.....+  . 
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~--~-  185 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLL--Q-  185 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHH--H-
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHH--H-
Confidence            455677899999999999998864    2112 346789999999999999999999888753     22111111  1 


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh----hhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCCCCc
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE----ITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFNAFD  171 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~  171 (352)
                        .++.+...|...|++++|...|++......-.++.    .++..+...+...|++++|...+++..+.    +..|..
T Consensus       186 --~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~  263 (383)
T 3ulq_A          186 --CHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSL  263 (383)
T ss_dssp             --HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGH
T ss_pred             --HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhH
Confidence              18889999999999999999999884332211222    37888999999999999999999988773    332326


Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccC-----CC-CHhhHHHHHHHHHcCCC---HHHHHHHHHHHHhcCCCCCcch
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVD-----RK-NLVSWTTIISGFAMHGM---GKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-----~~-~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      ..++..+..+|.+.|++++|.+.+++....     .| ....++.+...+...|+   +++|..++++..          
T Consensus       264 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~----------  333 (383)
T 3ulq_A          264 PQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKM----------  333 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTT----------
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCc----------
Confidence            778999999999999999999999986543     12 12335677788888898   666666666541          


Q ss_pred             hhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          243 RIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       243 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                                       ..+.....+..+...|.+.|++++|.+.+++..
T Consensus       334 -----------------~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          334 -----------------LYADLEDFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             -----------------CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -----------------CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                             112234577789999999999999999887653

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.22  E-value=4.5e-10  Score=99.00  Aligned_cols=255  Identities=7%  Similarity=-0.061  Sum_probs=182.6

Q ss_pred             HHHHHHHHhCCCCch----hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhcCC
Q 042593           45 QLHAVFSKVGFQSHV----YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRMNR  115 (352)
Q Consensus        45 ~~~~~m~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~~~  115 (352)
                      +.++.+.....+.+.    ..+-.....+...|++++|...|++..+     ++... .+.+     +..+...|...|+
T Consensus        83 ~~l~~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~a~~-----~~~lg~~y~~~~~  156 (378)
T 3q15_A           83 ELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIE-KAEF-----HFKVAEAYYHMKQ  156 (378)
T ss_dssp             HHHHHHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHH-HHHH-----HHHHHHHHHHTTC
T ss_pred             HHHHHHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHH-HHHH-----HHHHHHHHHHcCC
Confidence            666666543312111    1233445566789999999999998754     23211 1111     8889999999999


Q ss_pred             HHHHHHHHHHhHhccCCCCC-----hhhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhC
Q 042593          116 SNEALALFRRMAACEYTEPS-----EITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       116 ~~~a~~~~~~m~~~~~~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g  186 (352)
                      ++.|...+++......-.++     ..+++.+..++...|++++|...+++..+.    +..+....++..+..+|...|
T Consensus       157 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~  236 (378)
T 3q15_A          157 THVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSG  236 (378)
T ss_dssp             HHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC
Confidence            99999999987433222222     347888999999999999999999888753    222213457888999999999


Q ss_pred             ChHHHHHHHHHhcc-----CCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          187 CIFSASKLFEDTSV-----DRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       187 ~~~~a~~~~~~~~~-----~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      ++++|.+.|++...     ..| ...++..+...+.+.|++++|...+++..+.....                     +
T Consensus       237 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~---------------------~  295 (378)
T 3q15_A          237 DDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITAR---------------------S  295 (378)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTT---------------------C
T ss_pred             CHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc---------------------C
Confidence            99999999998765     433 36778889999999999999999999988743221                     1


Q ss_pred             CCCChhhHHHHHHHHHHcCC---hhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          261 VLPDIKHYGCLIDILERAGR---LEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       261 ~~p~~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      .+.....+..+...|...|+   ..+|...+++....+.....+..+...|...|++++|...+.+.+.
T Consensus       296 ~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          296 HKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             CSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            22223345666667777777   8888888887543323345667788889999999999999888764

>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=99.20  E-value=1.9e-10  Score=109.16  Aligned_cols=162  Identities=9%  Similarity=-0.019  Sum_probs=142.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +..+|+.+..++.+.|++++|++.|++..+.. +-+..++..|..+|.+.|++++|++.|++..+  |+ ...       
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a-------   79 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADA-------   79 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH-------
Confidence            57889999999999999999999999999876 44678999999999999999999999999865  43 344       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                         |+.+..++...|++++|++.|++..+.   .|+ ...|..+..++.+.|++++|...+++..+....  +...+..+
T Consensus        80 ---~~nLg~~l~~~g~~~~A~~~~~kAl~l---~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~--~~~a~~~L  151 (723)
T 4gyw_A           80 ---YSNMGNTLKEMQDVQGALQCYTRAIQI---NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD--FPDAYCNL  151 (723)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC--CHHHHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--ChHHHhhh
Confidence               899999999999999999999998553   354 568999999999999999999999999988644  78899999


Q ss_pred             HHHHHhhCChHHHHHHHHHhcc
Q 042593          179 IDTYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~  200 (352)
                      ..+|...|++++|.+.+++..+
T Consensus       152 ~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          152 AHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHHHHHTTCCTTHHHHHHHHHH
T ss_pred             hhHHHhcccHHHHHHHHHHHHH
Confidence            9999999999999999887643

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.20  E-value=8.6e-10  Score=96.89  Aligned_cols=272  Identities=11%  Similarity=-0.008  Sum_probs=187.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHhCCCCch----hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHH
Q 042593           27 YSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV----YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVII   97 (352)
Q Consensus        27 ~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i   97 (352)
                      .......+...|++++|...++......-..+.    .+++.+...+...|++++|.+.+++..+     .+... ..  
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~--   93 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHY-AL--   93 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH-HH--
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHH-HH--
Confidence            344455667899999999999998875422222    2567778888899999999999998764     22211 11  


Q ss_pred             HHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc---CCC--CC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC--
Q 042593           98 TGLVKWTGIIDGYSRMNRSNEALALFRRMAACE---YTE--PS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA--  169 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~~--p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--  169 (352)
                      .   .++.+...+...|++++|...+++.....   +..  |. ...+..+...+...|++++|...+++..+.....  
T Consensus        94 ~---~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  170 (373)
T 1hz4_A           94 W---SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQP  170 (373)
T ss_dssp             H---HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCG
T ss_pred             H---HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCc
Confidence            1   16677788999999999999999874322   211  22 2356678888999999999999999887654321  


Q ss_pred             -CchhhHHHHHHHHHhhCChHHHHHHHHHhccC--CC-CHhhHH-----HHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          170 -FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--RK-NLVSWT-----TIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       170 -~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~-~~~~~~-----~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                       .....+..+...+...|++++|...+++....  .+ +...+.     ..+..+...|++++|...+++..+..  |. 
T Consensus       171 ~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~--~~-  247 (373)
T 1hz4_A          171 QQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPE--FA-  247 (373)
T ss_dssp             GGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCC--CT-
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCC--CC-
Confidence             02356778889999999999999999986432  21 111222     23345779999999999998876532  11 


Q ss_pred             chhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CC---Cc-hhhHHHHHHHHhccc
Q 042593          241 SWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---IT---NV-VVWRTGFLRLLINSY  313 (352)
Q Consensus       241 ~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~---~~-~~~~~li~~~~~~g~  313 (352)
                                         ........+..+...+...|++++|...+++....   .+   +. ..+..+...+...|+
T Consensus       248 -------------------~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~  308 (373)
T 1hz4_A          248 -------------------NNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGR  308 (373)
T ss_dssp             -------------------TCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             -------------------cchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCC
Confidence                               00111234566778888889999888888766433   11   11 255666777888888


Q ss_pred             ccCcccccccchh
Q 042593          314 FFSPITLNSQRLF  326 (352)
Q Consensus       314 ~~~a~~~~~~~~~  326 (352)
                      .++|...+.+.+.
T Consensus       309 ~~~A~~~l~~al~  321 (373)
T 1hz4_A          309 KSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            8888888877754

>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=3.2e-10  Score=95.01  Aligned_cols=158  Identities=13%  Similarity=0.029  Sum_probs=122.1

Q ss_pred             HhcCChhHHHHHhccCCC-------CC-chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc-----CCCCC-
Q 042593           70 VSLGFLKDSSKLFDELPE-------RN-LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACE-----YTEPS-  135 (352)
Q Consensus        70 ~~~g~~~~a~~~~~~m~~-------~~-~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~-  135 (352)
                      ...|++++|+.+|++..+       ++ .....+       |..+...+...|++++|...+++.....     +-.|. 
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~-------~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   84 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATM-------LNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAV   84 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH-------HHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHH
Confidence            356777777777776653       23 222222       8889999999999999999999984431     22232 


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhc------CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--------
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKR------GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--------  201 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--------  201 (352)
                      ..++..+...+...|++++|...+++..+.      ...|....++..+..+|...|++++|.+.+++....        
T Consensus        85 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  164 (283)
T 3edt_B           85 AATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPD  164 (283)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCC
Confidence            457899999999999999999999998765      222325778899999999999999999999987543        


Q ss_pred             CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          202 RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       202 ~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .| ...++..+...|...|++++|...+++..+.
T Consensus       165 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          165 DPNVAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            33 3567888999999999999999999998763

>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=99.14  E-value=1.2e-09  Score=88.92  Aligned_cols=195  Identities=11%  Similarity=0.043  Sum_probs=147.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      |+..+......+...|++++|...|+...+..-+++...+..+..++...|++++|++.|++..+.++.....       
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~-------   78 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANA-------   78 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHH-------
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHH-------
Confidence            6788999999999999999999999999988743777888789999999999999999999987533322222       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-------hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC--chh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-------ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF--DIH  173 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~  173 (352)
                      |..+...+...|++++|...|++..+...  .+.       ..|..+...+...|++++|...+++..+.  .|.  +..
T Consensus        79 ~~~l~~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~  154 (228)
T 4i17_A           79 YIGKSAAYRDMKNNQEYIATLTEGIKAVP--GNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTD  154 (228)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCC--CcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHH
Confidence            88899999999999999999999854332  223       45778888889999999999999998876  453  356


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      .+..+..+|...|+.     .++++... ..+...|.....  ...+.+++|...+++..+..
T Consensus       155 ~~~~l~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~--~~~~~~~~A~~~~~~a~~l~  210 (228)
T 4i17_A          155 ALYSLGVLFYNNGAD-----VLRKATPLASSNKEKYASEKA--KADAAFKKAVDYLGEAVTLS  210 (228)
T ss_dssp             HHHHHHHHHHHHHHH-----HHHHHGGGTTTCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHH-----HHHHHHhcccCCHHHHHHHHH--HHHHHHHHHHHHHHHHhhcC
Confidence            777888888766543     33443322 234444544432  34456889999999888753

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.14  E-value=2.6e-09  Score=90.62  Aligned_cols=206  Identities=7%  Similarity=-0.085  Sum_probs=149.9

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHh----CCCCc-hhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKV----GFQSH-VYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVII   97 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i   97 (352)
                      ..|......+...|++++|.+.|+...+.    |-+++ ..+|+.+..+|.+.|++++|+..|++..+  ++...+....
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            46888888999999999999999988764    32222 56899999999999999999999988754  1110001011


Q ss_pred             HHHHhHHHHHHHHHhc-CCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch
Q 042593           98 TGLVKWTGIIDGYSRM-NRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI  172 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  172 (352)
                      .   .|+.+...|... |++++|+..|++......-..+    ..++..+...+.+.|++++|...+++..+........
T Consensus       118 ~---~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~  194 (292)
T 1qqe_A          118 N---FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLS  194 (292)
T ss_dssp             H---HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTT
T ss_pred             H---HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcc
Confidence            1   188889999996 9999999999998442211111    3468889999999999999999999999876543121


Q ss_pred             -----hhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH------hhHHHHHHHHH--cCCCHHHHHHHHHHHHh
Q 042593          173 -----HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL------VSWTTIISGFA--MHGMGKEAVENFERMQK  233 (352)
Q Consensus       173 -----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~------~~~~~li~~~~--~~~~~~~a~~~~~~m~~  233 (352)
                           ..+..+..++...|++++|...|++.....|+.      ..+..++.++.  ..+++++|...|+++..
T Consensus       195 ~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~  268 (292)
T 1qqe_A          195 QWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (292)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             cHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCc
Confidence                 156788889999999999999999987665532      23445566664  45678888888876543

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.13  E-value=7.5e-09  Score=95.47  Aligned_cols=213  Identities=11%  Similarity=0.057  Sum_probs=167.0

Q ss_pred             hHHHHHHHHHHhCCCCchhhHHHHHHHHHh-------cCChh-------HHHHHhccCCC---CC-chhHHHHHHHHHhH
Q 042593           42 LGTQLHAVFSKVGFQSHVYVNTALGDMYVS-------LGFLK-------DSSKLFDELPE---RN-LVTWNVIITGLVKW  103 (352)
Q Consensus        42 ~a~~~~~~m~~~~~~~~~~~~~~li~~~~~-------~g~~~-------~a~~~~~~m~~---~~-~~~~~~~i~~~~~~  103 (352)
                      .+..+|+...... +.++..|..++..+.+       .|+++       +|..+|++..+   |+ ...          |
T Consensus       256 ~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l----------~  324 (530)
T 2ooe_A          256 RVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL----------Y  324 (530)
T ss_dssp             HHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHH----------H
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHH----------H
Confidence            6677888888764 5578888888888876       79987       89999998764   43 233          8


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh--hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEPSE--ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      ..++..+.+.|++++|..+|+++..   +.|+.  ..|...+..+.+.|++++|..+++...+....  +...|......
T Consensus       325 ~~~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~--~~~~~~~~a~~  399 (530)
T 2ooe_A          325 FAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART--RHHVYVTAALM  399 (530)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTC--CTHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhC---ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCC--chHHHHHHHHH
Confidence            8888999999999999999999954   34543  47888888888999999999999999876432  33444332222


Q ss_pred             -HHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhc
Q 042593          182 -YAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEEC  259 (352)
Q Consensus       182 -~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~  259 (352)
                       +...|+.++|.++|+...+..| +...|..++..+.+.|+.++|..+|++....+.                       
T Consensus       400 ~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~-----------------------  456 (530)
T 2ooe_A          400 EYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS-----------------------  456 (530)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCC-----------------------
T ss_pred             HHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccC-----------------------
Confidence             3468999999999998766644 688999999999999999999999999887531                       


Q ss_pred             CCCC--ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          260 EVLP--DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       260 ~~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                       ..|  ....|...+....+.|+.+.+..+.+++...
T Consensus       457 -~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          457 -LPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             -SCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             122  3457888888888999999999998887654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.12  E-value=9.6e-09  Score=86.41  Aligned_cols=198  Identities=15%  Similarity=0.016  Sum_probs=142.2

Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCc--hhHHHHHHHHHhHHHHHHHHHhcCCHHHHH
Q 042593           43 GTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNL--VTWNVIITGLVKWTGIIDGYSRMNRSNEAL  120 (352)
Q Consensus        43 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~--~~~~~~i~~~~~~~~li~~~~~~~~~~~a~  120 (352)
                      +...++...+.+ +++..++..+..++...|++++|++++.+...++.  .....       +..++..+.+.|+.+.|.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea-------~~l~vqi~L~~~r~d~A~  156 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTEL-------LLLAIEVALLNNNVSTAS  156 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHH-------HHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHH-------HHHHHHHHHHCCCHHHHH
Confidence            667777776655 55666667888999999999999999998754432  22222       777888999999999999


Q ss_pred             HHHHHhHhccCCCC-----ChhhHHHHHHHHH--h--CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHH
Q 042593          121 ALFRRMAACEYTEP-----SEITILAVLPAIW--K--NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       121 ~~~~~m~~~~~~~p-----~~~t~~~ll~~~~--~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      +.+++| ...  .|     +..+...+..++.  .  .++..+|..+|+++.+..  | +...-..++.++.+.|++++|
T Consensus       157 k~l~~~-~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p-~~~~~~lLln~~~~~g~~~eA  230 (310)
T 3mv2_B          157 TIFDNY-TNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--P-TWKTQLGLLNLHLQQRNIAEA  230 (310)
T ss_dssp             HHHHHH-HHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--C-SHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHH-Hhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--C-CcccHHHHHHHHHHcCCHHHH
Confidence            999999 433  46     3566666666633  2  338999999999987653  2 323334555589999999999


Q ss_pred             HHHHHHhccC-----------CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-hHhHHHHHHHHHHh
Q 042593          192 SKLFEDTSVD-----------RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-GEEGLKFFDKMVEE  258 (352)
Q Consensus       192 ~~~~~~~~~~-----------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-~~~a~~~~~~m~~~  258 (352)
                      ++.++.+.+.           +.|+.+...+|......|+  +|.+++.++++.  .|+..... ..+....|+++...
T Consensus       231 e~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~--~P~hp~i~d~~~k~~~Fd~~~~k  305 (310)
T 3mv2_B          231 QGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL--DHEHAFIKHHQEIDAKFDELVRK  305 (310)
T ss_dssp             HHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT--TCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh--CCCChHHHHHHHHHHHHHHHHHH
Confidence            9999876542           3367777566666666676  889999999884  46665555 77777777777764

>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=99.11  E-value=1.7e-09  Score=88.13  Aligned_cols=161  Identities=10%  Similarity=-0.127  Sum_probs=124.8

Q ss_pred             CChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHH
Q 042593          134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTII  212 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li  212 (352)
                      .|...+......+...|++++|...++...+....+ +...+..+..++...|++++|.+.|++.....| +...|..+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~-~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQ-DSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCC-CcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHH
Confidence            345678888888899999999999999998877534 667777789999999999999999998876655 567788899


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          213 SGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                      .+|...|++++|...+++..+..  |+...+.        ..         -...|..+...+.+.|++++|.+.+++..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~--------~~---------~~~~~~~~g~~~~~~~~~~~A~~~~~~al  144 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAV--PGNATIE--------KL---------YAIYYLKEGQKFQQAGNIEKAEENYKHAT  144 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHH--------HH---------HHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC--CCcHHHH--------HH---------HHHHHHHHhHHHHHhccHHHHHHHHHHHH
Confidence            99999999999999999988742  2210000        00         01457778888889999999999998888


Q ss_pred             CC-CC--CchhhHHHHHHHHhcccc
Q 042593          293 SQ-IT--NVVVWRTGFLRLLINSYF  314 (352)
Q Consensus       293 ~~-~~--~~~~~~~li~~~~~~g~~  314 (352)
                      .. +.  +...|..+...|...|+.
T Consensus       145 ~~~p~~~~~~~~~~l~~~~~~~~~~  169 (228)
T 4i17_A          145 DVTSKKWKTDALYSLGVLFYNNGAD  169 (228)
T ss_dssp             TSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCCcccHHHHHHHHHHHHHHHHH
Confidence            77 44  467888888888888877

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.08  E-value=6.7e-09  Score=91.47  Aligned_cols=230  Identities=12%  Similarity=-0.049  Sum_probs=168.1

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCC-CC----chhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGF-QS----HVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITG   99 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~-~~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~   99 (352)
                      ....+...|++++|...++...+... .+    ...++..+..+|...|+++.|...+++..+     ++....  ...+
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~--~~~~  184 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIR--TIQS  184 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHH--HHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhh--HHHH
Confidence            34455689999999999999886421 12    346788999999999999999998887653     221111  1111


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCCCCc
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFNAFD  171 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~  171 (352)
                         ++.+...|...|++++|.+.|++......-.++    ..++..+..++...|++++|...+++..+.    +.+. .
T Consensus       185 ---~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~-~  260 (378)
T 3q15_A          185 ---LFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDL-L  260 (378)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGG-H
T ss_pred             ---HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChh-H
Confidence               889999999999999999999987432211122    246888899999999999999999988762    2222 5


Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccC-----CC-CHhhHHHHHHHHHcCCC---HHHHHHHHHHHHhcCCCCCcch
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVD-----RK-NLVSWTTIISGFAMHGM---GKEAVENFERMQKVGLKPNRSW  242 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-----~~-~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~~  242 (352)
                      ..++..+..+|.+.|++++|.+.+++....     .+ ....++.+-..+...++   +.+|...+++   .+       
T Consensus       261 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~-------  330 (378)
T 3q15_A          261 PKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KN-------  330 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TT-------
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CC-------
Confidence            778889999999999999999999986442     22 23456666667777788   6666666665   11       


Q ss_pred             hhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCC
Q 042593          243 RIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIP  292 (352)
Q Consensus       243 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  292 (352)
                                       ..+.....+..+...|.+.|++++|.+.|++..
T Consensus       331 -----------------~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          331 -----------------LHAYIEACARSAAAVFESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             -----------------CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -----------------ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                             111234466789999999999999999988754

>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=99.08  E-value=6.7e-09  Score=76.27  Aligned_cols=128  Identities=14%  Similarity=0.178  Sum_probs=111.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|..+++++.. .. +.+...+..+...+...|++++|...++++.+.+..  +...+..+..++
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~l~~~~   79 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALE-LD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR--SAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHH-cC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC--chHHHHHHHHHH
Confidence            77888899999999999999999944 32 235668888999999999999999999999887643  677888999999


Q ss_pred             HhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          183 AKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...|++++|.+.++++.... .+...+..+...+...|++++|...++++.+.
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            99999999999999986654 46788999999999999999999999998874

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.03  E-value=3.5e-08  Score=86.54  Aligned_cols=242  Identities=13%  Similarity=0.028  Sum_probs=169.8

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCC-Cc----hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCc-hhHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQ-SH----VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNL-VTWN   94 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~-~~~~   94 (352)
                      +++.+...+...|++++|...++...+..-. .+    ..++..+...+...|++++|...+++..+     .+. ....
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  134 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMH  134 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHH
Confidence            4666777888999999999999987753211 11    23467788889999999999999988753     111 0001


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC-CCC--ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY-TEP--SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD  171 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  171 (352)
                      ...     +..+...+...|++++|...+++...... ..+  ...++..+...+...|++++|...+++.......+..
T Consensus       135 ~~~-----~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~  209 (373)
T 1hz4_A          135 EFL-----VRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKY  209 (373)
T ss_dssp             HHH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHH-----HHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCc
Confidence            111     67788889999999999999998743221 111  1246778888899999999999999988765322202


Q ss_pred             hhhHH-----HHHHHHHhhCChHHHHHHHHHhccCCCC-----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          172 IHVSN-----CLIDTYAKCGCIFSASKLFEDTSVDRKN-----LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       172 ~~~~~-----~li~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                      ...+.     ..+..+...|++++|...+++.....+.     ...+..+...+...|++++|...+++.....      
T Consensus       210 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~------  283 (373)
T 1hz4_A          210 HSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENA------  283 (373)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH------
T ss_pred             chhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH------
Confidence            11222     2345578999999999999998655332     2356777888999999999999999876531      


Q ss_pred             hhhhHhHHHHHHHHHHhcCCCCCh-hhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          242 WRIGEEGLKFFDKMVEECEVLPDI-KHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       242 ~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                                    ... +..++. ..+..+..++...|+.++|...+++...
T Consensus       284 --------------~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          284 --------------RSL-RLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             --------------HHT-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --------------HhC-cchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence                          011 222233 3666778889999999999998887654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.03  E-value=2.4e-08  Score=84.62  Aligned_cols=214  Identities=9%  Similarity=-0.066  Sum_probs=150.5

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhc
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRM  113 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~  113 (352)
                      ++++|...|+..               ...|...|++++|...|++..+     .+... .+.     .|+.+...|...
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~a~-----~~~~lg~~~~~~   90 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDE-AGN-----TYVEAYKCFKSG   90 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHH-HHH-----HHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHH-HHH-----HHHHHHHHHHHC
Confidence            366666666554               5567889999999999887653     12110 000     189999999999


Q ss_pred             CCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhC-CChhhHHHHHHHHHhcCCCCC----chhhHHHHHHHHHh
Q 042593          114 NRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKN-GEVRNCQLIHGYGEKRGFNAF----DIHVSNCLIDTYAK  184 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~~----~~~~~~~li~~~~~  184 (352)
                      |++++|+..|++......-..+    ..++..+...+... |++++|...+++..+......    ...+++.+..++.+
T Consensus        91 g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~  170 (292)
T 1qqe_A           91 GNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKAL  170 (292)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHH
Confidence            9999999999987432211112    34788899999996 999999999999876532110    14578889999999


Q ss_pred             hCChHHHHHHHHHhccCCCCH--------hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHH
Q 042593          185 CGCIFSASKLFEDTSVDRKNL--------VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMV  256 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~~~--------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~  256 (352)
                      .|++++|...|++.....|+.        ..|..+..++...|++++|...|++..+.  .|+.                
T Consensus       171 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~----------------  232 (292)
T 1qqe_A          171 DGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNF----------------  232 (292)
T ss_dssp             TTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC----------------------
T ss_pred             hCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCC----------------
Confidence            999999999999977654322        15677888899999999999999998763  2210                


Q ss_pred             HhcCCCCChhhHHHHHHHHH--HcCChhHHHHHHhcCCCC
Q 042593          257 EECEVLPDIKHYGCLIDILE--RAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       257 ~~~~~~p~~~~~~~li~~~~--~~g~~~~A~~~~~~m~~~  294 (352)
                         ........+..++.++.  ..+++++|...|+.+...
T Consensus       233 ---~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l  269 (292)
T 1qqe_A          233 ---ADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRL  269 (292)
T ss_dssp             --------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCC
T ss_pred             ---CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCcc
Confidence               00111234455666664  467799999999888765

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.02  E-value=3.7e-09  Score=100.46  Aligned_cols=169  Identities=12%  Similarity=-0.031  Sum_probs=140.4

Q ss_pred             HhcCCcchHHHHHHHHH--------HhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhH
Q 042593           35 VTLSYPNLGTQLHAVFS--------KVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKW  103 (352)
Q Consensus        35 ~~~g~~~~a~~~~~~m~--------~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~  103 (352)
                      ...|++++|++.++...        +.. +.+...+..+..++...|++++|++.|++..+  | +...          |
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a----------~  470 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRL----------V  470 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHH----------H
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHH----------H
Confidence            78899999999999988        332 45678899999999999999999999999876  3 3334          8


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      ..+..++...|++++|.+.|++..+.   .| +...+..+..++.+.|++++ ...+++..+.+..  +...|..+..++
T Consensus       471 ~~lg~~~~~~g~~~~A~~~~~~al~l---~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~--~~~a~~~lg~~~  544 (681)
T 2pzi_A          471 WYRAVAELLTGDYDSATKHFTEVLDT---FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG--VISAAFGLARAR  544 (681)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH---STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc--hHHHHHHHHHHH
Confidence            88889999999999999999998543   34 45688899999999999999 9999999987654  788999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCC-HhhHHHHHHHHHcCCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRKN-LVSWTTIISGFAMHGM  220 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~-~~~~~~li~~~~~~~~  220 (352)
                      .+.|++++|.+.|++.....|+ ...+..+..++...++
T Consensus       545 ~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          545 SAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            9999999999999998877665 6778888888777665

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.99  E-value=4.1e-09  Score=95.19  Aligned_cols=268  Identities=12%  Similarity=-0.025  Sum_probs=125.4

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCCh---hHHHHHhccCCCCCchhHHHHHHHHHhHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFL---KDSSKLFDELPERNLVTWNVIITGLVKWTGI  106 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~---~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~l  106 (352)
                      +...+.+.|++++|.++|+...+.|   ++..+..|...|...|+.   ++|...|++..+.++..          +..+
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A----------~~~L   75 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRA----------QARL   75 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC----------------------------C----------HHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHH----------HHHH
Confidence            5677788999999999999998887   344455567777778888   89999999987665555          5556


Q ss_pred             HHHHHhcC-----CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhh---HHHHHHHHHhcCC-----------
Q 042593          107 IDGYSRMN-----RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRN---CQLIHGYGEKRGF-----------  167 (352)
Q Consensus       107 i~~~~~~~-----~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~---a~~~~~~~~~~~~-----------  167 (352)
                      ...+...+     +.++|...|++. ...|. |  ..+..+...|...+..+.   +...+......|.           
T Consensus        76 g~~~~~~~~~~~~~~~~A~~~~~~A-a~~g~-~--~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y  151 (452)
T 3e4b_A           76 GRLLAAKPGATEAEHHEAESLLKKA-FANGE-G--NTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLY  151 (452)
T ss_dssp             HHHHHTC--CCHHHHHHHHHHHHHH-HHTTC-S--SCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHH
T ss_pred             HHHHHhCCCCCCcCHHHHHHHHHHH-HHCCC-H--HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            66454544     788999999998 44332 2  245555555554443222   2233332222221           


Q ss_pred             ---------------------CCCchhhHHHHHHHHHhhC---ChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcC----
Q 042593          168 ---------------------NAFDIHVSNCLIDTYAKCG---CIFSASKLFEDTSVD-RKNLVSWTTIISGFAMH----  218 (352)
Q Consensus       168 ---------------------~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~----  218 (352)
                                           .. ++..+..|...|.+.|   +.++|.+.|+..... .++...+..|...|...    
T Consensus       152 ~~~~~~~~~~~~a~~~~~~a~~~-~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~  230 (452)
T 3e4b_A          152 RTQGTYDQHLDDVERICKAALNT-TDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGT  230 (452)
T ss_dssp             HHHTCGGGGHHHHHHHHHHHTTT-CTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSS
T ss_pred             HcCCCcccCHHHHHHHHHHHHcC-CHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCC
Confidence                                 11 2234445555555555   555555555554333 23333334444444333    


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCcch------h------hhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcC-----Ch
Q 042593          219 GMGKEAVENFERMQKVGLKPNRSW------R------IGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAG-----RL  281 (352)
Q Consensus       219 ~~~~~a~~~~~~m~~~~~~p~~~~------~------~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g-----~~  281 (352)
                      ++.++|...|++.. .|.. ....      +      ..++|..+|++..+. |   +...+..|...|. .|     +.
T Consensus       231 ~d~~~A~~~~~~aa-~g~~-~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~-g---~~~A~~~Lg~~y~-~G~g~~~d~  303 (452)
T 3e4b_A          231 PDEKTAQALLEKIA-PGYP-ASWVSLAQLLYDFPELGDVEQMMKYLDNGRAA-D---QPRAELLLGKLYY-EGKWVPADA  303 (452)
T ss_dssp             CCHHHHHHHHHHHG-GGST-HHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHH-HCSSSCCCH
T ss_pred             CCHHHHHHHHHHHc-CCCH-HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHH-cCCCCCCCH
Confidence            45555555555554 2111 1000      0      045555555555544 3   3444445555554 33     56


Q ss_pred             hHHHHHHhcCCCCCCCchhhHHHHHHHHh----cccccCcccccccc
Q 042593          282 EQAEEVASGIPSQITNVVVWRTGFLRLLI----NSYFFSPITLNSQR  324 (352)
Q Consensus       282 ~~A~~~~~~m~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~  324 (352)
                      ++|.+.|++..  +.+...+..|...|..    ..++++|+..+.+.
T Consensus       304 ~~A~~~~~~Aa--~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A  348 (452)
T 3e4b_A          304 KAAEAHFEKAV--GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTA  348 (452)
T ss_dssp             HHHHHHHHTTT--TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHH
Confidence            66666666555  2344555555544444    22444555544444

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.99  E-value=1.3e-08  Score=74.67  Aligned_cols=128  Identities=13%  Similarity=0.105  Sum_probs=108.2

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~  216 (352)
                      .+..+...+...|++++|..+++++.+....  +...+..+...+...|++++|.+.++++... +.+...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPR--SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCc--chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHH
Confidence            4677888899999999999999999887543  6778888999999999999999999987655 446778889999999


Q ss_pred             cCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          217 MHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      ..|++++|...++++.+..                          +.+...+..+...+.+.|++++|...++++..
T Consensus        81 ~~~~~~~A~~~~~~~~~~~--------------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELD--------------------------PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--------------------------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhC--------------------------CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            9999999999999988742                          22566788899999999999999999987643

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.98  E-value=3.8e-08  Score=81.83  Aligned_cols=166  Identities=12%  Similarity=0.030  Sum_probs=90.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHhccCCC--CCch-hHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-
Q 042593           60 YVNTALGDMYVSLGFLKDSSKLFDELPE--RNLV-TWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-  135 (352)
Q Consensus        60 ~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~-~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  135 (352)
                      ..+-.+...+.+.|++++|...|+++.+  |+.. ...+       +..+..++.+.|++++|...|++......-.|. 
T Consensus        16 ~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a-------~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~   88 (261)
T 3qky_A           16 QEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADA-------QFYLARAYYQNKEYLLAASEYERFIQIYQIDPRV   88 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHH-------HHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchh
Confidence            3334444444555555555555555443  2210 0111       444445555555555555555555332211112 


Q ss_pred             hhhHHHHHHHHHh--------CCChhhHHHHHHHHHhcCCCCCchhhH-----------------HHHHHHHHhhCChHH
Q 042593          136 EITILAVLPAIWK--------NGEVRNCQLIHGYGEKRGFNAFDIHVS-----------------NCLIDTYAKCGCIFS  190 (352)
Q Consensus       136 ~~t~~~ll~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~-----------------~~li~~~~~~g~~~~  190 (352)
                      ...+..+..++..        .|++++|...++++.+....  +....                 ..+..+|.+.|++++
T Consensus        89 ~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~--~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  166 (261)
T 3qky_A           89 PQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPN--HELVDDATQKIRELRAKLARKQYEAARLYERRELYEA  166 (261)
T ss_dssp             HHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTT--CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcC--chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHH
Confidence            1234444444444        55555555555555544322  22222                 456777888888888


Q ss_pred             HHHHHHHhccCCCC----HhhHHHHHHHHHcC----------CCHHHHHHHHHHHHhc
Q 042593          191 ASKLFEDTSVDRKN----LVSWTTIISGFAMH----------GMGKEAVENFERMQKV  234 (352)
Q Consensus       191 a~~~~~~~~~~~~~----~~~~~~li~~~~~~----------~~~~~a~~~~~~m~~~  234 (352)
                      |...|+.+....|+    ...+..+..+|...          |++++|...|+++.+.
T Consensus       167 A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          167 AAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            88888887655443    34566677777655          7788888888887764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.98  E-value=9e-09  Score=85.63  Aligned_cols=172  Identities=7%  Similarity=-0.094  Sum_probs=134.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCc---hhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSH---VYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVI   96 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~   96 (352)
                      +...+-.....+.+.|++++|...|+.+.+.. +.+   ...+..+..+|.+.|++++|+..|++..+  |+. ....+ 
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a-   91 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA-   91 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH-
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH-
Confidence            56777788889999999999999999998865 223   57788899999999999999999999875  432 22122 


Q ss_pred             HHHHHhHHHHHHHHHh--------cCCHHHHHHHHHHhHhccCCCCCh-hhH-----------------HHHHHHHHhCC
Q 042593           97 ITGLVKWTGIIDGYSR--------MNRSNEALALFRRMAACEYTEPSE-ITI-----------------LAVLPAIWKNG  150 (352)
Q Consensus        97 i~~~~~~~~li~~~~~--------~~~~~~a~~~~~~m~~~~~~~p~~-~t~-----------------~~ll~~~~~~~  150 (352)
                            +..+..++..        .|++++|...|++.....   |+. ...                 ..+...+.+.|
T Consensus        92 ------~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~---p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g  162 (261)
T 3qky_A           92 ------EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY---PNHELVDDATQKIRELRAKLARKQYEAARLYERRE  162 (261)
T ss_dssp             ------HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC---TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ------HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC---cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence                  6677788888        999999999999995533   332 233                 56678899999


Q ss_pred             ChhhHHHHHHHHHhcCCCCC-chhhHHHHHHHHHhh----------CChHHHHHHHHHhccCCCCH
Q 042593          151 EVRNCQLIHGYGEKRGFNAF-DIHVSNCLIDTYAKC----------GCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       151 ~~~~a~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~  205 (352)
                      ++++|...++.+.+.....+ ....+..+..+|...          |++++|...|+.+....|+.
T Consensus       163 ~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          163 LYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             CHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            99999999999988754321 345777888888866          88999999999987666654

>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=98.97  E-value=1.7e-08  Score=78.61  Aligned_cols=157  Identities=9%  Similarity=-0.044  Sum_probs=89.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhh
Q 042593           62 NTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEIT  138 (352)
Q Consensus        62 ~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t  138 (352)
                      +..+...+...|++++|+..|++..+  | +...          |..+...+...|++++|...|++.....   |+...
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a----------~~~la~~~~~~g~~~~A~~~~~~a~~~~---p~~~~   75 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQSRGDV----------KLAKADCLLETKQFELAQELLATIPLEY---QDNSY   75 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHH----------HHHHHHHHHHTTCHHHHHHHHTTCCGGG---CCHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHH----------HHHHHHHHHHCCCHHHHHHHHHHhhhcc---CChHH
Confidence            33445555666666666666666654  2 2222          5556666666666666666666662222   22222


Q ss_pred             HHHHHHH-HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC---HhhHHHHHHH
Q 042593          139 ILAVLPA-IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN---LVSWTTIISG  214 (352)
Q Consensus       139 ~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~li~~  214 (352)
                      +...... +...+...++...++...+....  +...+..+..++...|++++|.+.|++.....|+   ...+..+...
T Consensus        76 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~P~--~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~  153 (176)
T 2r5s_A           76 KSLIAKLELHQQAAESPELKRLEQELAANPD--NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDI  153 (176)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHH
Confidence            2111111 11222233456666666655433  5666777777777777777777777776655443   4466777777


Q ss_pred             HHcCCCHHHHHHHHHHHHh
Q 042593          215 FAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~  233 (352)
                      +...|+.++|...|++...
T Consensus       154 ~~~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          154 LSALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             HHHHCSSCHHHHHHHHHHH
T ss_pred             HHHhCCCCcHHHHHHHHHH
Confidence            7777777777777766543

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.92  E-value=1.7e-07  Score=78.90  Aligned_cols=245  Identities=9%  Similarity=0.002  Sum_probs=159.3

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGY  110 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~  110 (352)
                      ++-.--.|++..++.-   ..+..-......---+.++|...|+.+...     -..|....          ...+ ..|
T Consensus        20 ikn~fy~G~yq~~i~e---~~~~~~~~~~~~~~~~~Rs~iAlg~~~~~~-----~~~~~~~a----------~~~l-a~~   80 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQE---IEKFSKVTDNTLLFYKAKTLLALGQYQSQD-----PTSKLGKV----------LDLY-VQF   80 (310)
T ss_dssp             HHHHHTTTCHHHHTHH---HHTSSCCCCHHHHHHHHHHHHHTTCCCCCC-----SSSTTHHH----------HHHH-HHH
T ss_pred             HHHHHHhhHHHHHHHH---HHhcCccchHHHHHHHHHHHHHcCCCccCC-----CCCHHHHH----------HHHH-HHH
Confidence            4555567888777762   222111111122223457888888876421     11133222          2222 222


Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS  190 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  190 (352)
                      ...+    |+..|++. ...+ .++..++..+..++...|+.++|.+++.+....+..+.+...+..++..+.+.|+.+.
T Consensus        81 ~~~~----a~~~l~~l-~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~  154 (310)
T 3mv2_B           81 LDTK----NIEELENL-LKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVST  154 (310)
T ss_dssp             HTTT----CCHHHHHT-TTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHH
T ss_pred             hccc----HHHHHHHH-HhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHH
Confidence            2322    77888887 4333 4566667788899999999999999999987776522378889999999999999999


Q ss_pred             HHHHHHHhccCCC-----CHhhHHHHHHH--HHcCC--CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCC
Q 042593          191 ASKLFEDTSVDRK-----NLVSWTTIISG--FAMHG--MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEV  261 (352)
Q Consensus       191 a~~~~~~~~~~~~-----~~~~~~~li~~--~~~~~--~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~  261 (352)
                      |.+.++.|.+..|     +-.+...|..+  ....|  +.++|..+|+++.+.                           
T Consensus       155 A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~---------------------------  207 (310)
T 3mv2_B          155 ASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT---------------------------  207 (310)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT---------------------------
T ss_pred             HHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh---------------------------
Confidence            9999999977677     35555666655  33334  899999999998753                           


Q ss_pred             CCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-----------CCCchhhHHHHHHHHhcccccCcccccccchhhhh
Q 042593          262 LPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-----------ITNVVVWRTGFLRLLINSYFFSPITLNSQRLFFFP  329 (352)
Q Consensus       262 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-----------~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  329 (352)
                      .|+..+-..++.++.+.|++++|++.++.+...           +.|..+.-.+|......|+  +|.++..+.....|
T Consensus       208 ~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P  284 (310)
T 3mv2_B          208 FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLDH  284 (310)
T ss_dssp             SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTC
T ss_pred             CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCC
Confidence            234333344455899999999999999765432           2355666455555555676  77777777665444

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.91  E-value=9.7e-08  Score=77.53  Aligned_cols=186  Identities=10%  Similarity=-0.065  Sum_probs=114.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCC-C-chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchh-HHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQ-S-HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVT-WNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~~i   97 (352)
                      +...+......+.+.|++++|...|+.+.+..-. | ....+..+..+|.+.|++++|+..|+++.+  |+... ..+  
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a--   80 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYV--   80 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH--
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHH--
Confidence            3445556667777888888888888888775411 1 134666777788888888888888888764  43322 112  


Q ss_pred             HHHHhHHHHHHHHHh------------------cCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHH
Q 042593           98 TGLVKWTGIIDGYSR------------------MNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLI  158 (352)
Q Consensus        98 ~~~~~~~~li~~~~~------------------~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~  158 (352)
                           +..+..++..                  .|++++|...|+++.+.   .|+.. .......              
T Consensus        81 -----~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~---~P~~~~a~~a~~~--------------  138 (225)
T 2yhc_A           81 -----MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG---YPNSQYTTDATKR--------------  138 (225)
T ss_dssp             -----HHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT---CTTCTTHHHHHHH--------------
T ss_pred             -----HHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH---CcCChhHHHHHHH--------------
Confidence                 3333334433                  34555555555555221   12221 1111000              


Q ss_pred             HHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH----hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          159 HGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL----VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...+...     .......+...|.+.|++++|...|+++....|+.    ..+..+..++.+.|+.++|.+.++.+...
T Consensus       139 l~~~~~~-----~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          139 LVFLKDR-----LAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             HHHHHHH-----HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             HHHHHHH-----HHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence            0000000     01111355678889999999999999987766643    56888899999999999999999998886


Q ss_pred             CCC
Q 042593          235 GLK  237 (352)
Q Consensus       235 ~~~  237 (352)
                      +..
T Consensus       214 ~~~  216 (225)
T 2yhc_A          214 SSN  216 (225)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            543

>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=98.91  E-value=3.6e-08  Score=76.77  Aligned_cols=162  Identities=12%  Similarity=0.012  Sum_probs=124.6

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCc-hhHHHHHHHHHh
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNL-VTWNVIITGLVK  102 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~~~~~~i~~~~~  102 (352)
                      ...+......+.+.|++++|...++...+.. +.+...+..+..++...|++++|+..|++..+.++ ..+         
T Consensus         6 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~---------   75 (176)
T 2r5s_A            6 DEQLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSY---------   75 (176)
T ss_dssp             CTTHHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHH---------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHH---------
Confidence            3456777788999999999999999888765 45678899999999999999999999999876322 121         


Q ss_pred             HHHHHH-HHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          103 WTGIID-GYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       103 ~~~li~-~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      +..+.. .+...++..+|...+++...   ..| +...+..+..++...|++++|...++++.+....+.+...+..+..
T Consensus        76 ~~~~~~~~~~~~~~~~~a~~~~~~al~---~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~  152 (176)
T 2r5s_A           76 KSLIAKLELHQQAAESPELKRLEQELA---ANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMD  152 (176)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHH
Confidence            111111 11222333457888888744   235 4678889999999999999999999999988765424668899999


Q ss_pred             HHHhhCChHHHHHHHHHh
Q 042593          181 TYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~  198 (352)
                      ++...|+.++|...|++.
T Consensus       153 ~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          153 ILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HHHHHCSSCHHHHHHHHH
T ss_pred             HHHHhCCCCcHHHHHHHH
Confidence            999999999999999865

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.89  E-value=8.3e-08  Score=81.10  Aligned_cols=163  Identities=11%  Similarity=-0.020  Sum_probs=123.0

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCC
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYT  132 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  132 (352)
                      +.+...+..+...+...|++++|+..|++..+  |+ ...          +..+...+.+.|++++|...+++... .  
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a----------~~~la~~~~~~g~~~~A~~~l~~~~~-~--  180 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEI----------GLLLAETLIALNRSEDAEAVLXTIPL-Q--  180 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHH----------HHHHHHHHHHTTCHHHHHHHHTTSCG-G--
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhH----------HHHHHHHHHHCCCHHHHHHHHHhCch-h--
Confidence            55566777788888888999999999888764  43 333          77788888889999999999888833 2  


Q ss_pred             CCChhh-HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC---HhhH
Q 042593          133 EPSEIT-ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN---LVSW  208 (352)
Q Consensus       133 ~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~  208 (352)
                      .|+... .......+...++.++|...+++..+....  +...+..+..++...|++++|.+.|+++....|+   ...+
T Consensus       181 ~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~--~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~  258 (287)
T 3qou_A          181 DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPE--DAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTR  258 (287)
T ss_dssp             GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHH
T ss_pred             hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCc--cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHH
Confidence            344432 223333466777788888888888877544  7788888889999999999999999887766553   5678


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          209 TTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       209 ~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..+...+...|+.++|...+++...
T Consensus       259 ~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          259 XTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            8888889899998888888877553

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.88  E-value=3.2e-08  Score=83.69  Aligned_cols=162  Identities=7%  Similarity=-0.038  Sum_probs=108.4

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHh
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVK  102 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~  102 (352)
                      ..+..+...+.+.|++++|...++...+.. +-+...+..+..++...|++++|...+++...  |+...  .       
T Consensus       118 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~--~-------  187 (287)
T 3qou_A          118 ELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRY--Q-------  187 (287)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHH--H-------
T ss_pred             hhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHH--H-------
Confidence            445555666677788888888888777765 44566777777788888888888888887765  43221  0       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      .......+...++.++|...+++.....  +.+...+..+...+...|++++|...+.++.+......+...+..+..++
T Consensus       188 ~~~~~~~l~~~~~~~~a~~~l~~al~~~--P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~  265 (287)
T 3qou_A          188 GLVAQIELLXQAADTPEIQQLQQQVAEN--PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEIL  265 (287)
T ss_dssp             HHHHHHHHHHHHTSCHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccCccHHHHHHHHhcC--CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHH
Confidence            2222233556666777777777763322  23455677777777888888888888888777655432366777788888


Q ss_pred             HhhCChHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDT  198 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~  198 (352)
                      ...|+.++|...+++.
T Consensus       266 ~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          266 AALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHHCTTCHHHHHHHHH
T ss_pred             HHcCCCCcHHHHHHHH
Confidence            8888877777777653

>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=98.87  E-value=1.8e-08  Score=95.65  Aligned_cols=174  Identities=14%  Similarity=-0.010  Sum_probs=143.3

Q ss_pred             HhcCCHHHHHHHHHHhHh-----ccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh
Q 042593          111 SRMNRSNEALALFRRMAA-----CEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~-----~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  184 (352)
                      ...|++++|++.+++...     .....| +...+..+..++...|++++|...+++..+....  +...|..+..+|..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~--~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGW--RWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcc--hHHHHHHHHHHHHH
Confidence            788999999999999841     112234 4567888999999999999999999999987544  78899999999999


Q ss_pred             hCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCC
Q 042593          185 CGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLP  263 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p  263 (352)
                      .|++++|.+.|++..+..| +...|..+..++.+.|++++ .+.|++..+..  |                        -
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~--P------------------------~  532 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTN--D------------------------G  532 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC--T------------------------T
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC--C------------------------c
Confidence            9999999999999876655 67889999999999999999 99999988742  2                        2


Q ss_pred             ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhccc
Q 042593          264 DIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSY  313 (352)
Q Consensus       264 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~  313 (352)
                      +...|..+..++.+.|++++|.+.|++.... +.+...|..+...+...++
T Consensus       533 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          533 VISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            5678899999999999999999999999887 5556788888888877665

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.87  E-value=5.1e-08  Score=78.18  Aligned_cols=178  Identities=6%  Similarity=-0.064  Sum_probs=84.0

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTG  105 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~  105 (352)
                      .+-.....+.+.|++++|...|+...+.. +-+...+...     ..             .. .......+      ++.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~-----~~-------------~~-~~~~~~~~------~~~   59 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALN-IDRTEMYYWT-----NV-------------DK-NSEISSKL------ATE   59 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-HHHHHHHHHH-----HS-------------CT-TSHHHHHH------HHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHh-----hh-------------cc-hhhhhHHH------HHH
Confidence            34445567778999999999999988765 2234444430     00             00 00000000      333


Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC  185 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  185 (352)
                      +..++.+.|++++|...|++..+..  +-+...+..+..++...|++++|...+++..+....  +..++..+..+|...
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~--~~~a~~~lg~~~~~~  135 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKA--PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEAD--NLAANIFLGNYYYLT  135 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--CHHHHHHHHHHHHHH
Confidence            4445555555555555555552211  112334555555555555555555555555554332  445555555554433


Q ss_pred             CC--hHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          186 GC--IFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       186 g~--~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      |+  .+.+...++......|....+...-.++...|++++|...|++..+
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~  185 (208)
T 3urz_A          136 AEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL  185 (208)
T ss_dssp             HHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            32  2333444444322222222222333334445555555555555554

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.85  E-value=1.1e-07  Score=76.17  Aligned_cols=176  Identities=12%  Similarity=0.058  Sum_probs=118.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHH
Q 042593           61 VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITIL  140 (352)
Q Consensus        61 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~  140 (352)
                      .+-.....+...|++++|+..|++..+.++.....       |..     .....               ..........
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------~~~-----~~~~~---------------~~~~~~~~~~   58 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEM-------YYW-----TNVDK---------------NSEISSKLAT   58 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHH-------HHH-----HHSCT---------------TSHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHH-------HHH-----hhhcc---------------hhhhhHHHHH
Confidence            33445566778999999999999986533332111       111     00000               0011122344


Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG  219 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~  219 (352)
                      .+..++.+.|++++|...+++..+....  +...+..+..+|...|++++|.+.|++.....| +...|..+..+|...|
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~  136 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQKAPN--NVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTA  136 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHh
Confidence            5788899999999999999999988654  789999999999999999999999999876655 6788888888876665


Q ss_pred             C--HHHHHHHHHHHHhcCCCCCcch---hh----------hHhHHHHHHHHHHhcCCCCChhhHHHHH
Q 042593          220 M--GKEAVENFERMQKVGLKPNRSW---RI----------GEEGLKFFDKMVEECEVLPDIKHYGCLI  272 (352)
Q Consensus       220 ~--~~~a~~~~~~m~~~~~~p~~~~---~~----------~~~a~~~~~~m~~~~~~~p~~~~~~~li  272 (352)
                      +  .+.+...++...    .|+...   +.          +++|...|++.++   +.|+......+.
T Consensus       137 ~~~~~~~~~~~~~~~----~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~---l~P~~~~~~~l~  197 (208)
T 3urz_A          137 EQEKKKLETDYKKLS----SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL---RFPSTEAQKTLD  197 (208)
T ss_dssp             HHHHHHHHHHHC-------CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT---TSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh----CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCHHHHHHHH
Confidence            4  445566666543    233221   11          7889999998874   467765544443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.84  E-value=1.8e-07  Score=75.98  Aligned_cols=169  Identities=14%  Similarity=-0.005  Sum_probs=112.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch-hhHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI-HVSNCLID  180 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~li~  180 (352)
                      +..+...+.+.|++++|...|+++.....-.|. ...+..+..++.+.|++++|...++.+.+.....+.. ..+..+..
T Consensus         7 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~   86 (225)
T 2yhc_A            7 IYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGL   86 (225)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHH
Confidence            555667788999999999999999543322222 3467888899999999999999999998876543111 23444444


Q ss_pred             HHHh------------------hCChHHHHHHHHHhccCCCCH-hhH-----------------HHHHHHHHcCCCHHHH
Q 042593          181 TYAK------------------CGCIFSASKLFEDTSVDRKNL-VSW-----------------TTIISGFAMHGMGKEA  224 (352)
Q Consensus       181 ~~~~------------------~g~~~~a~~~~~~~~~~~~~~-~~~-----------------~~li~~~~~~~~~~~a  224 (352)
                      ++.+                  .|+.++|...|+++....|+. ..+                 ..+...|.+.|++++|
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A  166 (225)
T 2yhc_A           87 TNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAV  166 (225)
T ss_dssp             HHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHH
Confidence            5543                  467888888888877665543 222                 1234456667777777


Q ss_pred             HHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          225 VENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       225 ~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      ...|+++.+.-  |                     +.+.....+..+..+|.+.|+.++|.+.++.+...
T Consensus       167 ~~~~~~~l~~~--p---------------------~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          167 VNRVEGMLRDY--P---------------------DTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             HHHHHHHHHHS--T---------------------TSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHC--c---------------------CCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence            77777766531  1                     10111245677788888888888888888766544

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.83  E-value=2.2e-07  Score=83.80  Aligned_cols=211  Identities=10%  Similarity=0.030  Sum_probs=142.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCC---ChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNG---EVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                      +..+...|...+.++++....... ...-...+...+..+...+...|   +.++|...++...+.|..  +...+..+.
T Consensus       144 ~~~Lg~~y~~~~~~~~~~~~a~~~-~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~--~a~~~~~Lg  220 (452)
T 3e4b_A          144 GLAQVLLYRTQGTYDQHLDDVERI-CKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTV--TAQRVDSVA  220 (452)
T ss_dssp             HHHHHHHHHHHTCGGGGHHHHHHH-HHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS--CHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccCHHHHHHH-HHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH--HHHHHHHHH
Confidence            445555566656444333332222 11112233447888888888899   899999999999988855  566556777


Q ss_pred             HHHHhh----CChHHHHHHHHHhccCCCCHhhHHHHHHH-H--HcCCCHHHHHHHHHHHHhcCCCCCcchhh--------
Q 042593          180 DTYAKC----GCIFSASKLFEDTSVDRKNLVSWTTIISG-F--AMHGMGKEAVENFERMQKVGLKPNRSWRI--------  244 (352)
Q Consensus       180 ~~~~~~----g~~~~a~~~~~~~~~~~~~~~~~~~li~~-~--~~~~~~~~a~~~~~~m~~~~~~p~~~~~~--------  244 (352)
                      ..|...    ++.++|.+.|+...  +-++..+..|-.. +  ...++.++|...|++..+.|. |+.....        
T Consensus       221 ~~y~~g~~~~~d~~~A~~~~~~aa--~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~-~~A~~~Lg~~y~~G~  297 (452)
T 3e4b_A          221 RVLGDATLGTPDEKTAQALLEKIA--PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQ-PRAELLLGKLYYEGK  297 (452)
T ss_dssp             HHHTCGGGSSCCHHHHHHHHHHHG--GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHCS
T ss_pred             HHHhCCCCCCCCHHHHHHHHHHHc--CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCC-HHHHHHHHHHHHcCC
Confidence            777655    79999999999986  4456667776666 4  568899999999999888762 1111111        


Q ss_pred             -----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH----cCChhHHHHHHhcCCCCCCCchhhHHHHHHHHh----c
Q 042593          245 -----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILER----AGRLEQAEEVASGIPSQITNVVVWRTGFLRLLI----N  311 (352)
Q Consensus       245 -----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~----~  311 (352)
                           .++|..+|++..     .-+...+..|...|..    ..+.++|.+.|++.... .+......|...|..    .
T Consensus       298 g~~~d~~~A~~~~~~Aa-----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~-g~~~A~~~Lg~~y~~G~g~~  371 (452)
T 3e4b_A          298 WVPADAKAAEAHFEKAV-----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARN-GQNSADFAIAQLFSQGKGTK  371 (452)
T ss_dssp             SSCCCHHHHHHHHHTTT-----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTT-TCTTHHHHHHHHHHSCTTBC
T ss_pred             CCCCCHHHHHHHHHHHh-----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhh-ChHHHHHHHHHHHHhCCCCC
Confidence                 667777777655     2356677777777776    34999999999987665 456677777777664    3


Q ss_pred             ccccCcccccccch
Q 042593          312 SYFFSPITLNSQRL  325 (352)
Q Consensus       312 g~~~~a~~~~~~~~  325 (352)
                      .+..+|...+....
T Consensus       372 ~d~~~A~~~~~~A~  385 (452)
T 3e4b_A          372 PDPLNAYVFSQLAK  385 (452)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            46666776666654

>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=98.82  E-value=5.1e-07  Score=76.39  Aligned_cols=213  Identities=10%  Similarity=0.062  Sum_probs=143.8

Q ss_pred             HHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHh
Q 042593           47 HAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus        47 ~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      +.....-...|+..+...+...+.-.  +   ..++..-...+......       +...+..+...|++++|..++++.
T Consensus        34 ~s~~e~g~~~~~~~~l~~i~~~l~~~--~---~~~~~~~~~~~~~~~~~-------l~~~i~~~~~~~~y~~a~~~~~~~  101 (293)
T 3u3w_A           34 VSRIESGAVYPSMDILQGIAAKLQIP--I---IHFYEVLIYSDIERKKQ-------FKDQVIMLCKQKRYKEIYNKVWNE  101 (293)
T ss_dssp             HHHHHTTSCCCCHHHHHHHHHHHTCC--T---HHHHHTTTSSCHHHHHH-------HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCCCCCHHHHHHHHHHhCcC--H---HHHhCCCCCCcchhHHH-------HHHHHHHHHHHhhHHHHHHHHHHH
Confidence            34443333467777776666655422  1   22333322222222111       444567788999999999999998


Q ss_pred             HhccCCCCChh----hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc----hhhHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          127 AACEYTEPSEI----TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD----IHVSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       127 ~~~~~~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      .......|+..    .+..+...+...+++++|...++...+......+    ..+++.+..+|...|++++|.+.|++.
T Consensus       102 l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~a  181 (293)
T 3u3w_A          102 LKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQI  181 (293)
T ss_dssp             HTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            44333334422    3334666677788999999999999875433213    336899999999999999999999987


Q ss_pred             cc-------CCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCC-hhhHH
Q 042593          199 SV-------DRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPD-IKHYG  269 (352)
Q Consensus       199 ~~-------~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~  269 (352)
                      ..       ..+ ...+|..+...|.+.|++++|...+++..+..                    .+. +..+. ..+|.
T Consensus       182 l~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~--------------------~~~-~~~~~~~~~~~  240 (293)
T 3u3w_A          182 LKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEIS--------------------CRI-NSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--------------------HHT-TBCTTHHHHHH
T ss_pred             HHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH--------------------HHc-CcHHHHHHHHH
Confidence            63       122 23578899999999999999999999877631                    111 22232 57888


Q ss_pred             HHHHHHHHcCC-hhHHHHHHhcCC
Q 042593          270 CLIDILERAGR-LEQAEEVASGIP  292 (352)
Q Consensus       270 ~li~~~~~~g~-~~~A~~~~~~m~  292 (352)
                      .+..+|.+.|+ .++|.+.+++..
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHH
Confidence            99999999995 688888777654

>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=98.79  E-value=4.8e-07  Score=72.35  Aligned_cols=125  Identities=11%  Similarity=-0.090  Sum_probs=109.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +..+...+...|++++|...|++.     +.|+...+..+..++.+.|++++|...++...+....  +...+..+..+|
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a-----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~--~~~~~~~lg~~~   81 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH--LAVAYFQRGMLY   81 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH-----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc--chHHHHHHHHHH
Confidence            566777888999999999999988     3678889999999999999999999999999887643  788999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-C----------------HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-N----------------LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~----------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...|++++|.+.|++.....| +                ...+..+..+|...|++++|...|++..+.
T Consensus        82 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            999999999999999766433 2                277888999999999999999999998874

>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=98.79  E-value=1.7e-07  Score=87.17  Aligned_cols=155  Identities=6%  Similarity=-0.043  Sum_probs=113.3

Q ss_pred             cCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC
Q 042593           72 LGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGE  151 (352)
Q Consensus        72 ~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~  151 (352)
                      .|++++|++.|++..+.++.....       |..+...+...|++++|.+.|++..+..  +-+...+..+..++...|+
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~-------~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~   72 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVA-------WLMLADAELGMGDTTAGEMAVQRGLALH--PGHPEAVARLGRVRWTQQR   72 (568)
T ss_dssp             -------------------CCHHH-------HHHHHHHHHHHTCHHHHHHHHHHHHTTS--TTCHHHHHHHHHHHHHTTC
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCC
Confidence            478889999999887632222122       8888899999999999999999984422  2345688899999999999


Q ss_pred             hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcC---CCHHHHHHH
Q 042593          152 VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMH---GMGKEAVEN  227 (352)
Q Consensus       152 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~---~~~~~a~~~  227 (352)
                      +++|...+++..+....  +...+..+..+|.+.|++++|.+.|++..+..| +...+..+..++...   |+.++|.+.
T Consensus        73 ~~~A~~~~~~al~~~p~--~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~  150 (568)
T 2vsy_A           73 HAEAAVLLQQASDAAPE--HPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQ  150 (568)
T ss_dssp             HHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHH
Confidence            99999999999887644  788999999999999999999999999766544 678889999999999   999999999


Q ss_pred             HHHHHhcCCC
Q 042593          228 FERMQKVGLK  237 (352)
Q Consensus       228 ~~~m~~~~~~  237 (352)
                      +++..+.+..
T Consensus       151 ~~~al~~~p~  160 (568)
T 2vsy_A          151 VRAAVAQGVG  160 (568)
T ss_dssp             HHHHHHHTCC
T ss_pred             HHHHHhcCCc
Confidence            9998886543

>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=98.78  E-value=8.3e-08  Score=89.25  Aligned_cols=156  Identities=8%  Similarity=-0.091  Sum_probs=113.6

Q ss_pred             cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCH
Q 042593           37 LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRS  116 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~  116 (352)
                      .|++++|.+.++...+.. +.+...+..+...+...|++++|.+.|++..+.++.....       |..+...+...|++
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------~~~lg~~~~~~g~~   73 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEA-------VARLGRVRWTQQRH   73 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHH-------HHHHHHHHHHTTCH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH-------HHHHHHHHHHCCCH
Confidence            478899999999887764 4467889999999999999999999999987633222222       88888999999999


Q ss_pred             HHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh---CChHHHHH
Q 042593          117 NEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC---GCIFSASK  193 (352)
Q Consensus       117 ~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~---g~~~~a~~  193 (352)
                      ++|.+.|++..+..  +-+...+..+..++.+.|++++|...+++..+....  +...+..+..++...   |+.++|.+
T Consensus        74 ~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           74 AEAAVLLQQASDAA--PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE--EPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHhhccccHHHHHH
Confidence            99999999984432  234568899999999999999999999999988654  778889999999999   99999999


Q ss_pred             HHHHhccCCCC
Q 042593          194 LFEDTSVDRKN  204 (352)
Q Consensus       194 ~~~~~~~~~~~  204 (352)
                      .+++.....|+
T Consensus       150 ~~~~al~~~p~  160 (568)
T 2vsy_A          150 QVRAAVAQGVG  160 (568)
T ss_dssp             HHHHHHHHTCC
T ss_pred             HHHHHHhcCCc
Confidence            99987665443

>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=98.78  E-value=4.6e-07  Score=72.51  Aligned_cols=133  Identities=11%  Similarity=-0.052  Sum_probs=105.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHH
Q 042593           61 VNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITIL  140 (352)
Q Consensus        61 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~  140 (352)
                      .+..+...+...|++++|...|++...++...          |..+...+...|++++|...|++.....  +.+...+.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~----------~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~   75 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQDPHSRI----------CFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYF   75 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHcCCChHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchHHHH
Confidence            34556777788899999999999887776555          8888888899999999999998884432  23456788


Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCC--------------CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFN--------------AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~--------------~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .+..++...|++++|...++...+....              |.....+..+..+|.+.|++++|.+.|+......|+.
T Consensus        76 ~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~  154 (213)
T 1hh8_A           76 QRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  154 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc
Confidence            8888899999999999999988875432              1133788899999999999999999999987776754

>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=98.77  E-value=1.1e-07  Score=81.24  Aligned_cols=189  Identities=7%  Similarity=-0.073  Sum_probs=134.4

Q ss_pred             cCCcchHHHHHHHHHHhC------CCCch----hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHH
Q 042593           37 LSYPNLGTQLHAVFSKVG------FQSHV----YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLV  101 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~------~~~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~  101 (352)
                      .|++++|.++++...+..      ..++.    ..|+.....|...|++++|...|.+..+     .+...   ...   
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~---~a~---   77 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFH---AAK---   77 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH---HHH---
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHH---HHH---
Confidence            456667777777665421      12332    3567777888899999999998887653     11110   011   


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccC--CCCC--hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC----CCchh
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEY--TEPS--EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN----AFDIH  173 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~--~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~  173 (352)
                      .|+.+...|...|++++|+..|++......  -.|.  ..++..+...+.. |++++|...+++..+....    .....
T Consensus        78 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~  156 (307)
T 2ifu_A           78 AFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAE  156 (307)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHH
Confidence            188889999999999999999998733211  1122  3467888888888 9999999999988754211    10246


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      +++.+..+|.+.|++++|.+.|++....   .++    ...+..+..++...|++++|...|++..
T Consensus       157 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          157 LIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            7888999999999999999999987543   121    2366777778888899999999999987

>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=98.77  E-value=3.7e-07  Score=73.36  Aligned_cols=178  Identities=12%  Similarity=-0.019  Sum_probs=139.3

Q ss_pred             chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCC-CchhHHHHHHHHHhHHHHHHHHHhcC----C
Q 042593           41 NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPER-NLVTWNVIITGLVKWTGIIDGYSRMN----R  115 (352)
Q Consensus        41 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~i~~~~~~~~li~~~~~~~----~  115 (352)
                      .+|.+.|+...+.|   ++..+..|...|...+++++|.+.|++..+. +...          +..|-..|.. +    +
T Consensus         3 ~eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a----------~~~lg~~y~~-~g~~~~   68 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDA----------LALLAQLKIR-NPQQAD   68 (212)
T ss_dssp             -CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHH----------HHHHHHHTTS-STTSCC
T ss_pred             chHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHH----------HHHHHHHHHc-CCCCCC
Confidence            35778888888775   6777888899999999999999999987654 3444          6667777777 6    8


Q ss_pred             HHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh----hCC
Q 042593          116 SNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK----CGC  187 (352)
Q Consensus       116 ~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~  187 (352)
                      .++|...|++. ...+   +...+..+...+..    .++.++|...+++..+.|.....+..+..|-..|..    .++
T Consensus        69 ~~~A~~~~~~A-~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d  144 (212)
T 3rjv_A           69 YPQARQLAEKA-VEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPED  144 (212)
T ss_dssp             HHHHHHHHHHH-HHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCC
T ss_pred             HHHHHHHHHHH-HHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCC
Confidence            99999999998 4433   55677788888877    889999999999998887531136778888888988    889


Q ss_pred             hHHHHHHHHHhccCCCCHhhHHHHHHHHHcC-C-----CHHHHHHHHHHHHhcCC
Q 042593          188 IFSASKLFEDTSVDRKNLVSWTTIISGFAMH-G-----MGKEAVENFERMQKVGL  236 (352)
Q Consensus       188 ~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~-~-----~~~~a~~~~~~m~~~~~  236 (352)
                      .++|.+.|++......+...+..|-..|... |     +.++|...|++..+.|.
T Consensus       145 ~~~A~~~~~~A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          145 DVKASEYFKGSSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHHHHHHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            9999999999765545666777777777643 3     89999999999888763

>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=98.77  E-value=4e-08  Score=74.35  Aligned_cols=144  Identities=7%  Similarity=-0.148  Sum_probs=102.1

Q ss_pred             HHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHH
Q 042593           65 LGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVL  143 (352)
Q Consensus        65 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll  143 (352)
                      |...+...|++++|+..++.....++.....       +..+...|.+.|++++|.+.|++..+.   .| +..+|..+.
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~p~~~~~-------~~~la~~y~~~~~~~~A~~~~~~al~~---~p~~~~a~~~lg   72 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSPRQKSIK-------GFYFAKLYYEAKEYDLAKKYICTYINV---QERDPKAHRFLG   72 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSHHHHHTT-------HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHH
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccCcccHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHH
Confidence            3445556778888888888876533221111       667788888999999999999888442   34 456888888


Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHH-HHHhccCCC-CHhhHHHHHHHHHcCCC
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKL-FEDTSVDRK-NLVSWTTIISGFAMHGM  220 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~-~~~~~~~~~-~~~~~~~li~~~~~~~~  220 (352)
                      .++.+.|++++|...++...+....  +..++..+..+|.+.|+.++|.+. +++..+..| ++..|......+...|+
T Consensus        73 ~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           73 LLYELEENTDKAVECYRRSVELNPT--QKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHcCchHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            8889999999999999988887544  778888888889999988776655 466544444 56777776666666654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.76  E-value=7.4e-07  Score=75.49  Aligned_cols=236  Identities=9%  Similarity=-0.018  Sum_probs=174.6

Q ss_pred             HhcCCc-chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC--ChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHH-
Q 042593           35 VTLSYP-NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG--FLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGY-  110 (352)
Q Consensus        35 ~~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g--~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~-  110 (352)
                      .+.|.. ++|+++++.++... +-+...|+.--.++...|  ++++++++++.+...++..|.+       |+.--..+ 
T Consensus        43 ~~~~e~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~a-------W~~R~~iL~  114 (306)
T 3dra_A           43 MKAEEYSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQI-------WNYRQLIIG  114 (306)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHH-------HHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHH-------HHHHHHHHH
Confidence            345555 68999999999876 345566888888888888  9999999999987633333333       55444444 


Q ss_pred             ---Hhc---CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChh--hHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          111 ---SRM---NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVR--NCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       111 ---~~~---~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                         ...   +++++++++++++....  +-+..+|+.-.-.+.+.|.++  ++...++.+.+..+.  +.+.|+.-..++
T Consensus       115 ~~~~~l~~~~~~~~EL~~~~~~l~~~--pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~--N~sAW~~R~~ll  190 (306)
T 3dra_A          115 QIMELNNNDFDPYREFDILEAMLSSD--PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK--NNSAWSHRFFLL  190 (306)
T ss_dssp             HHHHHTTTCCCTHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHhccccCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence               444   78999999999995432  245668888888888889888  999999999998766  888898887777


Q ss_pred             HhhCC------hHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCH-HHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHH
Q 042593          183 AKCGC------IFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMG-KEAVENFERMQKVGLKPNRSWRIGEEGLKFFDK  254 (352)
Q Consensus       183 ~~~g~------~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~  254 (352)
                      .+.|+      ++++++.++..... +-|...|+-+-..+.+.|+. +++..+..+..+.+ .                 
T Consensus       191 ~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~-~-----------------  252 (306)
T 3dra_A          191 FSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLE-K-----------------  252 (306)
T ss_dssp             HSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGG-G-----------------
T ss_pred             HhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhcc-C-----------------
Confidence            77776      88899998887655 45788898888888888874 33555666655432 0                 


Q ss_pred             HHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC--CCCchhhHHHH
Q 042593          255 MVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ--ITNVVVWRTGF  305 (352)
Q Consensus       255 m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~~~li  305 (352)
                           .-..+...+..+..+|.+.|+.++|.++++.+..+  +....-|+..+
T Consensus       253 -----~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~~~Dpir~~yW~~~~  300 (306)
T 3dra_A          253 -----DQVTSSFALETLAKIYTQQKKYNESRTVYDLLKSKYNPIRSNFWDYQI  300 (306)
T ss_dssp             -----TEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHHHHHHHH
T ss_pred             -----CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHhccChHHHHHHHHHH
Confidence                 11346788899999999999999999999998753  44445555443

>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=98.70  E-value=2.1e-08  Score=75.93  Aligned_cols=121  Identities=9%  Similarity=-0.096  Sum_probs=76.2

Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG  186 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  186 (352)
                      ..+...|++++|+..+++. ..  ..|+ ...+..+...|.+.|++++|...+++..+....  +..+|..+..+|.+.|
T Consensus         5 ~~~~~~~~~e~ai~~~~~a-~~--~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~--~~~a~~~lg~~~~~~~   79 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGS-TP--SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER--DPKAHRFLGLLYELEE   79 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHH-SC--SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTT
T ss_pred             HHHHHcChHHHHHHHHHHh-cc--cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHcC
Confidence            3444556777777777666 21  1122 235556677777777777777777777766433  6677777777777777


Q ss_pred             ChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHH-HHHHHh
Q 042593          187 CIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVEN-FERMQK  233 (352)
Q Consensus       187 ~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~-~~~m~~  233 (352)
                      ++++|...|++.....| +...|..+...|.+.|++++|... +++..+
T Consensus        80 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~  128 (150)
T 4ga2_A           80 NTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAK  128 (150)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            77777777777655444 466677777777777776655444 355554

>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=98.70  E-value=3.9e-06  Score=70.90  Aligned_cols=169  Identities=7%  Similarity=-0.135  Sum_probs=124.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHhccCCCC--CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh---
Q 042593           62 NTALGDMYVSLGFLKDSSKLFDELPER--NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE---  136 (352)
Q Consensus        62 ~~~li~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~---  136 (352)
                      +...+..+...|++++|.+++++..+.  ........+..   +..+...+...+++++|+..|++......-.++.   
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~  154 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQW---QYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHH---HHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHH---HHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHH
Confidence            334477888999999999999987652  11111111111   5567778888899999999999995532223332   


Q ss_pred             -hhHHHHHHHHHhCCChhhHHHHHHHHHh----c-CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC------CCC
Q 042593          137 -ITILAVLPAIWKNGEVRNCQLIHGYGEK----R-GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD------RKN  204 (352)
Q Consensus       137 -~t~~~ll~~~~~~~~~~~a~~~~~~~~~----~-~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~------~~~  204 (352)
                       .+++.+..++...|++++|...++++.+    . +..+....++..+..+|.+.|++++|.+.+++....      .+.
T Consensus       155 ~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~  234 (293)
T 3u3w_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHH
Confidence             2689999999999999999999999874    1 222213458889999999999999999999876432      122


Q ss_pred             -HhhHHHHHHHHHcCCC-HHHHHHHHHHHHh
Q 042593          205 -LVSWTTIISGFAMHGM-GKEAVENFERMQK  233 (352)
Q Consensus       205 -~~~~~~li~~~~~~~~-~~~a~~~~~~m~~  233 (352)
                       ..+|..+..+|.+.|+ +++|.+.+++...
T Consensus       235 ~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence             5778899999999995 6999999988765

>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=98.69  E-value=4.3e-07  Score=77.45  Aligned_cols=195  Identities=7%  Similarity=-0.072  Sum_probs=138.0

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCC---CC--chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGF---QS--HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIIT   98 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~---~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~   98 (352)
                      .|+.....+...|++++|.+.|+...+...   .+  -..+|+.+..+|.+.|++++|+..|++..+  +..........
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            678888889999999999999998875421   11  145788999999999999999998887643  11000011111


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCC----CCC
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGF----NAF  170 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~----~~~  170 (352)
                         .++.+...|.. |++++|+..|++......-..+    ..++..+...+.+.|++++|...+++..+...    .+.
T Consensus       118 ---~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  193 (307)
T 2ifu_A          118 ---ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPT  193 (307)
T ss_dssp             ---HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             ---HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhH
Confidence               18888888988 9999999999987432211111    35788899999999999999999999876421    110


Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH------hhHHHHHHHHHcCCCHHHHHH
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL------VSWTTIISGFAMHGMGKEAVE  226 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~------~~~~~li~~~~~~~~~~~a~~  226 (352)
                      ....+..+..++...|++++|...|++.. ..|+.      .....++.++ ..|+.+.+.+
T Consensus       194 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          194 CYKKCIAQVLVQLHRADYVAAQKCVRESY-SIPGFSGSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHh-CCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence            12366777788888899999999999987 64421      2344555555 5677666655

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.66  E-value=8e-07  Score=75.19  Aligned_cols=172  Identities=5%  Similarity=-0.164  Sum_probs=124.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCC--CC
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYT--EP  134 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--~p  134 (352)
                      ...+...+..+...|++++|.+.+++..+  +........+..   +..+...+...|++++|+..+++.......  .+
T Consensus        75 ~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~  151 (293)
T 2qfc_A           75 KKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQW---QYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDV  151 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHH---HHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCT
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHH---HHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCch
Confidence            44566678889999999999999886543  221111111111   445667788889999999999988432211  12


Q ss_pred             C--hhhHHHHHHHHHhCCChhhHHHHHHHHHhc---CCCCC--chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC----
Q 042593          135 S--EITILAVLPAIWKNGEVRNCQLIHGYGEKR---GFNAF--DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK----  203 (352)
Q Consensus       135 ~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----  203 (352)
                      .  ..+++.+...+...|++++|...+++..+.   ....+  ...++..+..+|.+.|++++|.+.+++.....+    
T Consensus       152 ~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~  231 (293)
T 2qfc_A          152 YQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINS  231 (293)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTB
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCc
Confidence            2  347889999999999999999999988732   21110  125888999999999999999999998643311    


Q ss_pred             ---CHhhHHHHHHHHHcCCCHHHH-HHHHHHHHh
Q 042593          204 ---NLVSWTTIISGFAMHGMGKEA-VENFERMQK  233 (352)
Q Consensus       204 ---~~~~~~~li~~~~~~~~~~~a-~~~~~~m~~  233 (352)
                         -..+|..+..+|.+.|+.++| ...+++...
T Consensus       232 ~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          232 MALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             CSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence               257788999999999999999 777887654

>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=98.62  E-value=2.2e-06  Score=80.60  Aligned_cols=204  Identities=8%  Similarity=-0.082  Sum_probs=153.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHH-HHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-------------C
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGT-QLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------------R   88 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~-~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------------~   88 (352)
                      +...|-..+..+.+.|+.+.|. ++++.....- +.+...|-..+...-+.|++++|.++|+.+.+             |
T Consensus       342 ~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~-P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p  420 (679)
T 4e6h_A          342 APEIWFNMANYQGEKNTDSTVITKYLKLGQQCI-PNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDP  420 (679)
T ss_dssp             CHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHST
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccC
Confidence            5566777777777889999996 9999998643 55666777888889999999999999998764             2


Q ss_pred             Cch------h-HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC-CChhhHHHHHH
Q 042593           89 NLV------T-WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN-GEVRNCQLIHG  160 (352)
Q Consensus        89 ~~~------~-~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~-~~~~~a~~~~~  160 (352)
                      +..      . -...     .|-..++...+.|+.+.|..+|.+..+..+ .+....|...+..-.+. ++.+.|..+|+
T Consensus       421 ~~~~~~~~~~~~~~~-----vWi~y~~~erR~~~l~~AR~vf~~A~~~~~-~~~~~lyi~~A~lE~~~~~d~e~Ar~ife  494 (679)
T 4e6h_A          421 TNESAINQLKSKLTY-----VYCVYMNTMKRIQGLAASRKIFGKCRRLKK-LVTPDIYLENAYIEYHISKDTKTACKVLE  494 (679)
T ss_dssp             TCHHHHHHHHHHHHH-----HHHHHHHHHHHHHCHHHHHHHHHHHHHTGG-GSCTHHHHHHHHHHHTTTSCCHHHHHHHH
T ss_pred             cchhhhhhhccchHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            100      0 0111     177788888888999999999999954412 11223333332222333 55899999999


Q ss_pred             HHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC----CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          161 YGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK----NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       161 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      ...+.-  |.+...+...++.....|+.+.|..+|+......|    ....|...+..-.+.|+.+.+..+.+++.+.-
T Consensus       495 ~~Lk~~--p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          495 LGLKYF--ATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHHHHH--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             HHHHHC--CCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            998872  32777888999999999999999999999877655    34778888888899999999999999999863

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.58  E-value=2.6e-06  Score=71.96  Aligned_cols=168  Identities=13%  Similarity=0.078  Sum_probs=123.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh----hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc----hhh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE----ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD----IHV  174 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~  174 (352)
                      +...+..+...|++++|.+.+++........++.    ..+..+...+...|++++|...++...+......+    ..+
T Consensus        78 l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            5567778899999999999998874433221211    22444566677889999999999988754322111    458


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhcc---CCCC-----HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhH
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSV---DRKN-----LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGE  246 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~  246 (352)
                      ++.+...|...|++++|.+.|++...   ..|+     ..+++.+...|...|++++|...+++..+..           
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~-----------  226 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEIS-----------  226 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHH-----------
Confidence            88999999999999999999998652   2222     2688899999999999999999999977631           


Q ss_pred             hHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHH-HHHHhcC
Q 042593          247 EGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQA-EEVASGI  291 (352)
Q Consensus       247 ~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A-~~~~~~m  291 (352)
                               ... +... -..+|..+..+|.+.|+.++| ...+++.
T Consensus       227 ---------~~~-~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          227 ---------CRI-NSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             ---------HHT-TBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             ---------Hhc-CcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence                     011 2222 256788899999999999999 6666654

>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=98.55  E-value=1e-06  Score=74.15  Aligned_cols=94  Identities=10%  Similarity=-0.132  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~  216 (352)
                      .+..+...+.+.|++++|...++...+....  +...|..+..+|.+.|++++|.+.+++.....| +...+..+..+|.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPL--VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc--cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            3444444455555555555555555444322  444455555555555555555555555443322 3444555555555


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 042593          217 MHGMGKEAVENFERMQK  233 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (352)
                      ..|++++|...|++..+
T Consensus        84 ~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           84 EMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            55555555555555443

>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=98.54  E-value=5.1e-07  Score=75.95  Aligned_cols=195  Identities=8%  Similarity=-0.096  Sum_probs=131.3

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      +...+..+...+.+.|++++|...|+...+.. +.+...|..+..+|.+.|++++|+..+++..+-++....+       
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~-------   74 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKA-------   74 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHH-------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHH-------
Confidence            56778888999999999999999999999875 4578889999999999999999999999987633322222       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+..++...|++++|...|++......-.+.  .+...+....+..   .... +.......... +......+.. +
T Consensus        75 ~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~--~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~-~~~i~~~l~~-l  146 (281)
T 2c2l_A           75 HFFLGQCQLEMESYDEAIANLQRAYSLAKEQRL--NFGDDIPSALRIA---KKKR-WNSIEERRIHQ-ESELHSYLTR-L  146 (281)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC--CCCSHHHHHHHHH---HHHH-HHHHHHTCCCC-CCHHHHHHHH-H
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCccchh--hHHHHHHHHHHHH---HHHH-HHHHHHHHHhh-hHHHHHHHHH-H
Confidence            888899999999999999999998443211111  1111222211111   1111 11222222332 4444444433 2


Q ss_pred             HhhCChHHHHHHHHHhccCCCCH-hhHHHHHHHHHcC-CCHHHHHHHHHHHHhc
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNL-VSWTTIISGFAMH-GMGKEAVENFERMQKV  234 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~-~~~~~li~~~~~~-~~~~~a~~~~~~m~~~  234 (352)
                       ..|+.++|.+.++......|+. .....+-..+.+. +.+++|.++|.+..+.
T Consensus       147 -~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          147 -IAAERERELEECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             -HHHHHHHHHTTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             -HHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence             3689999999998887666654 3334444444444 6688999999987664

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.53  E-value=4.1e-06  Score=66.13  Aligned_cols=159  Identities=9%  Similarity=-0.055  Sum_probs=108.4

Q ss_pred             HHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC----CCchhHHHHHHHHHhHHHHHHH
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE----RNLVTWNVIITGLVKWTGIIDG  109 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~~i~~~~~~~~li~~  109 (352)
                      +...|++++|.++++.+.. ........+..+...+...|++++|...+++..+    .+........     ++.+...
T Consensus         2 ~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~-----~~~l~~~   75 (203)
T 3gw4_A            2 AFEAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRA-----LHQVGMV   75 (203)
T ss_dssp             -----CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHH-----HHHHHHH
T ss_pred             ccccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHH-----HHHHHHH
Confidence            3467899999996655543 2124567899999999999999999999988754    1111111111     8888899


Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCC-C----hhhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCCCCchhhHHHHHH
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEP-S----EITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFNAFDIHVSNCLID  180 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p-~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~li~  180 (352)
                      +...|++++|...+++......-.+ +    ...+..+...+...|++++|...+++..+.    +.......++..+..
T Consensus        76 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~  155 (203)
T 3gw4_A           76 ERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGD  155 (203)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHH
Confidence            9999999999999998744311122 2    235777788888889999998888877643    211101334567778


Q ss_pred             HHHhhCChHHHHHHHHHh
Q 042593          181 TYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       181 ~~~~~g~~~~a~~~~~~~  198 (352)
                      ++...|++++|.+.+++.
T Consensus       156 ~~~~~g~~~~A~~~~~~a  173 (203)
T 3gw4_A          156 LAQQEKNLLEAQQHWLRA  173 (203)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHCcCHHHHHHHHHHH
Confidence            888888888888888776

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.52  E-value=1.5e-05  Score=67.50  Aligned_cols=198  Identities=5%  Similarity=-0.079  Sum_probs=155.2

Q ss_pred             cccHHHHHHHHHhcC--CcchHHHHHHHHHHhCCCCchhhHHHHHHHH----Hhc---CChhHHHHHhccCCCCCchhHH
Q 042593           24 SFTYSFLIRTCVTLS--YPNLGTQLHAVFSKVGFQSHVYVNTALGDMY----VSL---GFLKDSSKLFDELPERNLVTWN   94 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g--~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~----~~~---g~~~~a~~~~~~m~~~~~~~~~   94 (352)
                      ..+|+.--.++...|  ++++++++++.+.... +-+..+|+.--..+    .+.   +++++++++++++.+.++..|.
T Consensus        67 ~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~pkny~  145 (306)
T 3dra_A           67 YTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSDPKNHH  145 (306)
T ss_dssp             HHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhCCCCHH
Confidence            445666667777788  9999999999999876 45666777666666    555   7899999999999875555555


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHH--HHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC------hhhHHHHHHHHHhcC
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSN--EALALFRRMAACEYTEPSEITILAVLPAIWKNGE------VRNCQLIHGYGEKRG  166 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~------~~~a~~~~~~~~~~~  166 (352)
                      +       |+.-.-.+.+.|.++  ++++.++++.. .. .-|...|+.-...+.+.+.      ++++.+.++.+....
T Consensus       146 a-------W~~R~~vl~~l~~~~~~~EL~~~~~~i~-~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~  216 (306)
T 3dra_A          146 V-------WSYRKWLVDTFDLHNDAKELSFVDKVID-TD-LKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC  216 (306)
T ss_dssp             H-------HHHHHHHHHHTTCTTCHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC
T ss_pred             H-------HHHHHHHHHHhcccChHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC
Confidence            5       777777778888888  99999999944 32 2456678777777777776      888999999988886


Q ss_pred             CCCCchhhHHHHHHHHHhhCChHH-HHHHHHHhccC----CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          167 FNAFDIHVSNCLIDTYAKCGCIFS-ASKLFEDTSVD----RKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       167 ~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +.  +...|+-+-..+.+.|+... +.++.+++...    ..+...+..+...|.+.|+.++|.++++.+.+
T Consensus       217 p~--n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          217 PQ--NPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             SS--CHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CC--CccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            65  89999999999999888544 55677765543    34778899999999999999999999999876

>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=98.52  E-value=2.9e-06  Score=64.59  Aligned_cols=127  Identities=8%  Similarity=-0.072  Sum_probs=104.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...|++.....  +.+..++..+..++...|++++|...++...+....  +...+..+..++
T Consensus        16 ~~~~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~~a~~~   91 (166)
T 1a17_A           16 LKTQANDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK--YIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc--cHHHHHHHHHHH
Confidence            7888889999999999999999984432  235678889999999999999999999999887543  788899999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHH--HHHHHHcCCCHHHHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTT--IISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~--li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ...|++++|.+.|++.....| +...+..  +...+...|++++|...+.....
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            999999999999999766544 4555533  44447788999999999987654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.51  E-value=1.5e-06  Score=68.63  Aligned_cols=154  Identities=11%  Similarity=-0.035  Sum_probs=112.0

Q ss_pred             HhcCChhHHHH---HhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhc---cCCCC-ChhhHHHH
Q 042593           70 VSLGFLKDSSK---LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC---EYTEP-SEITILAV  142 (352)
Q Consensus        70 ~~~g~~~~a~~---~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~p-~~~t~~~l  142 (352)
                      ...|++++|.+   ++..-.......          ++.+...+...|++++|...+++....   .+..| ...++..+
T Consensus         3 ~~~g~~~~A~~~~~~~~~~~~~~~~~----------~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l   72 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAHPATASGA----------RFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQV   72 (203)
T ss_dssp             ----CHHHHHHHHHHHHTSTTTHHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHhcCChHHHHHH----------HHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            46799999999   554422112222          888889999999999999999987432   11122 23468888


Q ss_pred             HHHHHhCCChhhHHHHHHHHHhc----CCCC-CchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----HhhHHH
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKR----GFNA-FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LVSWTT  210 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~~~~~  210 (352)
                      ...+...|++++|...+++..+.    +..+ .....+..+..++...|++++|.+.+++....   ..+    ..++..
T Consensus        73 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  152 (203)
T 3gw4_A           73 GMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRG  152 (203)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            88999999999999999987764    2111 13556888899999999999999999886532   222    244678


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHh
Q 042593          211 IISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +...+...|++++|...+++..+
T Consensus       153 la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          153 LGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHH
Confidence            88899999999999999998765

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.51  E-value=3.9e-06  Score=60.21  Aligned_cols=96  Identities=16%  Similarity=0.141  Sum_probs=63.4

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~  215 (352)
                      ..+..+...+...|++++|...++++.+....  +..++..+..++.+.|++++|...|+++... +.+..++..+...+
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPN--NAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC--cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            45666666666777777777777766665432  5566666777777777777777777765544 33556666777777


Q ss_pred             HcCCCHHHHHHHHHHHHhc
Q 042593          216 AMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...|++++|...++++.+.
T Consensus        88 ~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHh
Confidence            7777777777777776653

>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=98.50  E-value=4.3e-07  Score=78.54  Aligned_cols=129  Identities=10%  Similarity=-0.095  Sum_probs=108.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-------------hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-------------EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-------------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  169 (352)
                      |..+...+.+.|++++|...|++......-.++             ...|..+..++.+.|++++|...++...+.... 
T Consensus       150 ~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-  228 (336)
T 1p5q_A          150 VKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN-  228 (336)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-
Confidence            888899999999999999999998443221110             378999999999999999999999999988644 


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHH-HHHHHHHHh
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEA-VENFERMQK  233 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a-~~~~~~m~~  233 (352)
                       +...+..+..+|...|++++|...|++.....| +...+..+..++.+.|+.++| ...++.|..
T Consensus       229 -~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          229 -NEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFE  293 (336)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             788999999999999999999999999876655 678888999999999999888 556777654

>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=98.50  E-value=7.1e-06  Score=65.74  Aligned_cols=157  Identities=8%  Similarity=-0.090  Sum_probs=127.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC----ChhHHHHHhccCCCC-CchhHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG----FLKDSSKLFDELPER-NLVTWNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g----~~~~a~~~~~~m~~~-~~~~~~~~i   97 (352)
                      ++..+..+...+...+++++|.+.|+...+.|   ++..+..|...|.. +    ++++|.+.|++..++ +...     
T Consensus        17 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g~~~a-----   87 (212)
T 3rjv_A           17 DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAGSKSG-----   87 (212)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTTCHHH-----
T ss_pred             CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCCCHHH-----
Confidence            78889999999999999999999999998876   56777788888887 6    899999999998654 3444     


Q ss_pred             HHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCCCCC---hhhHHHHHHHHHh----CCChhhHHHHHHHHHhcC
Q 042593           98 TGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYTEPS---EITILAVLPAIWK----NGEVRNCQLIHGYGEKRG  166 (352)
Q Consensus        98 ~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~p~---~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~  166 (352)
                           +..|...|..    .+++++|...|++. ...+  |+   ...+..+...|..    .++.++|...++...+.+
T Consensus        88 -----~~~Lg~~y~~g~g~~~d~~~A~~~~~~A-~~~~--~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~  159 (212)
T 3rjv_A           88 -----EIVLARVLVNRQAGATDVAHAITLLQDA-ARDS--ESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS  159 (212)
T ss_dssp             -----HHHHHHHHTCGGGSSCCHHHHHHHHHHH-TSST--TSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS
T ss_pred             -----HHHHHHHHHcCCCCccCHHHHHHHHHHH-HHcC--CCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC
Confidence                 6677777776    88999999999999 5444  32   5688888888888    889999999999998872


Q ss_pred             CCCCchhhHHHHHHHHHhh-C-----ChHHHHHHHHHhc
Q 042593          167 FNAFDIHVSNCLIDTYAKC-G-----CIFSASKLFEDTS  199 (352)
Q Consensus       167 ~~~~~~~~~~~li~~~~~~-g-----~~~~a~~~~~~~~  199 (352)
                      -   +...+..|..+|... |     +.++|.+.|+...
T Consensus       160 ~---~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~  195 (212)
T 3rjv_A          160 R---TGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSC  195 (212)
T ss_dssp             C---TTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHH
T ss_pred             C---CHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHH
Confidence            2   445667777777654 3     8999999998763

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.50  E-value=1.7e-06  Score=65.25  Aligned_cols=99  Identities=12%  Similarity=0.006  Sum_probs=64.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +..+...+.+.|++++|...|++.....  +-+...|..+..++...|++++|...+++..+....  ++..|..+..+|
T Consensus        39 ~~~lg~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~--~~~~~~~lg~~~  114 (151)
T 3gyz_A           39 IYSYAYDFYNKGRIEEAEVFFRFLCIYD--FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN--DYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS--CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC--CcHHHHHHHHHH
Confidence            5666666777777777777777763322  123456666777777777777777777777666433  566666777777


Q ss_pred             HhhCChHHHHHHHHHhccCCCCH
Q 042593          183 AKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .+.|++++|.+.|+......|+.
T Consensus       115 ~~lg~~~eA~~~~~~al~l~~~~  137 (151)
T 3gyz_A          115 LRLKAPLKAKECFELVIQHSNDE  137 (151)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCCCH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCH
Confidence            77777777777777665445554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.50  E-value=6.2e-07  Score=65.51  Aligned_cols=94  Identities=10%  Similarity=-0.070  Sum_probs=54.8

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~  216 (352)
                      .+......+.+.|++++|...|++..+....  +...|..+..+|.+.|++++|++.|++.... +.+...|..+..++.
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~   92 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRDPE--NAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLV   92 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            4555556666666666666666666555432  5555666666666666666666666654433 234555666666666


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 042593          217 MHGMGKEAVENFERMQK  233 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (352)
                      ..|++++|.+.|++..+
T Consensus        93 ~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           93 AMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHH
Confidence            66666666666666554

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.49  E-value=1.2e-05  Score=69.04  Aligned_cols=231  Identities=12%  Similarity=0.035  Sum_probs=161.6

Q ss_pred             HHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC-ChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHH
Q 042593           32 RTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG-FLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGY  110 (352)
Q Consensus        32 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~  110 (352)
                      ....+.+..++|+++++.+.... +-+..+|+.--.++...| ++++++++++.+...++..|.+       |+.-...+
T Consensus        62 ~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~a-------W~hR~wlL  133 (349)
T 3q7a_A           62 AIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQV-------WHHRLLLL  133 (349)
T ss_dssp             HHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHH-------HHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHH-------HHHHHHHH
Confidence            33344556678999999999876 445667888888888888 5999999999998766666555       77777777


Q ss_pred             Hhc-C-CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChh--------hHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          111 SRM-N-RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVR--------NCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       111 ~~~-~-~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      .+. + ++++++++++++.. .. +-|...|+.-.-.+.+.|.++        ++.+.++.+.+..+.  +...|+....
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~-~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~--N~SAW~~R~~  209 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLL-PD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGR--NNSAWGWRWY  209 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTS-SC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHH
T ss_pred             HHhcCCChHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCC--CHHHHHHHHH
Confidence            666 6 88999999999943 22 234556766665666666666        889999999988765  8889998888


Q ss_pred             HHHhhCC-------hHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCH--------------------HHHHHHHHHHH
Q 042593          181 TYAKCGC-------IFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMG--------------------KEAVENFERMQ  232 (352)
Q Consensus       181 ~~~~~g~-------~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~--------------------~~a~~~~~~m~  232 (352)
                      ++.+.++       ++++++.+++.... +-|...|+-+-..+.+.|+.                    .+..+...++.
T Consensus       210 lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  289 (349)
T 3q7a_A          210 LRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMP  289 (349)
T ss_dssp             HHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCC
T ss_pred             HHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHH
Confidence            8888876       67888888776555 44777787766666665543                    11111111111


Q ss_pred             hcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          233 KVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       233 ~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      ..+. ++                  . .-.++......|++.|...|+.++|.++++.+..+
T Consensus       290 ~~~~-~~------------------~-~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          290 SDPL-PE------------------D-TPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             C-CC-CS------------------S-CCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             hccc-cc------------------c-cCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            1100 00                  0 11357788899999999999999999999998644

>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=98.48  E-value=4.5e-06  Score=78.52  Aligned_cols=230  Identities=7%  Similarity=-0.107  Sum_probs=155.1

Q ss_pred             HHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHH-HHhccCCC--CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHH
Q 042593           43 GTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSS-KLFDELPE--RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEA  119 (352)
Q Consensus        43 a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~-~~~~~m~~--~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a  119 (352)
                      +..+|+.+...- +-+...|-..+..+...|+.++|. ++|+....  |....    +     |-..+...-+.|++++|
T Consensus       328 v~~~Ye~aL~~~-p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P~s~~----L-----wl~~a~~ee~~~~~e~a  397 (679)
T 4e6h_A          328 MTYVYMQAAQHV-CFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIPNSAV----L-----AFSLSEQYELNTKIPEI  397 (679)
T ss_dssp             HHHHHHHHHHHT-TTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCTTCHH----H-----HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHc-CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCCHH----H-----HHHHHHHHHHhCCHHHH
Confidence            456788887753 557788888888888899999996 99988764  43221    1     66777778889999999


Q ss_pred             HHHHHHhHhcc---------CCCCC------------hhhHHHHHHHHHhCCChhhHHHHHHHHHhc-CCCCCchhhHHH
Q 042593          120 LALFRRMAACE---------YTEPS------------EITILAVLPAIWKNGEVRNCQLIHGYGEKR-GFNAFDIHVSNC  177 (352)
Q Consensus       120 ~~~~~~m~~~~---------~~~p~------------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~  177 (352)
                      .++|+++....         .. |+            ...|...++...+.|..+.|..++....+. +..  ...+|..
T Consensus       398 R~iyek~l~~l~~~~~~~~~~~-p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~--~~~lyi~  474 (679)
T 4e6h_A          398 ETTILSCIDRIHLDLAALMEDD-PTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLV--TPDIYLE  474 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGS--CTHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhcc-CcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCC--ChHHHHH
Confidence            99999984321         11 42            235777788778889999999999998876 322  3344433


Q ss_pred             HHHHHHhh-CChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHH
Q 042593          178 LIDTYAKC-GCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKM  255 (352)
Q Consensus       178 li~~~~~~-g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m  255 (352)
                      ....--+. ++.+.|.++|+...+..| +...|...+......|+.+.|..+|++.......+.                
T Consensus       475 ~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~----------------  538 (679)
T 4e6h_A          475 NAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSH----------------  538 (679)
T ss_dssp             HHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTT----------------
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHH----------------
Confidence            33333344 458999999998766644 566677888878888999999999999887432111                


Q ss_pred             HHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHH
Q 042593          256 VEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRL  308 (352)
Q Consensus       256 ~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~  308 (352)
                             -....|...+..-.+.|+.+.+.++.+++....|+......++.-|
T Consensus       539 -------~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          539 -------LLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVNKLEEFTNKY  584 (679)
T ss_dssp             -------HHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCCHHHHHHHHT
T ss_pred             -------HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHh
Confidence                   0234555556666666666666666666654434444444444433

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.48  E-value=1.3e-06  Score=63.43  Aligned_cols=95  Identities=11%  Similarity=-0.042  Sum_probs=54.6

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      ..+..+...+...|++++|...++...+....  +...+..+..++...|++++|.+.++......| +...+..+...+
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELNPA--NAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcCCC--CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHH
Confidence            34555555566666666666666666554322  455555666666666666666666665543322 355555555666


Q ss_pred             HcCCCHHHHHHHHHHHHh
Q 042593          216 AMHGMGKEAVENFERMQK  233 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~  233 (352)
                      ...|++++|...+++..+
T Consensus        91 ~~~~~~~~A~~~~~~~~~  108 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALE  108 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHh
Confidence            666666666666665554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.48  E-value=1.6e-06  Score=63.32  Aligned_cols=95  Identities=12%  Similarity=0.025  Sum_probs=52.9

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~  215 (352)
                      ..+..+...+.+.|++++|...+++..+....  +...+..+..++...|++++|.+.+++..... .+...+..+..++
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~--~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~   94 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAIKRNPK--DAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAAL   94 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTT--CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHHH
Confidence            34555555556666666666666655554322  45555555555666666666666665544332 2345555555556


Q ss_pred             HcCCCHHHHHHHHHHHHh
Q 042593          216 AMHGMGKEAVENFERMQK  233 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~  233 (352)
                      ...|++++|...+++..+
T Consensus        95 ~~~~~~~~A~~~~~~~~~  112 (133)
T 2lni_A           95 EAMKDYTKAMDVYQKALD  112 (133)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHH
Confidence            666666666666655544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.46  E-value=3.6e-06  Score=61.30  Aligned_cols=113  Identities=4%  Similarity=-0.220  Sum_probs=92.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...|++... .. +.+...+..+..++...|++++|...+++..+....  +...+..+..++
T Consensus        19 ~~~~~~~~~~~~~~~~A~~~~~~al~-~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~la~~~   94 (133)
T 2lni_A           19 VKNKGNECFQKGDYPQAMKHYTEAIK-RN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT--FIKGYTRKAAAL   94 (133)
T ss_dssp             HHHHHHHHHHTTCSHHHHHHHHHHHT-TC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH-cC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--chHHHHHHHHHH
Confidence            78888999999999999999999843 22 235678889999999999999999999999887543  778899999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG  219 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~  219 (352)
                      .+.|++++|.+.|++.....| +...+..+..++...|
T Consensus        95 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           95 EAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHT
T ss_pred             HHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhc
Confidence            999999999999998765554 4556666666665544

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.46  E-value=4.6e-06  Score=59.83  Aligned_cols=111  Identities=13%  Similarity=0.101  Sum_probs=90.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|.+.|+++....  +.+..++..+...+.+.|++++|...++.+.+....  +..++..+..++
T Consensus        12 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~la~~~   87 (125)
T 1na0_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN--NAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCc--cHHHHHHHHHHH
Confidence            7788889999999999999999994432  235668889999999999999999999999887543  778889999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHc
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAM  217 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~  217 (352)
                      ...|++++|.+.|+++....| +...+..+...+..
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh
Confidence            999999999999999865544 45556555555443

>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=98.46  E-value=9.5e-07  Score=67.33  Aligned_cols=123  Identities=13%  Similarity=-0.045  Sum_probs=60.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh
Q 042593           61 VNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI  137 (352)
Q Consensus        61 ~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  137 (352)
                      .+..+...+...|++++|...|++..+  | +...          |..+...+...|++++|...+++.....  +.+..
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~----------~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~   82 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIY----------YGNRSLAYLRTECYGYALGDATRAIELD--KKYIK   82 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHhC--cccHH
Confidence            344444445555555555555554432  1 1222          4455555555556666666555552221  12334


Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhH--HHHHHHHHhhCChHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVS--NCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      .+..+..++...|++++|...+++..+....  +...+  ..+...+.+.|++++|.+.+..
T Consensus        83 ~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  142 (166)
T 1a17_A           83 GYYRRAASNMALGKFRAALRDYETVVKVKPH--DKDAKMKYQECNKIVKQKAFERAIAGDEH  142 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            5555555566666666666666665554332  33333  2233335555666666665554

>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=98.45  E-value=6.3e-07  Score=71.02  Aligned_cols=162  Identities=13%  Similarity=-0.019  Sum_probs=104.2

Q ss_pred             HHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC---------
Q 042593           65 LGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS---------  135 (352)
Q Consensus        65 li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~---------  135 (352)
                      .+......|+++++.+.++.-.+........       +..+...+...|++++|...|++......-.|+         
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~   82 (198)
T 2fbn_A           10 HSSGRENLYFQGAKKSIYDYTDEEKVQSAFD-------IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDK   82 (198)
T ss_dssp             ------------CCCSGGGCCHHHHHHHHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHH
T ss_pred             hhhhhhhhhhccccCchhhCCHHHHHHHHHH-------HHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHH
Confidence            4445556677777777776543211111111       777788889999999999999998543322221         


Q ss_pred             -----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHH
Q 042593          136 -----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWT  209 (352)
Q Consensus       136 -----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~  209 (352)
                           ...+..+..++.+.|++++|...++...+....  +...+..+..+|...|++++|.+.|++.....| +...+.
T Consensus        83 ~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~  160 (198)
T 2fbn_A           83 KKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKN--NVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRN  160 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc--cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHH
Confidence                 267888888999999999999999999887543  788888999999999999999999998765544 667777


Q ss_pred             HHHHHHHcCCCHHHHH-HHHHHHHhcC
Q 042593          210 TIISGFAMHGMGKEAV-ENFERMQKVG  235 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~-~~~~~m~~~~  235 (352)
                      .+..++...++.+++. ..+..|...+
T Consensus       161 ~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          161 SYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHHHHHHHHHC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            8877777777777666 5566665543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.44  E-value=1.3e-06  Score=72.59  Aligned_cols=190  Identities=7%  Similarity=-0.111  Sum_probs=137.3

Q ss_pred             hcCCcchHHHHHHHHHHhCCCCchhhHHHH-------HHHHHhcCChhHHHHHhccCCC--C-------C-chhH-----
Q 042593           36 TLSYPNLGTQLHAVFSKVGFQSHVYVNTAL-------GDMYVSLGFLKDSSKLFDELPE--R-------N-LVTW-----   93 (352)
Q Consensus        36 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~l-------i~~~~~~g~~~~a~~~~~~m~~--~-------~-~~~~-----   93 (352)
                      ..++...|.+.|....+.. +-....|..+       ...+.+.++..++...+..-.+  |       + ...|     
T Consensus        18 ~~~d~~~A~~~F~~a~~~d-P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            6899999999999999876 4456778777       4555555555555555554433  1       1 1111     


Q ss_pred             -----HHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC
Q 042593           94 -----NVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus        94 -----~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  168 (352)
                           ..+      +-.....+...|++++|.++|+.+ ...+  |+......+...+.+.+++++|+..++...+...+
T Consensus        97 ~v~~r~dl------~LayA~~L~~~g~y~eA~~~l~~~-~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~  167 (282)
T 4f3v_A           97 PVTSPLAI------TMGFAACEAAQGNYADAMEALEAA-PVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDK  167 (282)
T ss_dssp             ECSSHHHH------HHHHHHHHHHHTCHHHHHHHHTSS-CCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCH
T ss_pred             ccCCHhHH------HHHHHHHHHHCCCHHHHHHHHHHH-HhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCc
Confidence                 111      445667788999999999999999 4433  55446666666888999999999999866554311


Q ss_pred             CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC--CC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          169 AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR--KN--LVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       169 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~--~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      ......+..+-.++...|++++|++.|++.....  |.  .........++.+.|+.++|...|+++....
T Consensus       168 ~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          168 FLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             ccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            0013467788999999999999999999986432  53  3456677788999999999999999999854

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.44  E-value=4.9e-06  Score=60.25  Aligned_cols=115  Identities=5%  Similarity=-0.134  Sum_probs=96.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...|++.....  +.+...+..+...+...|++++|...++...+....  +...+..+..++
T Consensus        15 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~~~~   90 (131)
T 2vyi_A           15 LKTEGNEQMKVENFEAAVHFYGKAIELN--PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPA--YSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCcc--CHHHHHHHHHHH
Confidence            7778889999999999999999984432  235678889999999999999999999999887543  678899999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCH
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMG  221 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~  221 (352)
                      .+.|++++|.+.|++.....| +...+..+..++...|++
T Consensus        91 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcC
Confidence            999999999999998766544 677788888887777654

>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=98.42  E-value=2.3e-06  Score=66.27  Aligned_cols=118  Identities=8%  Similarity=0.029  Sum_probs=51.1

Q ss_pred             hcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH-HHhhCCh--
Q 042593          112 RMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT-YAKCGCI--  188 (352)
Q Consensus       112 ~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~-~~~~g~~--  188 (352)
                      ..|++++|...+++.....  +.+...+..+...+...|++++|...++...+....  +...+..+..+ +...|++  
T Consensus        22 ~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE--NAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             -----CCCCHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS--CHHHHHHHHHHHHHHTTTCCC
T ss_pred             hccCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC--CHHHHHHHHHHHHHhcCCcch
Confidence            3444555555554442211  122334444445555555555555555554444322  33444444444 4444544  


Q ss_pred             HHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          189 FSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ++|.+.|++.....| +...+..+...|...|++++|...+++..+
T Consensus        98 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A           98 AQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            555555544433322 334444444445555555555555554443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.41  E-value=2.1e-06  Score=64.83  Aligned_cols=102  Identities=12%  Similarity=0.030  Sum_probs=89.4

Q ss_pred             CCCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHH
Q 042593          132 TEPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWT  209 (352)
Q Consensus       132 ~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~  209 (352)
                      +.|+. ..+..+...+.+.|++++|...|+...+..+.  +...|..+..+|...|++++|.+.|++.....| ++..|.
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~--~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~  108 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY--NVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVF  108 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHH
Confidence            34543 47888888999999999999999999988654  889999999999999999999999999876655 678899


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          210 TIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      .+..+|...|++++|...|++..+..
T Consensus       109 ~lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          109 HTGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999999999999999999998853

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.40  E-value=5.5e-06  Score=58.21  Aligned_cols=99  Identities=8%  Similarity=-0.107  Sum_probs=83.3

Q ss_pred             ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC---CHhhHHHH
Q 042593          135 SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK---NLVSWTTI  211 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~~~~~l  211 (352)
                      +...+..+...+...|++++|...++...+....  +...+..+..++...|++++|.+.|++.....|   +...+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPE--ESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC--CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHH
Confidence            3456778888888999999999999998887543  677888899999999999999999998776644   57888889


Q ss_pred             HHHHHcC-CCHHHHHHHHHHHHhcC
Q 042593          212 ISGFAMH-GMGKEAVENFERMQKVG  235 (352)
Q Consensus       212 i~~~~~~-~~~~~a~~~~~~m~~~~  235 (352)
                      ..++... |++++|.+.+++..+..
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhhcc
Confidence            9999999 99999999999988764

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.40  E-value=6.7e-06  Score=59.89  Aligned_cols=106  Identities=9%  Similarity=-0.097  Sum_probs=89.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |......+.+.|++++|++.|++..+..  +.+...|..+..++.+.|++++|...++...+....  +...|..+..+|
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~--~~~a~~~lg~~~   91 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD--PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK--FIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh--hhHHHHHHHHHH
Confidence            7778889999999999999999984432  235678999999999999999999999999987654  788999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTII  212 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li  212 (352)
                      ...|++++|.+.|++..+..| +...+..+-
T Consensus        92 ~~~~~~~~A~~~~~~al~l~P~~~~a~~~l~  122 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQVDPSNEEAREGVR  122 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHCcCCHHHHHHHH
Confidence            999999999999999876655 455554443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.40  E-value=1.3e-06  Score=77.94  Aligned_cols=202  Identities=6%  Similarity=-0.088  Sum_probs=142.2

Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCCh---------------hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPSE---------------ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI  172 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~---------------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  172 (352)
                      ..+.+.|++++|++.|.++.+......+.               ..+..+...|...|++++|...+..+.+.-......
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            45678899999999999985543322221               137788999999999999999999886532111022


Q ss_pred             ----hhHHHHHHHHHhhCChHHHHHHHHHhccC------CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcc
Q 042593          173 ----HVSNCLIDTYAKCGCIFSASKLFEDTSVD------RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRS  241 (352)
Q Consensus       173 ----~~~~~li~~~~~~g~~~~a~~~~~~~~~~------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  241 (352)
                          .+.+.+-..+...|+.+.|.++++.....      .+ -..++..+...|...|++++|..++++....-...+  
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~--  169 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD--  169 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS--
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc--
Confidence                23334444455678899999998875432      22 246788899999999999999999998765321111  


Q ss_pred             hhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC---CCC-----chhhHHHHHHHHhccc
Q 042593          242 WRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ---ITN-----VVVWRTGFLRLLINSY  313 (352)
Q Consensus       242 ~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~-----~~~~~~li~~~~~~g~  313 (352)
                                        .-+-...++..++..|...|++++|..+++.....   .++     ...+..+...+...|+
T Consensus       170 ------------------~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  231 (434)
T 4b4t_Q          170 ------------------DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKD  231 (434)
T ss_dssp             ------------------CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSC
T ss_pred             ------------------cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHh
Confidence                              11113457888999999999999999998766433   122     2456667777888899


Q ss_pred             ccCcccccccchhhhh
Q 042593          314 FFSPITLNSQRLFFFP  329 (352)
Q Consensus       314 ~~~a~~~~~~~~~~~~  329 (352)
                      +++|...+.+.+..++
T Consensus       232 y~~A~~~~~~a~~~~~  247 (434)
T 4b4t_Q          232 YKTAFSYFFESFESYH  247 (434)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            9999888888765443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.37  E-value=6.1e-06  Score=61.41  Aligned_cols=96  Identities=11%  Similarity=-0.098  Sum_probs=74.0

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      ..+..+...+.+.|++++|...++...+....  +...|..+..+|.+.|++++|...|+......| +...+..+..+|
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLDHY--DARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhCCc--cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHH
Confidence            35566667777888888888888888776543  677788888888888888888888887665543 566777788888


Q ss_pred             HcCCCHHHHHHHHHHHHhc
Q 042593          216 AMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...|++++|...|++..+.
T Consensus        97 ~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            8888888888888887764

>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=98.36  E-value=5.5e-06  Score=62.26  Aligned_cols=96  Identities=10%  Similarity=-0.086  Sum_probs=78.1

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      ..+..+...+.+.|++++|...++...+....  +...|..+..+|...|++++|.+.|++.....| +...+..+..+|
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~   99 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLDHY--DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcCcc--cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            46667777888889999999999888877544  778888888888899999999999988765544 567788888888


Q ss_pred             HcCCCHHHHHHHHHHHHhc
Q 042593          216 AMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...|++++|...|++..+.
T Consensus       100 ~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            9999999999999887764

>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=98.35  E-value=3e-06  Score=63.70  Aligned_cols=98  Identities=9%  Similarity=-0.011  Sum_probs=83.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +..+...+.+.|++++|...|++.....  +.+...|..+..++...|++++|...++...+....  +...+..+..+|
T Consensus        24 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~--~~~~~~~lg~~~   99 (148)
T 2vgx_A           24 LYSLAFNQYQSGXYEDAHXVFQALCVLD--HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX--EPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CTHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC--CchHHHHHHHHH
Confidence            7778888999999999999999984432  235668889999999999999999999999987644  778889999999


Q ss_pred             HhhCChHHHHHHHHHhccCCCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      ...|++++|.+.|+......|+
T Consensus       100 ~~~g~~~~A~~~~~~al~~~p~  121 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQELIAN  121 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHcCCHHHHHHHHHHHHHHCcC
Confidence            9999999999999987655443

>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=98.33  E-value=2.1e-06  Score=66.49  Aligned_cols=122  Identities=11%  Similarity=0.021  Sum_probs=92.7

Q ss_pred             hcCChhHHHHHhccCCC--C-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHH-H
Q 042593           71 SLGFLKDSSKLFDELPE--R-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPA-I  146 (352)
Q Consensus        71 ~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~-~  146 (352)
                      ..|++++|...+++..+  | +...          |..+...+...|++++|...|++......  .+...+..+..+ +
T Consensus        22 ~~~~~~~A~~~~~~al~~~p~~~~~----------~~~lg~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~la~~l~   89 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRANPQNSEQ----------WALLGEYYLWQNDYSNSLLAYRQALQLRG--ENAELYAALATVLY   89 (177)
T ss_dssp             -----CCCCHHHHHHHHHCCSCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHHC--SCHHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHhCCCcHHH----------HHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHH
Confidence            45667777777766543  3 3334          88888999999999999999999844332  355677788888 7


Q ss_pred             HhCCCh--hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHh
Q 042593          147 WKNGEV--RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLV  206 (352)
Q Consensus       147 ~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  206 (352)
                      ...|++  ++|...++...+....  +...+..+..+|...|++++|...|++.....|+..
T Consensus        90 ~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~  149 (177)
T 2e2e_A           90 YQASQHMTAQTRAMIDKALALDSN--EITALMLLASDAFMQANYAQAIELWQKVMDLNSPRI  149 (177)
T ss_dssp             HHTTTCCCHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTS
T ss_pred             HhcCCcchHHHHHHHHHHHHhCCC--cHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCc
Confidence            789998  9999999999987644  678888999999999999999999999876655533

>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=98.32  E-value=5.6e-07  Score=71.30  Aligned_cols=154  Identities=12%  Similarity=-0.060  Sum_probs=105.1

Q ss_pred             HHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-C----------------Hhh
Q 042593          145 AIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-N----------------LVS  207 (352)
Q Consensus       145 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~----------------~~~  207 (352)
                      .....|+++.+...++.-.+....  ....+..+...+.+.|++++|.+.|++.....| +                ...
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~   90 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEEKVQ--SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISC   90 (198)
T ss_dssp             ---------CCCSGGGCCHHHHHH--HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHHHHH--HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHH
Confidence            344556666666666544332222  455677778888889999999999988765432 2                267


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHH
Q 042593          208 WTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEV  287 (352)
Q Consensus       208 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~  287 (352)
                      |..+..+|...|++++|...+++..+..                          +.+...+..+..+|...|++++|.+.
T Consensus        91 ~~~la~~~~~~~~~~~A~~~~~~al~~~--------------------------p~~~~~~~~lg~~~~~~~~~~~A~~~  144 (198)
T 2fbn_A           91 NLNLATCYNKNKDYPKAIDHASKVLKID--------------------------KNNVKALYKLGVANMYFGFLEEAKEN  144 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS--------------------------TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC--------------------------cccHHHHHHHHHHHHHcccHHHHHHH
Confidence            8888999999999999999999988741                          23667888899999999999999999


Q ss_pred             HhcCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          288 ASGIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       288 ~~~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      |++.... +.+...+..+...+...++.+++.......++
T Consensus       145 ~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          145 LYKAASLNPNNLDIRNSYELCVNKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             HHHHHHHSTTCHHHHHHHHHHHHHHHHHHC----------
T ss_pred             HHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9987665 55777888888888888888887744444333

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.28  E-value=3.6e-05  Score=68.51  Aligned_cols=197  Identities=10%  Similarity=-0.051  Sum_probs=143.5

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCC-c---------------hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CC
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQS-H---------------VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RN   89 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~-~---------------~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~   89 (352)
                      .+.+.+.|++++|.+.|..+.+..-.. +               ...+..|...|...|++++|.+.+..+.+     ++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            456788999999999999988754211 1               12477899999999999999999998764     11


Q ss_pred             chhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHh---ccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhc
Q 042593           90 LVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAA---CEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKR  165 (352)
Q Consensus        90 ~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  165 (352)
                      ... ..++     .+.+-..+...|+.++|..++++...   ..+..+. ..++..+...+...|++++|..+++++...
T Consensus        91 ~~~-~~~~-----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~  164 (434)
T 4b4t_Q           91 SKT-VKVL-----KTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLRE  164 (434)
T ss_dssp             HHH-HHHH-----HHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hHH-HHHH-----HHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHH
Confidence            111 1111     45555566677899999999888632   2223333 347788999999999999999999987643


Q ss_pred             ----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-----CC-C--HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          166 ----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-----RK-N--LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       166 ----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-----~~-~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                          +-.+....++..++..|...|++++|...++.....     .| .  ...+..+...+...|++++|...|.+..+
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          165 FKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             HTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             HHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence                222213568889999999999999999999876432     22 1  24566777788899999999998888765

>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=98.27  E-value=7.6e-06  Score=70.63  Aligned_cols=129  Identities=11%  Similarity=-0.050  Sum_probs=105.0

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc--------------hhhHHHHHHHHHhhCChHHHHHHHHHhccC
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD--------------IHVSNCLIDTYAKCGCIFSASKLFEDTSVD  201 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~--------------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  201 (352)
                      ...+..+...+.+.|++++|...|++..+..... .              ...|..+..+|.+.|++++|.+.+++....
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~-~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYE-SSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTC-CCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhcc-ccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4578888889999999999999999998876542 2              588899999999999999999999987665


Q ss_pred             C-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCC
Q 042593          202 R-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGR  280 (352)
Q Consensus       202 ~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  280 (352)
                      . .+...|..+..+|...|++++|...|++..+..  |                        -+...+..+..++.+.|+
T Consensus       226 ~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P------------------------~~~~a~~~l~~~~~~~~~  279 (336)
T 1p5q_A          226 DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY--P------------------------NNKAAKTQLAVCQQRIRR  279 (336)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--S------------------------SCHHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--C------------------------CCHHHHHHHHHHHHHHHH
Confidence            4 468889999999999999999999999988742  2                        255677788888888888


Q ss_pred             hhHHH-HHHhcC
Q 042593          281 LEQAE-EVASGI  291 (352)
Q Consensus       281 ~~~A~-~~~~~m  291 (352)
                      .++|. ..++.|
T Consensus       280 ~~~a~~~~~~~~  291 (336)
T 1p5q_A          280 QLAREKKLYANM  291 (336)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            88883 455544

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.27  E-value=1.3e-05  Score=59.53  Aligned_cols=113  Identities=11%  Similarity=0.000  Sum_probs=87.6

Q ss_pred             HHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHH
Q 042593           80 KLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIH  159 (352)
Q Consensus        80 ~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~  159 (352)
                      ..|++..+.++.....       +..+...+.+.|++++|...|++.....  +.+...|..+..++.+.|++++|...+
T Consensus         5 ~~l~~al~~~p~~~~~-------~~~~a~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~   75 (142)
T 2xcb_A            5 GTLAMLRGLSEDTLEQ-------LYALGFNQYQAGKWDDAQKIFQALCMLD--HYDARYFLGLGACRQSLGLYEQALQSY   75 (142)
T ss_dssp             ----CCTTCCHHHHHH-------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhHHHHHcCCHHHHHH-------HHHHHHHHHHHccHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            3455555544433222       6677788999999999999999984432  235668888999999999999999999


Q ss_pred             HHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      +...+....  +...+..+..+|...|++++|.+.|+......|
T Consensus        76 ~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  117 (142)
T 2xcb_A           76 SYGALMDIN--EPRFPFHAAECHLQLGDLDGAESGFYSARALAA  117 (142)
T ss_dssp             HHHHHHCTT--CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCC--CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            999988654  778888999999999999999999998765544

>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=98.24  E-value=2e-05  Score=57.83  Aligned_cols=99  Identities=11%  Similarity=-0.093  Sum_probs=83.5

Q ss_pred             CChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHH
Q 042593          134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTII  212 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li  212 (352)
                      .+...+..+...+...|++++|...++...+....  +...+..+..++...|++++|...++......| +...+..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL--VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcC--cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHH
Confidence            45667888888899999999999999998887644  678888999999999999999999988765544 578888899


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhc
Q 042593          213 SGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .++...|++++|...|++..+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            9999999999999999988764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.24  E-value=2.6e-05  Score=59.47  Aligned_cols=97  Identities=12%  Similarity=-0.065  Sum_probs=67.1

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISG  214 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~  214 (352)
                      ...+..+...+.+.|++++|...+++..+....  +...|..+..+|.+.|++++|...|++.....| +...|..+..+
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIAPA--NPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc--CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            345666666777777777777777777766433  566777777777777777777777777654433 46667777777


Q ss_pred             HHcCCCHHHHHHHHHHHHhc
Q 042593          215 FAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~  234 (352)
                      |...|++++|...|++..+.
T Consensus        89 ~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHh
Confidence            77777777777777776653

>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=98.23  E-value=1.6e-05  Score=57.61  Aligned_cols=94  Identities=10%  Similarity=-0.094  Sum_probs=56.4

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~  216 (352)
                      .+......+.+.|++++|...+++..+....  +...|..+..+|.+.|++++|.+.|++.....| +...|..+..++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRAPE--DARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC--ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            3444555556666666666666666555432  555666666666666666666666666544433 4555666666666


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 042593          217 MHGMGKEAVENFERMQK  233 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~  233 (352)
                      ..|++++|...|++..+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            66666666666666554

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.22  E-value=0.00017  Score=61.83  Aligned_cols=199  Identities=8%  Similarity=-0.061  Sum_probs=146.1

Q ss_pred             CcccHHHHHHHHHhcC-CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhc-C-ChhHHHHHhccCCCCCchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLS-YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSL-G-FLKDSSKLFDELPERNLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~-g-~~~~a~~~~~~m~~~~~~~~~~~i~~   99 (352)
                      +..+|+.--.++...| .+++++++++.+.... +-+..+|+.-..++.+. + ++++++++++++.+.|+..|.+    
T Consensus        87 ~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~dpkNy~A----  161 (349)
T 3q7a_A           87 HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPDPKNYHT----  161 (349)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSCTTCHHH----
T ss_pred             hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhCCCCHHH----
Confidence            3445666666677777 5999999999999866 55778888888888776 7 8999999999999866666555    


Q ss_pred             HHhHHHHHHHHHhcCCHH--------HHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC-------hhhHHHHHHHHHh
Q 042593          100 LVKWTGIIDGYSRMNRSN--------EALALFRRMAACEYTEPSEITILAVLPAIWKNGE-------VRNCQLIHGYGEK  164 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~--------~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~-------~~~a~~~~~~~~~  164 (352)
                         |+.-.-...+.|.++        ++++.++++.. .. .-|...|+.....+.+.+.       ++++.+.++....
T Consensus       162 ---W~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~-~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~  236 (349)
T 3q7a_A          162 ---WAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLR-VD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIH  236 (349)
T ss_dssp             ---HHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHhccccccchhhHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHH
Confidence               665555555555555        89999999844 32 2466688888888888776       5788888888888


Q ss_pred             cCCCCCchhhHHHHHHHHHhhCCh--------------------HHHHHHHHHhccC-------CCCHhhHHHHHHHHHc
Q 042593          165 RGFNAFDIHVSNCLIDTYAKCGCI--------------------FSASKLFEDTSVD-------RKNLVSWTTIISGFAM  217 (352)
Q Consensus       165 ~~~~~~~~~~~~~li~~~~~~g~~--------------------~~a~~~~~~~~~~-------~~~~~~~~~li~~~~~  217 (352)
                      ..+.  +...|+-+-..+.+.|+-                    ....++..++...       .+.......|...|..
T Consensus       237 ~~P~--n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~  314 (349)
T 3q7a_A          237 LIPH--NVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIE  314 (349)
T ss_dssp             HCTT--CHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHH
T ss_pred             hCCC--CHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHh
Confidence            7655  889998888788777754                    3344444444333       2567888899999999


Q ss_pred             CCCHHHHHHHHHHHHh
Q 042593          218 HGMGKEAVENFERMQK  233 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~  233 (352)
                      .|+.++|.++++.+.+
T Consensus       315 ~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          315 QNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHh
Confidence            9999999999999875

>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=98.22  E-value=1.3e-05  Score=58.35  Aligned_cols=110  Identities=9%  Similarity=0.055  Sum_probs=85.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--C-CchhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--R-NLVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~~i~~   99 (352)
                      ....+..+...+.+.|++++|++.|+...+.. |.+...|..+..+|.+.|++++|++.|++..+  | +...+..+..+
T Consensus         7 ~A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~   85 (127)
T 4gcn_A            7 AAIAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKA   85 (127)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHH
Confidence            34567889999999999999999999999876 55778899999999999999999999998764  2 11222222222


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITI  139 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~  139 (352)
                         |..+..++...|++++|++.|++...   ..||..+.
T Consensus        86 ---~~~lg~~~~~~~~~~~A~~~~~kal~---~~~~~~~~  119 (127)
T 4gcn_A           86 ---MSRAGNAFQKQNDLSLAVQWFHRSLS---EFRDPELV  119 (127)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHH---HSCCHHHH
T ss_pred             ---HHHHHHHHHHcCCHHHHHHHHHHHHh---hCcCHHHH
Confidence               77888889999999999999998744   23555443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.20  E-value=2e-05  Score=58.54  Aligned_cols=63  Identities=10%  Similarity=-0.082  Sum_probs=32.0

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +...+..+...+...|++++|.+.|++.....|+    ...|..+..+|...|++++|...+++..+
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~   93 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIE   93 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHh
Confidence            3444444555555555555555555554444443    34445555555555555555555555443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.20  E-value=5.8e-06  Score=63.16  Aligned_cols=97  Identities=8%  Similarity=-0.019  Sum_probs=71.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|.+.|+...+.. +.+...|..+..+|.+.|++++|+..|++..+  |+ ...       
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~-------   81 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKA-------   81 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHH-------
Confidence            45667777778888888888888888887765 44667777888888888888888888887654  32 233       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhcc
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACE  130 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  130 (352)
                         |..+..++...|++++|...|++.....
T Consensus        82 ---~~~lg~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           82 ---WSRLGLARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence               7777777888888888888888774433

>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=98.20  E-value=5.2e-05  Score=53.51  Aligned_cols=93  Identities=13%  Similarity=-0.052  Sum_probs=44.9

Q ss_pred             HHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHc
Q 042593          139 ILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAM  217 (352)
Q Consensus       139 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~  217 (352)
                      +..+...+...|++++|...++...+....  +...+..+..++...|++++|...+++.....| +...+..+..++..
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~   84 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLDPH--NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEF   84 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCCC--cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            334444444455555555555554443322  344444555555555555555555554433322 34444555555555


Q ss_pred             CCCHHHHHHHHHHHHh
Q 042593          218 HGMGKEAVENFERMQK  233 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~  233 (352)
                      .|++++|...+++..+
T Consensus        85 ~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           85 LNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             TTCHHHHHHHHHHHHT
T ss_pred             HhhHHHHHHHHHHHHH
Confidence            5555555555555443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.20  E-value=8.5e-06  Score=57.20  Aligned_cols=95  Identities=9%  Similarity=0.021  Sum_probs=81.2

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC---chhHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN---LVTWNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~---~~~~~~~i   97 (352)
                      +...+..+...+.+.|++++|...++...+.. +.+...+..+..++...|++++|...|++..+  |+   ...     
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~-----   78 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDV-----   78 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHH-----
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHH-----
Confidence            56778888899999999999999999998876 45678888999999999999999999998764  33   333     


Q ss_pred             HHHHhHHHHHHHHHhc-CCHHHHHHHHHHhHh
Q 042593           98 TGLVKWTGIIDGYSRM-NRSNEALALFRRMAA  128 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~  128 (352)
                           |..+...+... |++++|.+.+++...
T Consensus        79 -----~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           79 -----WAAKADALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             -----HHHHHHHHTTCSSCSHHHHHHHHHHGG
T ss_pred             -----HHHHHHHHHHHhCCHHHHHHHHHHHhh
Confidence                 88888999999 999999999999843

>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=98.20  E-value=6.4e-06  Score=60.06  Aligned_cols=91  Identities=12%  Similarity=0.043  Sum_probs=39.5

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC----C----HhhHHHHH
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK----N----LVSWTTII  212 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----~----~~~~~~li  212 (352)
                      .+...+.+.|++++|...|++..+....  +...|..+..+|.+.|++++|++.+++.....|    +    ..+|..+-
T Consensus        13 ~lG~~~~~~~~~~~A~~~y~~Al~~~p~--~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg   90 (127)
T 4gcn_A           13 DLGNAAYKQKDFEKAHVHYDKAIELDPS--NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAG   90 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHH
Confidence            3344444444444444444444443221  344444444444444444444444444322211    0    12344444


Q ss_pred             HHHHcCCCHHHHHHHHHHHHh
Q 042593          213 SGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .++...|++++|.+.|++..+
T Consensus        91 ~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           91 NAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHh
Confidence            445555555555555555443

>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=98.19  E-value=4.2e-05  Score=55.32  Aligned_cols=96  Identities=8%  Similarity=-0.128  Sum_probs=83.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+.+.|++++|+..|++.....  +.+...|..+..++.+.|++++|...++...+....  +...+..+..++
T Consensus         7 ~~~~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~   82 (126)
T 3upv_A            7 ARLEGKEYFTKSDWPNAVKAYTEMIKRA--PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN--FVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC--cHHHHHHHHHHH
Confidence            7778888999999999999999984432  235678999999999999999999999999988644  788899999999


Q ss_pred             HhhCChHHHHHHHHHhccCC
Q 042593          183 AKCGCIFSASKLFEDTSVDR  202 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~  202 (352)
                      ...|++++|.+.|++.....
T Consensus        83 ~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhC
Confidence            99999999999999876544

>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=98.19  E-value=7.2e-05  Score=52.76  Aligned_cols=105  Identities=8%  Similarity=-0.095  Sum_probs=87.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...|++.....  +.+...+..+...+...|++++|...+++..+....  +...+..+..++
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~a~~~   82 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD--WGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcc--cHHHHHHHHHHH
Confidence            7778888999999999999999984432  235668888999999999999999999999887544  788899999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTI  211 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~l  211 (352)
                      ...|++++|.+.++......| +...+..+
T Consensus        83 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l  112 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKHEANNPQLKEGL  112 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHcCCCCHHHHHHH
Confidence            999999999999999876655 44444443

>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=98.19  E-value=1.1e-05  Score=58.37  Aligned_cols=96  Identities=8%  Similarity=0.039  Sum_probs=76.1

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC----C----HhhH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK----N----LVSW  208 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----~----~~~~  208 (352)
                      ..+..+...+...|++++|...++...+....  +...+..+..++...|++++|...+++.....|    +    ..++
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELDPT--NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc--cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            35666777778888888888888888776533  677788888888889999999988888655422    2    6778


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          209 TTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       209 ~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+..++...|++++|...|++..+.
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            88889999999999999999998874

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.18  E-value=5.1e-05  Score=62.95  Aligned_cols=138  Identities=9%  Similarity=-0.090  Sum_probs=102.5

Q ss_pred             HHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC--hhhHH
Q 042593           63 TALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS--EITIL  140 (352)
Q Consensus        63 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~t~~  140 (352)
                      -.+..++...|++++|.++|+.+...++... .       ...+...+.+.+++++|+..|+.. .... .|.  ...+.
T Consensus       106 LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~-~-------~~~~a~l~~~~~r~~dA~~~l~~a-~~~~-d~~~~~~a~~  175 (282)
T 4f3v_A          106 MGFAACEAAQGNYADAMEALEAAPVAGSEHL-V-------AWMKAVVYGAAERWTDVIDQVKSA-GKWP-DKFLAGAAGV  175 (282)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHTSSCCTTCHHH-H-------HHHHHHHHHHTTCHHHHHHHHTTG-GGCS-CHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhcCCchH-H-------HHHHHHHHHHcCCHHHHHHHHHHh-hccC-CcccHHHHHH
Confidence            3466778899999999999999986433221 1       455556889999999999999876 3221 121  23678


Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCC-chhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHH
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAF-DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTT  210 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  210 (352)
                      .+-.++.+.|+.++|...|++.......|. ..........++.+.|+.++|..+|+++....|+...+..
T Consensus       176 ~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~~~~~~a  246 (282)
T 4f3v_A          176 AHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPEPKVAAA  246 (282)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCCHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHH
Confidence            889999999999999999999875443241 2345667788999999999999999999776777333333

>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=98.17  E-value=8.1e-06  Score=59.97  Aligned_cols=96  Identities=8%  Similarity=-0.147  Sum_probs=84.0

Q ss_pred             CCcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHH
Q 042593           22 FDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIIT   98 (352)
Q Consensus        22 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~   98 (352)
                      .+...+..+...+...|++++|...|+...+.. +.+...+..+..++...|++++|...|++..+  |+ ...      
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~------   79 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKA------   79 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH------
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHH------
Confidence            378889999999999999999999999998876 55678899999999999999999999998865  33 333      


Q ss_pred             HHHhHHHHHHHHHhcCCHHHHHHHHHHhHh
Q 042593           99 GLVKWTGIIDGYSRMNRSNEALALFRRMAA  128 (352)
Q Consensus        99 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  128 (352)
                          |..+..++...|++++|...|++...
T Consensus        80 ----~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           80 ----HFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             ----HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                88889999999999999999999843

>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=98.15  E-value=1.2e-05  Score=58.26  Aligned_cols=110  Identities=9%  Similarity=0.086  Sum_probs=88.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC-CCc----hhhHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN-AFD----IHVSNC  177 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~----~~~~~~  177 (352)
                      |..+...+...|++++|...|++.....  +.+...+..+...+...|++++|...++...+.... +.+    ..++..
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELD--PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHH
Confidence            7788889999999999999999984432  235668889999999999999999999998876432 102    678889


Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHH
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISG  214 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~  214 (352)
                      +..++.+.|++++|.+.|+......|+......+...
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~  121 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQA  121 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            9999999999999999999987666776655555443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.12  E-value=2.3e-05  Score=58.90  Aligned_cols=132  Identities=10%  Similarity=-0.022  Sum_probs=65.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC
Q 042593           60 YVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP  134 (352)
Q Consensus        60 ~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p  134 (352)
                      .++..+...+...|++++|...+++..+     ++...   ...   .+..+...+...|++++|...+++......-.+
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~---~~~---~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~   83 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAA---ERI---AYSNLGNAYIFLGEFETASEYYKKTLLLARQLK   83 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH---HHH---HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchH---HHH---HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhC
Confidence            3455566666666666666666665543     11110   000   066666777777777777777776532111111


Q ss_pred             C----hhhHHHHHHHHHhCCChhhHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          135 S----EITILAVLPAIWKNGEVRNCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       135 ~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      +    ...+..+...+...|++++|...+++..+.    +..+.....+..+..++...|++++|.+.+++
T Consensus        84 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  154 (164)
T 3ro3_A           84 DRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEK  154 (164)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            1    224445555555666666666555554432    11110123344444444455555555444443

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.12  E-value=3.2e-05  Score=55.79  Aligned_cols=90  Identities=12%  Similarity=-0.083  Sum_probs=42.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh
Q 042593          106 IIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC  185 (352)
Q Consensus       106 li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  185 (352)
                      +...+.+.|++++|...|++..+..  +-+...+..+..++...|++++|...+++..+....  +...+..+..+|.+.
T Consensus        23 ~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~--~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           23 EGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK--DIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHc
Confidence            3344445555555555555542211  112334444444555555555555555555444322  344444555555555


Q ss_pred             CChHHHHHHHHHhc
Q 042593          186 GCIFSASKLFEDTS  199 (352)
Q Consensus       186 g~~~~a~~~~~~~~  199 (352)
                      |++++|.+.|++..
T Consensus        99 g~~~~A~~~~~~al  112 (121)
T 1hxi_A           99 HNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            55555555555443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.11  E-value=9.2e-06  Score=73.28  Aligned_cols=129  Identities=12%  Similarity=-0.100  Sum_probs=103.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-------------hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-------------EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-------------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  169 (352)
                      |..+...+.+.|++++|...|++......-.++             ...|..+..++.+.|++++|...+++..+.... 
T Consensus       271 ~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-  349 (457)
T 1kt0_A          271 VKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA-  349 (457)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-
Confidence            888889999999999999999998553322211             468889999999999999999999999987644 


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHH-HHHHHHHh
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAV-ENFERMQK  233 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~-~~~~~m~~  233 (352)
                       +...|..+..+|...|++++|...|++.....| +...+..+..++.+.++.+++. ..+..|..
T Consensus       350 -~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          350 -NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             -cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             788899999999999999999999999877755 5677888888888888887775 44555544

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.09  E-value=0.00011  Score=54.38  Aligned_cols=104  Identities=9%  Similarity=-0.037  Sum_probs=80.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCL  178 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  178 (352)
                      +..+...+...|++++|...|++...   ..|+    ...+..+..++...|++++|...++...+....  +...+..+
T Consensus        31 ~~~~a~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~  105 (148)
T 2dba_A           31 LRKEGNELFKCGDYGGALAAYTQALG---LDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG--DVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC--CHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH---HcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc--CHHHHHHH
Confidence            77788888899999999999998833   3455    467788888888899999999999888876433  67778888


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCCC-HhhHHHH
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRKN-LVSWTTI  211 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l  211 (352)
                      ..++...|++++|.+.|++.....|+ ...+..+
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l  139 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVSLEPKNKVFQEAL  139 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHH
Confidence            88888999999999998887655443 3444333

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.09  E-value=9.8e-07  Score=79.65  Aligned_cols=147  Identities=9%  Similarity=-0.093  Sum_probs=111.8

Q ss_pred             ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----------------HhhHHHHHHH
Q 042593          151 EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----------------LVSWTTIISG  214 (352)
Q Consensus       151 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----------------~~~~~~li~~  214 (352)
                      ++++|...++...+..  |.....+..+...|.+.|++++|...|++.....|+                ...|..+..+
T Consensus       249 ~~~~A~~~~~~~~~~~--~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~  326 (457)
T 1kt0_A          249 SFEKAKESWEMDTKEK--LEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMC  326 (457)
T ss_dssp             EEECCCCGGGSCHHHH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccCcchhhcCHHHH--HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHH
Confidence            4445555554443332  215667888899999999999999999987655333                5889999999


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      |.+.|++++|...+++.++..  |                        -+...|..+..+|...|++++|...|++....
T Consensus       327 ~~~~g~~~~A~~~~~~al~~~--p------------------------~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l  380 (457)
T 1kt0_A          327 YLKLREYTKAVECCDKALGLD--S------------------------ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  380 (457)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS--T------------------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHhcCHHHHHHHHHHHHhcC--C------------------------ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999988742  2                        26778889999999999999999999988777


Q ss_pred             -CCCchhhHHHHHHHHhcccccCcccccccch
Q 042593          295 -ITNVVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       295 -~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                       +.+...+..+...+...++.++|.+...+.+
T Consensus       381 ~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          381 NPQNKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             C----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             6677888999999999998887775544443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.07  E-value=8.2e-06  Score=61.45  Aligned_cols=133  Identities=14%  Similarity=0.050  Sum_probs=75.8

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCC----CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC---CCC----Hh
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFN----AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD---RKN----LV  206 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~----~~  206 (352)
                      ++..+...+...|++++|...+++..+....    .....++..+...+...|++++|.+.+++....   .++    ..
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            3444455555555555555555554432111    001235566666777777777777777664332   111    34


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCC-CChhhHHHHHHHHHHcCChhHHH
Q 042593          207 SWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVL-PDIKHYGCLIDILERAGRLEQAE  285 (352)
Q Consensus       207 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~-p~~~~~~~li~~~~~~g~~~~A~  285 (352)
                      .+..+...+...|++++|...+++..+..                    ... +.. .....+..+...+...|++++|.
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--------------------~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~  149 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIA--------------------QEL-KDRIGEGRACWSLGNAYTALGNHDQAM  149 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH--------------------HHT-TCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHH--------------------HHc-cchHhHHHHHHHHHHHHHHccCHHHHH
Confidence            56666777777888888888777765421                    000 111 12345667777778888888887


Q ss_pred             HHHhcC
Q 042593          286 EVASGI  291 (352)
Q Consensus       286 ~~~~~m  291 (352)
                      +.+++.
T Consensus       150 ~~~~~a  155 (164)
T 3ro3_A          150 HFAEKH  155 (164)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.06  E-value=0.00041  Score=63.06  Aligned_cols=287  Identities=8%  Similarity=-0.107  Sum_probs=164.9

Q ss_pred             CcccHHHHHHHHHhcCC-cchHHHHHHHHHHh-CCC-CchhhHHHHHHHHH----hcCChhHHHHHhccCCC-CCchhHH
Q 042593           23 DSFTYSFLIRTCVTLSY-PNLGTQLHAVFSKV-GFQ-SHVYVNTALGDMYV----SLGFLKDSSKLFDELPE-RNLVTWN   94 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~-~~~a~~~~~~m~~~-~~~-~~~~~~~~li~~~~----~~g~~~~a~~~~~~m~~-~~~~~~~   94 (352)
                      +...|...++...+.+. .+.+..+|+..... |.. .+...|...+..+.    ..++++.+.++|+.... |... ..
T Consensus        46 s~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~-~~  124 (493)
T 2uy1_A           46 NLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGS-LS  124 (493)
T ss_dssp             CHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTT-HH
T ss_pred             CHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhh-HH
Confidence            88888888888877763 46677888887764 533 35677777776543    24568889999988754 3211 11


Q ss_pred             HHHHHHH------------------------------------------hHHHHHHHHHhc--CC-----HHHHHHHHHH
Q 042593           95 VIITGLV------------------------------------------KWTGIIDGYSRM--NR-----SNEALALFRR  125 (352)
Q Consensus        95 ~~i~~~~------------------------------------------~~~~li~~~~~~--~~-----~~~a~~~~~~  125 (352)
                      .+-..+.                                          .|...+.--...  +-     .+.+..+|++
T Consensus       125 ~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~  204 (493)
T 2uy1_A          125 ELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNY  204 (493)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHH
Confidence            1111110                                          011111100000  00     1234445555


Q ss_pred             hHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHH-HHHHHhcc----
Q 042593          126 MAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSAS-KLFEDTSV----  200 (352)
Q Consensus       126 m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~-~~~~~~~~----  200 (352)
                      +....  +.+...|...+.-+.+.|+.+.|..++++....   |.+...+.    .|+...+.++.. ++.+....    
T Consensus       205 al~~~--p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~---P~~~~l~~----~y~~~~e~~~~~~~l~~~~~~~~~~  275 (493)
T 2uy1_A          205 ILDSF--YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM---SDGMFLSL----YYGLVMDEEAVYGDLKRKYSMGEAE  275 (493)
T ss_dssp             HHHHT--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHH----HHHHHTTCTHHHHHHHHHTC-----
T ss_pred             HHHcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---CCcHHHHH----HHHhhcchhHHHHHHHHHHHhhccc
Confidence            52211  223445555666666777777777777777766   31333322    222221111111 11111100    


Q ss_pred             -----C-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh------------hHhHHHHHHHHHHhcCCC
Q 042593          201 -----D-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI------------GEEGLKFFDKMVEECEVL  262 (352)
Q Consensus       201 -----~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~~~~~~  262 (352)
                           . ......|-..+....+.+..+.|..+|++. +.. ..+...+.            .+.|..+|+...+.++- 
T Consensus       276 ~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~-  352 (493)
T 2uy1_A          276 SAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPD-  352 (493)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTT-
T ss_pred             hhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCC-
Confidence                 0 001234555566666778899999999998 321 12222222            66788999998886332 


Q ss_pred             CChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          263 PDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       263 p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                       ++..+...++...+.|+.+.|..+|+++..   ....|...+.--...|+.+.+..++.+++.
T Consensus       353 -~~~~~~~yid~e~~~~~~~~aR~l~er~~k---~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          353 -STLLKEEFFLFLLRIGDEENARALFKRLEK---TSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHSCC---BHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             344567778888899999999999999853   577888888877888998888887777764

>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=2.8e-05  Score=56.08  Aligned_cols=95  Identities=7%  Similarity=-0.094  Sum_probs=83.5

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFA  216 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~  216 (352)
                      .+..+...+.+.|++++|...++...+....  +...|..+..++...|++++|...|++.....| +...+..+..++.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~--~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPE--REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHT   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            4566777888999999999999999987654  788999999999999999999999999876655 6788999999999


Q ss_pred             cCCCHHHHHHHHHHHHhc
Q 042593          217 MHGMGKEAVENFERMQKV  234 (352)
Q Consensus       217 ~~~~~~~a~~~~~~m~~~  234 (352)
                      ..|++++|...+++..+.
T Consensus        97 ~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            999999999999998864

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.03  E-value=0.00026  Score=60.38  Aligned_cols=181  Identities=9%  Similarity=-0.006  Sum_probs=122.1

Q ss_pred             cHHHHHHHH---HhcCCcc-hHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC----------hhHHHHHhccCCCCCch
Q 042593           26 TYSFLIRTC---VTLSYPN-LGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF----------LKDSSKLFDELPERNLV   91 (352)
Q Consensus        26 ~~~~ll~~~---~~~g~~~-~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~   91 (352)
                      .|..+...+   .+.|.+. +|+++.+.+.... |-+..+|+.--..+...+.          +++++.+++.+...++.
T Consensus        28 ~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~n-P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PK  106 (331)
T 3dss_A           28 LYQSATQAVFQKRQAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK  106 (331)
T ss_dssp             HHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCC
Confidence            444444433   3566666 7899999988765 3334446554444433332          57888888888764444


Q ss_pred             hHHHHHHHHHhHHHHHHHHHhcC--CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC-hhhHHHHHHHHHhcCCC
Q 042593           92 TWNVIITGLVKWTGIIDGYSRMN--RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGE-VRNCQLIHGYGEKRGFN  168 (352)
Q Consensus        92 ~~~~~i~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~~~~~~~~  168 (352)
                      .|.+       |+.-...+.+.+  ++++++.+++++....  +-|...|+.-.-.+...|. ++++...++.+.+..+.
T Consensus       107 ny~a-------W~hR~wlL~~l~~~~~~~EL~~~~k~l~~d--prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~  177 (331)
T 3dss_A          107 SYGT-------WHHRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS  177 (331)
T ss_dssp             CHHH-------HHHHHHHHHHCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC
T ss_pred             CHHH-------HHHHHHHHhccCcccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC
Confidence            4444       777767777777  4899999999995433  2456678777777778888 58999999999988765


Q ss_pred             CCchhhHHHHHHHHHhh--------------CChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcC
Q 042593          169 AFDIHVSNCLIDTYAKC--------------GCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMH  218 (352)
Q Consensus       169 ~~~~~~~~~li~~~~~~--------------g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~  218 (352)
                        +...|+....++.+.              +.++++++.++..... +-|...|+-+-..+.+.
T Consensus       178 --N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~  240 (331)
T 3dss_A          178 --NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAG  240 (331)
T ss_dssp             --CHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSS
T ss_pred             --CHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence              888888877777665              4577888888876544 44677776444434333

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.02  E-value=7.6e-05  Score=53.96  Aligned_cols=89  Identities=13%  Similarity=0.011  Sum_probs=42.6

Q ss_pred             HHHHHhCCChhhHHHHHHHHHhcCCCCCch---hhHHHHHHHHHhhCChHHHHHHHHHhccCCCC----HhhHHHHHHHH
Q 042593          143 LPAIWKNGEVRNCQLIHGYGEKRGFNAFDI---HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN----LVSWTTIISGF  215 (352)
Q Consensus       143 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~li~~~  215 (352)
                      ...+...|++++|...++...+....  +.   ..+..+..++.+.|++++|...|+......|+    ...+..+..++
T Consensus         9 a~~~~~~~~~~~A~~~~~~~~~~~p~--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~   86 (129)
T 2xev_A            9 AFDALKNGKYDDASQLFLSFLELYPN--GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSS--STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHCCC--CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHH
Confidence            33444455555555555554443322  12   34444455555555555555555554333222    33444455555


Q ss_pred             HcCCCHHHHHHHHHHHHh
Q 042593          216 AMHGMGKEAVENFERMQK  233 (352)
Q Consensus       216 ~~~~~~~~a~~~~~~m~~  233 (352)
                      ...|++++|...|+++.+
T Consensus        87 ~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            555555555555555544

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.02  E-value=0.00011  Score=53.07  Aligned_cols=101  Identities=7%  Similarity=-0.142  Sum_probs=80.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc---hhhHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD---IHVSNCL  178 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~~l  178 (352)
                      +..+...+...|++++|...|++......-.+. ...+..+..++.+.|++++|...++...+....  +   ...+..+
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~--~~~~~~~~~~l   82 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT--HDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--STTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC--CcccHHHHHHH
Confidence            445567788999999999999998443321111 147788889999999999999999999887644  4   6678889


Q ss_pred             HHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      ..++.+.|++++|.+.|+.+....|+.
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~~~p~~  109 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVATQYPGS  109 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence            999999999999999999987666653

>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=97.99  E-value=1.1e-05  Score=73.12  Aligned_cols=124  Identities=12%  Similarity=0.006  Sum_probs=91.1

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG  219 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~  219 (352)
                      .+...+.+.|++++|...+++..+....  +...+..+..+|.+.|++++|.+.+++..+..| +...|..+..+|...|
T Consensus        11 ~lg~~~~~~g~~~~A~~~~~~Al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g   88 (477)
T 1wao_1           11 TQANDYFKAKDYENAIKFYSQAIELNPS--NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALG   88 (477)
T ss_dssp             SSSSSTTTTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhCCc--cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            3344567889999999999988887543  688888999999999999999999988776644 5788888888999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHH--HHHcCChhHHHHHHhcCC
Q 042593          220 MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDI--LERAGRLEQAEEVASGIP  292 (352)
Q Consensus       220 ~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~--~~~~g~~~~A~~~~~~m~  292 (352)
                      ++++|.+.+++..+..  |                        -+...+..+..+  +.+.|++++|.+.+++..
T Consensus        89 ~~~eA~~~~~~al~~~--p------------------------~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~~  137 (477)
T 1wao_1           89 KFRAALRDYETVVKVK--P------------------------HDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  137 (477)
T ss_dssp             CHHHHHHHHHHHHHHS--T------------------------TCTTHHHHHHHHHHHHHHHHHCCC------CC
T ss_pred             CHHHHHHHHHHHHHhC--C------------------------CCHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            9999999999887642  1                        133445555555  788899999998887543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.97  E-value=6.6e-06  Score=58.94  Aligned_cols=85  Identities=12%  Similarity=0.069  Sum_probs=58.2

Q ss_pred             hcCCcchHHHHHHHHHHhC--CCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHHHHhHHHHHHHH
Q 042593           36 TLSYPNLGTQLHAVFSKVG--FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITGLVKWTGIIDGY  110 (352)
Q Consensus        36 ~~g~~~~a~~~~~~m~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~~~~~~~li~~~  110 (352)
                      ..|++++|+..|+...+.+  -+.+...+..+..+|...|++++|+..|++..+  |+. ..          +..+..++
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~----------~~~l~~~~   71 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQAL----------RVFYAMVL   71 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH----------HHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHH----------HHHHHHHH
Confidence            4577888888888887754  233556777888888888888888888887764  332 22          67777788


Q ss_pred             HhcCCHHHHHHHHHHhHhcc
Q 042593          111 SRMNRSNEALALFRRMAACE  130 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~  130 (352)
                      ...|++++|...|++.....
T Consensus        72 ~~~g~~~~A~~~~~~al~~~   91 (117)
T 3k9i_A           72 YNLGRYEQGVELLLKIIAET   91 (117)
T ss_dssp             HHHTCHHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC
Confidence            88888888888888774433

>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=97.92  E-value=3.4e-05  Score=69.93  Aligned_cols=122  Identities=9%  Similarity=-0.054  Sum_probs=94.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhHhccCCCC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          104 TGIIDGYSRMNRSNEALALFRRMAACEYTEP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       104 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      ..+...+.+.|++++|.+.|++..+.   .| +..++..+..++.+.|++++|...+++..+....  +...+..+..+|
T Consensus        10 ~~lg~~~~~~g~~~~A~~~~~~Al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~--~~~~~~~lg~~~   84 (477)
T 1wao_1           10 KTQANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK--YIKGYYRRAASN   84 (477)
T ss_dssp             SSSSSSTTTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence            33445678899999999999998443   34 4678999999999999999999999999987544  788999999999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHH--HHcCCCHHHHHHHHHH
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISG--FAMHGMGKEAVENFER  230 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~--~~~~~~~~~a~~~~~~  230 (352)
                      .+.|++++|.+.|++..+..| +...+..+..+  +.+.|++++|.+.+++
T Consensus        85 ~~~g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~  135 (477)
T 1wao_1           85 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEH  135 (477)
T ss_dssp             HHHTCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC------
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            999999999999999766544 44555555555  7788888888888765

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.90  E-value=2.9e-05  Score=67.01  Aligned_cols=131  Identities=8%  Similarity=-0.131  Sum_probs=71.9

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH------------------hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL------------------VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~------------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+..+...+.+.|++++|...|++.....|+.                  ..|..+..+|.+.|++++|...+++.++.
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  259 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTE  259 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            334455555556666666666666544333332                  27888999999999999999999998873


Q ss_pred             CCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHH-HHhcc
Q 042593          235 GLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLR-LLINS  312 (352)
Q Consensus       235 ~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~-~~~~g  312 (352)
                      .                          +-+...|..+..+|...|++++|...|++.... +.+...+..+... ....+
T Consensus       260 ~--------------------------p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~  313 (338)
T 2if4_A          260 E--------------------------EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKA  313 (338)
T ss_dssp             C--------------------------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC---------------------
T ss_pred             C--------------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Confidence            2                          226778899999999999999999999999877 4555666666554 34456


Q ss_pred             cccCcccccccchhhhh
Q 042593          313 YFFSPITLNSQRLFFFP  329 (352)
Q Consensus       313 ~~~~a~~~~~~~~~~~~  329 (352)
                      ..+++...+..++...|
T Consensus       314 ~~~~a~~~~~~~l~~~p  330 (338)
T 2if4_A          314 LYQKQKEMYKGIFKGKD  330 (338)
T ss_dssp             -----------------
T ss_pred             HHHHHHHHHHHhhCCCC
Confidence            66677777777665444

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.88  E-value=3.2e-05  Score=69.93  Aligned_cols=131  Identities=5%  Similarity=-0.161  Sum_probs=97.9

Q ss_pred             HHhCCChhhHHHHHHHHHhc-----CCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--------CCC-HhhHHH
Q 042593          146 IWKNGEVRNCQLIHGYGEKR-----GFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--------RKN-LVSWTT  210 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~-----~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--------~~~-~~~~~~  210 (352)
                      +...|++++|+.++++..+.     |.. |....+++.|..+|...|++++|+.++++....        .|+ ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            55789999999999887653     222 213568899999999999999999999875432        454 467999


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhc
Q 042593          211 IISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASG  290 (352)
Q Consensus       211 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  290 (352)
                      |...|...|++++|+.++++..+                 +++..... ..+-...+.+.+-.++...|.+++|+.++.+
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~-----------------i~~~~lG~-~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~  460 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYA-----------------ILLVTHGP-SHPITKDLEAMRMQTEMELRMFRQNEFMYHK  460 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH-----------------HHHHHTCT-TSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHH-----------------HHHHHhCC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998665                 22222211 2222345667778888899999999999988


Q ss_pred             CCCC
Q 042593          291 IPSQ  294 (352)
Q Consensus       291 m~~~  294 (352)
                      +++.
T Consensus       461 ~~~~  464 (490)
T 3n71_A          461 MREA  464 (490)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7653

>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=97.85  E-value=3.6e-05  Score=67.30  Aligned_cols=125  Identities=10%  Similarity=-0.141  Sum_probs=88.7

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhcc----------------C-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSV----------------D-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~----------------~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      ..+..+...+.+.|++++|.+.|++...                . +.+...|..+..+|.+.|++++|...+++..+..
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            3466677777888888888888877654                2 2245677778888888888888888888877631


Q ss_pred             CCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccc
Q 042593          236 LKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYF  314 (352)
Q Consensus       236 ~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~  314 (352)
                        |                        -+...+..+..+|.+.|++++|.+.|++.... +.+...+..+...+...++.
T Consensus       304 --p------------------------~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~  357 (370)
T 1ihg_A          304 --P------------------------SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQ  357 (370)
T ss_dssp             --T------------------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             --c------------------------hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence              2                        25667777888888888888888888877655 44566777777777777777


Q ss_pred             cCccccccc
Q 042593          315 FSPITLNSQ  323 (352)
Q Consensus       315 ~~a~~~~~~  323 (352)
                      +++.+...+
T Consensus       358 ~~a~k~~~~  366 (370)
T 1ihg_A          358 KDKEKAAYA  366 (370)
T ss_dssp             HHHHHCCC-
T ss_pred             HHHHHHHHH
Confidence            666554433

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.85  E-value=6.4e-05  Score=64.87  Aligned_cols=127  Identities=9%  Similarity=-0.065  Sum_probs=78.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh------------------hHHHHHHHHHhCCChhhHHHHHHHHHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI------------------TILAVLPAIWKNGEVRNCQLIHGYGEK  164 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~------------------t~~~ll~~~~~~~~~~~a~~~~~~~~~  164 (352)
                      |..+...+.+.|++++|...|++....   .|+..                  .|..+..++.+.|++++|...++...+
T Consensus       182 ~~~~g~~~~~~g~~~~A~~~y~~Al~~---~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~  258 (338)
T 2if4_A          182 RKMDGNSLFKEEKLEEAMQQYEMAIAY---MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLT  258 (338)
T ss_dssp             HHHHHHHTCSSSCCHHHHHHHHHHHHH---SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHH---hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            778888899999999999999997442   24433                  778888889999999999999999888


Q ss_pred             cCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHH-HHcCCCHHHHHHHHHHHHhc
Q 042593          165 RGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISG-FAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       165 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ....  +...|..+..+|...|++++|.+.|++.....| +...+..+... ....+..+++...|..|...
T Consensus       259 ~~p~--~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          259 EEEK--NPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             HCTT--CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------------------------
T ss_pred             hCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            7543  788888999999999999999999999876655 44555555544 33455677888888887754

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.83  E-value=3.6e-05  Score=55.01  Aligned_cols=85  Identities=11%  Similarity=-0.073  Sum_probs=47.7

Q ss_pred             CCChhhHHHHHHHHHhcCCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHH
Q 042593          149 NGEVRNCQLIHGYGEKRGFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVE  226 (352)
Q Consensus       149 ~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~  226 (352)
                      .|++++|...+++..+.+.. |.+...+..+..+|.+.|++++|.+.|++.....| +...+..+..++...|++++|..
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHH
Confidence            45566666666666554311 21445566666666666666666666666544433 45556666666666666666666


Q ss_pred             HHHHHHh
Q 042593          227 NFERMQK  233 (352)
Q Consensus       227 ~~~~m~~  233 (352)
                      .+++..+
T Consensus        83 ~~~~al~   89 (117)
T 3k9i_A           83 LLLKIIA   89 (117)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6666554

>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=97.83  E-value=0.00019  Score=62.63  Aligned_cols=90  Identities=11%  Similarity=0.039  Sum_probs=63.5

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHH
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGL  249 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~  249 (352)
                      +..+|..+..+|.+.|++++|.+.+++.....| +...|..+..+|...|++++|...|++..+..  |           
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~--P-----------  338 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA--P-----------  338 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--C-----------
Confidence            566777788888888888888888887766544 56777778888888888888888888877631  2           


Q ss_pred             HHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHH
Q 042593          250 KFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEE  286 (352)
Q Consensus       250 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~  286 (352)
                                   -+...+..+..++.+.++.+++.+
T Consensus       339 -------------~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          339 -------------EDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             -------------TCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -------------CCHHHHHHHHHHHHHHHHHHHHHH
Confidence                         144555566666666666665543

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.80  E-value=8.3e-05  Score=52.06  Aligned_cols=96  Identities=13%  Similarity=-0.009  Sum_probs=78.1

Q ss_pred             CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhH
Q 042593          204 NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQ  283 (352)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  283 (352)
                      +...+..+...+...|++++|...|++..+..                          +.+...+..+..++.+.|++++
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--------------------------p~~~~~~~~lg~~~~~~g~~~~   56 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ--------------------------PQNPVGYSNKAMALIKLGEYTQ   56 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--------------------------TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--------------------------CCCHHHHHHHHHHHHHhcCHHH
Confidence            45677888889999999999999999988742                          2256788899999999999999


Q ss_pred             HHHHHhcCCCC-CCC------chhhHHHHHHHHhcccccCcccccccch
Q 042593          284 AEEVASGIPSQ-ITN------VVVWRTGFLRLLINSYFFSPITLNSQRL  325 (352)
Q Consensus       284 A~~~~~~m~~~-~~~------~~~~~~li~~~~~~g~~~~a~~~~~~~~  325 (352)
                      |.+.+++.... +.+      ...+..+...+...|+++.|+..+.+..
T Consensus        57 A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           57 AIQMCQQGLRYTSTAEHVAIRSKLQYRLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             HHHHHHHHHTSCSSTTSHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHhHhhhHhHHHHhH
Confidence            99999988766 334      5677788888889999999988777643

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.80  E-value=0.00021  Score=64.62  Aligned_cols=128  Identities=9%  Similarity=-0.157  Sum_probs=98.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhc--cCC---CCCh-hhHHHHHHHHHhCCChhhHHHHHHHHHhc-----CCC-CCchhh
Q 042593          107 IDGYSRMNRSNEALALFRRMAAC--EYT---EPSE-ITILAVLPAIWKNGEVRNCQLIHGYGEKR-----GFN-AFDIHV  174 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~--~~~---~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~~~~~  174 (352)
                      +..+...|++++|+.++++.+..  .-+   .|+. .+++.+..+|...|++++|..++++..+.     |.. |....+
T Consensus       316 a~~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~  395 (490)
T 3n71_A          316 IDKARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMA  395 (490)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            34566889999999999887432  112   2332 47999999999999999999999987642     433 214568


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccC--------CCCH-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVD--------RKNL-VSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~--------~~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ++.|...|...|++++|+.++++....        .|++ .+.+.+-.++...+.+++|+.++.++.+.
T Consensus       396 l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          396 VMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999875432        3443 45667778888999999999999998763

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.74  E-value=0.00022  Score=54.07  Aligned_cols=64  Identities=13%  Similarity=0.046  Sum_probs=45.9

Q ss_pred             chhhHHHHHHHHHhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +...|..+..+|.+.|++++|...++...... .+...|..+..+|...|++++|...|++..+.
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            45667777777777777777777777765443 35677777777777777888777777777653

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.74  E-value=0.00032  Score=53.10  Aligned_cols=101  Identities=7%  Similarity=-0.109  Sum_probs=83.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhcc-------CC--------CC-ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcC
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACE-------YT--------EP-SEITILAVLPAIWKNGEVRNCQLIHGYGEKRG  166 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~-------~~--------~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  166 (352)
                      +......+.+.|++++|+..|.+.....       ..        .| +...|..+..++.+.|++++|...++...+..
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            7778888999999999999999984430       00        12 23578889999999999999999999999885


Q ss_pred             CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          167 FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       167 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      ..  +...|..+..+|...|++++|.+.|+......|+.
T Consensus        94 p~--~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~  130 (162)
T 3rkv_A           94 ET--NEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAA  130 (162)
T ss_dssp             TT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGG
T ss_pred             Cc--chHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCC
Confidence            44  78899999999999999999999999987666653

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.62  E-value=0.00096  Score=61.68  Aligned_cols=176  Identities=9%  Similarity=-0.023  Sum_probs=134.2

Q ss_pred             hcCCc-chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC----------hhHHHHHhccCCCCCchhHHHHHHHHHhHH
Q 042593           36 TLSYP-NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF----------LKDSSKLFDELPERNLVTWNVIITGLVKWT  104 (352)
Q Consensus        36 ~~g~~-~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~----------~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~  104 (352)
                      +.|.+ ++|++.++.+.... +-+..+|+.--.++.+.|+          ++++.+.++++.+.++..|.+       |+
T Consensus        40 ~~~~~~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~a-------W~  111 (567)
T 1dce_A           40 QAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGT-------WH  111 (567)
T ss_dssp             HTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHH-------HH
T ss_pred             HcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHH-------HH
Confidence            44444 57799999999876 4455667777777777666          899999999998755555555       88


Q ss_pred             HHHHHHHhcC--CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCC-ChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          105 GIIDGYSRMN--RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNG-EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       105 ~li~~~~~~~--~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      .-...+.+.+  +++++++.++++.+..  +-+...|+.-..++.+.| ..+++.+.++.+.+..+.  +...|+....+
T Consensus       112 hR~w~l~~l~~~~~~~el~~~~k~l~~d--~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~--n~saW~~r~~l  187 (567)
T 1dce_A          112 HRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS--NYSSWHYRSCL  187 (567)
T ss_dssp             HHHHHHHTCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC--CHHHHHHHHHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHhhc--cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCC--CccHHHHHHHH
Confidence            8888888888  7799999999995533  246678888888888888 889999999999887655  88899888888


Q ss_pred             HHhh--------------CChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHH
Q 042593          182 YAKC--------------GCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKE  223 (352)
Q Consensus       182 ~~~~--------------g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~  223 (352)
                      +.+.              +.++++.+.++......| |...|+-+-..+.+.++.++
T Consensus       188 l~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          188 LPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             HHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             HHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence            7764              557888888887655444 67788877777777776444

>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=97.61  E-value=0.0022  Score=54.64  Aligned_cols=181  Identities=8%  Similarity=-0.087  Sum_probs=129.5

Q ss_pred             cchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC--hhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCC-H
Q 042593           40 PNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF--LKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNR-S  116 (352)
Q Consensus        40 ~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~--~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~-~  116 (352)
                      +++++.+++.+.... +-+..+|+.-..++.+.++  +++++.+++++.+.|+..|.+       |+.-.-.....|. +
T Consensus        90 l~~EL~~~~~~L~~~-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~A-------W~~R~~vl~~l~~~~  161 (331)
T 3dss_A           90 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHC-------WDYRRFVAAQAAVAP  161 (331)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHH-------HHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHH-------HHHHHHHHHHhCcCH
Confidence            577888888888765 5678889888888888884  899999999998755555554       7777777777787 6


Q ss_pred             HHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC--------------CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          117 NEALALFRRMAACEYTEPSEITILAVLPAIWKN--------------GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       117 ~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +++++.++++.. .. +-|...|+.....+.+.              +.++++.+.+.......+.  |...|+-+-..+
T Consensus       162 ~eel~~~~~~I~-~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~--d~SaW~Y~r~ll  237 (331)
T 3dss_A          162 AEELAFTDSLIT-RN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPN--DQSAWFYHRWLL  237 (331)
T ss_dssp             HHHHHHHHHHHH-HC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence            899999999944 32 23555677666665554              4567888888888887654  888888766666


Q ss_pred             Hhh-----------CChHHHHHHHHHhccCCCCHhhHHHHHH-----HHHcCCCHHHHHHHHHHHHh
Q 042593          183 AKC-----------GCIFSASKLFEDTSVDRKNLVSWTTIIS-----GFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       183 ~~~-----------g~~~~a~~~~~~~~~~~~~~~~~~~li~-----~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+.           +.++++++.++++....||. .|..+-.     +....|..+++...+.++.+
T Consensus       238 ~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          238 GAGSGRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HhccCccccchHHHHHHHHHHHHHHHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            655           45788999999887667764 3432221     22245666777777777765

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.57  E-value=0.00023  Score=49.74  Aligned_cols=65  Identities=9%  Similarity=-0.133  Sum_probs=36.8

Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      ..+..+...+.+.|++++|...+++..+....  +...+..+..++.+.|++++|.+.+++.....|
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p   69 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQPQ--NPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTS   69 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC
Confidence            34455555555666666666666665554332  455555666666666666666666666554444

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.53  E-value=0.0016  Score=60.21  Aligned_cols=173  Identities=8%  Similarity=-0.094  Sum_probs=129.4

Q ss_pred             cCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCC----------hhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          113 MNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGE----------VRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      ....++|++.++++..   ..|+.. .|+.--.++.+.|+          ++++...++.+.+....  +..+|+.-..+
T Consensus        42 ~~~~eeal~~~~~~l~---~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK--~y~aW~hR~w~  116 (567)
T 1dce_A           42 GELDESVLELTSQILG---ANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK--SYGTWHHRCWL  116 (567)
T ss_dssp             TCCSHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH---HCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC--CHHHHHHHHHH
Confidence            3345678999999844   335544 56666666666666          89999999999987655  88899988888


Q ss_pred             HHhhC--ChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHH
Q 042593          182 YAKCG--CIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHG-MGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVE  257 (352)
Q Consensus       182 ~~~~g--~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~  257 (352)
                      +.+.|  +++++++.++++.+. +.|...|+.-...+.+.| .++++.+.++++.+..  |                   
T Consensus       117 l~~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~--p-------------------  175 (567)
T 1dce_A          117 LSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN--F-------------------  175 (567)
T ss_dssp             HHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT--C-------------------
T ss_pred             HHHcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC--C-------------------
Confidence            88999  779999999998766 457888888877778888 8889999888887642  2                   


Q ss_pred             hcCCCCChhhHHHHHHHHHHc--------------CChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhcccccC
Q 042593          258 ECEVLPDIKHYGCLIDILERA--------------GRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSYFFS  316 (352)
Q Consensus       258 ~~~~~p~~~~~~~li~~~~~~--------------g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~~~~  316 (352)
                           -|...|+.....+.+.              +.++++.+.++..... +.|...|+.+--.+...++.++
T Consensus       176 -----~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          176 -----SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             -----CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             -----CCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence                 2566666666665553              4567888888776655 6688899988777777777665

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.53  E-value=0.013  Score=53.10  Aligned_cols=192  Identities=10%  Similarity=0.008  Sum_probs=127.1

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHH-HHHhccCCC-C------CchhHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDS-SKLFDELPE-R------NLVTWN   94 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a-~~~~~~m~~-~------~~~~~~   94 (352)
                      +...|-..+..+.+.|+++.|.++++.....  |.+...+.    .|+...+.++. ..+.+.... .      ......
T Consensus       212 ~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~  285 (493)
T 2uy1_A          212 AEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----YYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKEL  285 (493)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----HHHHHTTCTHHHHHHHHHTC----------CHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----HHHhhcchhHHHHHHHHHHHhhccchhhhhccccc
Confidence            5667777778888899999999999999987  44443332    23322222221 122221110 0      001111


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHH-hCCChhhHHHHHHHHHhcCCCCCchh
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIW-KNGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                      ..+     |-..+....+.++.+.|..+|++. +..+  .+...|......-. ..++.+.|..+++...+.-..  ++.
T Consensus       286 ~~l-----w~~y~~~~~r~~~~~~AR~i~~~A-~~~~--~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~--~~~  355 (493)
T 2uy1_A          286 DLL-----RINHLNYVLKKRGLELFRKLFIEL-GNEG--VGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPD--STL  355 (493)
T ss_dssp             HHH-----HHHHHHHHHHHHCHHHHHHHHHHH-TTSC--CCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTT--CHH
T ss_pred             HHH-----HHHHHHHHHHcCCHHHHHHHHHHh-hCCC--CChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCC--CHH
Confidence            111     777777777788899999999999 5332  23334432222212 234799999999999886432  556


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+...++...+.|+.+.|..+|+...   .....|...+.-=...|+.+.+..++++..+
T Consensus       356 ~~~~yid~e~~~~~~~~aR~l~er~~---k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          356 LKEEFFLFLLRIGDEENARALFKRLE---KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHSC---CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            67778888899999999999999983   3577888888877888999999999988765

>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=97.52  E-value=0.0016  Score=48.81  Aligned_cols=105  Identities=18%  Similarity=0.119  Sum_probs=63.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +......+.+.|++++|+..|++......-.|+..                 +         ....|.+...|..+..++
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~-----------------a---------~~~~~~~a~a~~n~g~al   67 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEE-----------------A---------FDHAGFDAFCHAGLAEAL   67 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTS-----------------C---------CCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchh-----------------h---------hhhccchHHHHHHHHHHH
Confidence            55666778888999999999998855332222210                 0         000000233566666666


Q ss_pred             HhhCChHHHHHHHHHhccC-------CCC-HhhH----HHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDTSVD-------RKN-LVSW----TTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-------~~~-~~~~----~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+.|++++|+..+++....       .|+ ...|    ...-.++...|++++|+..|++..+
T Consensus        68 ~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           68 AGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            6666666666666655444       453 4556    6666777777777777777777665

>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=97.52  E-value=0.001  Score=49.86  Aligned_cols=86  Identities=14%  Similarity=0.052  Sum_probs=61.0

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccCCCC-------------HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc-----
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN-------------LVSWTTIISGFAMHGMGKEAVENFERMQKV-----  234 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----  234 (352)
                      ..+......+.+.|++++|.+.|++.....|+             ...|+.+-.++.+.|++++|+..+++.++.     
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            34455566666777777777777765444333             338999999999999999999999998874     


Q ss_pred             CCCCCcc-hh-----h----------hHhHHHHHHHHHHh
Q 042593          235 GLKPNRS-WR-----I----------GEEGLKFFDKMVEE  258 (352)
Q Consensus       235 ~~~p~~~-~~-----~----------~~~a~~~~~~m~~~  258 (352)
                      .+.|+.. .+     .          .++|+..|++..+.
T Consensus        92 e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel  131 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  131 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            2256542 22     3          88999999887753

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.48  E-value=0.00071  Score=47.76  Aligned_cols=77  Identities=14%  Similarity=0.009  Sum_probs=38.1

Q ss_pred             HHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          155 CQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       155 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      +...++...+....  +...+..+..+|...|++++|.+.|++.....| +...|..+..+|...|++++|...|++..+
T Consensus         4 a~~~~~~al~~~p~--~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            4 ITERLEAMLAQGTD--NMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHTTTCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCC--cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444443222  444555555555555555555555555433322 344555555555555555555555555443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.45  E-value=0.0002  Score=50.69  Aligned_cols=75  Identities=11%  Similarity=0.099  Sum_probs=50.0

Q ss_pred             chHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHHhHHHHHHHHHhcCCHH
Q 042593           41 NLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLVKWTGIIDGYSRMNRSN  117 (352)
Q Consensus        41 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~~li~~~~~~~~~~  117 (352)
                      +.+++.++...+.. +.+...+..+..+|...|++++|+..|++..+  |+ ...          |..+..++...|+++
T Consensus         2 ~~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~----------~~~la~~~~~~g~~~   70 (115)
T 2kat_A            2 QAITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVA----------WKWLGKTLQGQGDRA   70 (115)
T ss_dssp             CCHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH----------HHHHHHHHHHHTCHH
T ss_pred             hHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHH----------HHHHHHHHHHcCCHH
Confidence            34566666666544 34566777777777777777777777777654  32 222          666777777777777


Q ss_pred             HHHHHHHHh
Q 042593          118 EALALFRRM  126 (352)
Q Consensus       118 ~a~~~~~~m  126 (352)
                      +|...|++.
T Consensus        71 ~A~~~~~~a   79 (115)
T 2kat_A           71 GARQAWESG   79 (115)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777776

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.25  E-value=0.0018  Score=43.08  Aligned_cols=76  Identities=13%  Similarity=-0.004  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      .+..+...+...|++++|...+++..+....  +...+..+..++.+.|++++|.+.|++.....| +...+..+..++
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~   87 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDPN--NAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCCC--CHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            4555555566666666666666666555322  455556666666666666666666665543333 344444444443

>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=97.25  E-value=0.0076  Score=44.17  Aligned_cols=113  Identities=11%  Similarity=-0.033  Sum_probs=91.2

Q ss_pred             cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh----hCCh
Q 042593          113 MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK----CGCI  188 (352)
Q Consensus       113 ~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~  188 (352)
                      .++.++|++.|++. ...| .|+..    +-..|...+.+++|...++...+.|    +...+..|-..|..    .++.
T Consensus         8 ~~d~~~A~~~~~~a-a~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g----~~~a~~~Lg~~y~~G~g~~~d~   77 (138)
T 1klx_A            8 KKDLKKAIQYYVKA-CELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN----SGNGCRFLGDFYENGKYVKKDL   77 (138)
T ss_dssp             HHHHHHHHHHHHHH-HHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCH
T ss_pred             ccCHHHHHHHHHHH-HcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC----CHHHHHHHHHHHHcCCCCCccH
Confidence            35788999999999 5555 33333    6667777788899999999998875    66778888888888    8899


Q ss_pred             HHHHHHHHHhccCCCCHhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcCC
Q 042593          189 FSASKLFEDTSVDRKNLVSWTTIISGFAM----HGMGKEAVENFERMQKVGL  236 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~  236 (352)
                      ++|.+.|++..+. -++..+..|-..|..    .++.++|...|++..+.|.
T Consensus        78 ~~A~~~~~~Aa~~-g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           78 RKAAQYYSKACGL-NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHHHT-TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcC-CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            9999999987543 567778888888888    8899999999999988763

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.17  E-value=0.0018  Score=44.46  Aligned_cols=61  Identities=10%  Similarity=-0.018  Sum_probs=42.1

Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      ...+..+..++.+.|++++|...++...+....  +...|..+..+|.+.|++++|.+.|++.
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~--~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETDPD--YVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT--CTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--cHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            445666677777777777777777777766543  5566777777777777777777777665

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.07  E-value=0.0077  Score=39.82  Aligned_cols=80  Identities=14%  Similarity=0.186  Sum_probs=64.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+...|++++|...|++.....  +.+...+..+..++.+.|++++|...+++..+....  +...+..+..++
T Consensus        12 ~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~--~~~~~~~l~~~~   87 (91)
T 1na3_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN--NAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC--CHHHHHHHHHHH
Confidence            7778888999999999999999984432  234568889999999999999999999999887543  677777777776


Q ss_pred             HhhC
Q 042593          183 AKCG  186 (352)
Q Consensus       183 ~~~g  186 (352)
                      .+.|
T Consensus        88 ~~~g   91 (91)
T 1na3_A           88 QKQG   91 (91)
T ss_dssp             HHHC
T ss_pred             HhcC
Confidence            6543

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.05  E-value=0.0017  Score=44.62  Aligned_cols=63  Identities=17%  Similarity=0.156  Sum_probs=56.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      +...+..+...+.+.|++++|...|+...+.. +.+...|..+..+|...|++++|.+.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            67788899999999999999999999999876 5567889999999999999999999987754

>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=97.00  E-value=0.0011  Score=58.92  Aligned_cols=91  Identities=8%  Similarity=-0.115  Sum_probs=68.5

Q ss_pred             hhCChHHHHHHHHHhccC--------CCC-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHH
Q 042593          184 KCGCIFSASKLFEDTSVD--------RKN-LVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDK  254 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~--------~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~  254 (352)
                      ..|++++|+.++++....        .|+ ..+++.|..+|...|++++|+.++++..+-                 +++
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i-----------------~~~  372 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKP-----------------YSK  372 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------------HHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH-----------------HHH
Confidence            357889999998875331        343 477999999999999999999999997652                 222


Q ss_pred             HHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          255 MVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       255 m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                      ...  .-.| ...+++.|...|...|++++|+.++++...
T Consensus       373 ~lG--~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          373 HYP--VYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HSC--SSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HcC--CCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            111  1223 346799999999999999999999887644

>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=96.98  E-value=0.002  Score=48.24  Aligned_cols=44  Identities=14%  Similarity=0.022  Sum_probs=20.0

Q ss_pred             HHHHHHHHhccCCC-CHhhHHHHHHHHHcCC-----------CHHHHHHHHHHHHh
Q 042593          190 SASKLFEDTSVDRK-NLVSWTTIISGFAMHG-----------MGKEAVENFERMQK  233 (352)
Q Consensus       190 ~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~-----------~~~~a~~~~~~m~~  233 (352)
                      +|+..|++.....| +...|..+-.+|...|           ++++|...|++.++
T Consensus        64 eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           64 EAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH
Confidence            44444444433332 3344444444444432           45555555555444

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.95  E-value=0.0016  Score=57.96  Aligned_cols=86  Identities=7%  Similarity=-0.038  Sum_probs=68.9

Q ss_pred             hCCChhhHHHHHHHHHhc-----CCC-CCchhhHHHHHHHHHhhCChHHHHHHHHHhccC--------CCCH-hhHHHHH
Q 042593          148 KNGEVRNCQLIHGYGEKR-----GFN-AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--------RKNL-VSWTTII  212 (352)
Q Consensus       148 ~~~~~~~a~~~~~~~~~~-----~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--------~~~~-~~~~~li  212 (352)
                      ..|++++|+.++++..+.     |.. |....+++.|..+|...|++++|+.++++....        .|++ .+++.|.
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            457889999999887653     222 113578899999999999999999999886432        4543 6799999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHh
Q 042593          213 SGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..|...|++++|+.++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999998765

>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=96.94  E-value=0.0017  Score=47.75  Aligned_cols=112  Identities=8%  Similarity=-0.111  Sum_probs=79.8

Q ss_pred             cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchhHHHHHHHHHhHHHHHHHHHh---
Q 042593           37 LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVTWNVIITGLVKWTGIIDGYSR---  112 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~i~~~~~~~~li~~~~~---  112 (352)
                      .+++++|.+.|+...+.| .|+..    |...|...+.+++|.+.|++..+ .+...          ++.|-..|..   
T Consensus         8 ~~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a----------~~~Lg~~y~~G~g   72 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELNSGNG----------CRFLGDFYENGKY   72 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHH----------HHHHHHHHHHCSS
T ss_pred             ccCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHH----------HHHHHHHHHcCCC
Confidence            346778888888888887 33333    66677777778888888887654 34444          6666666766   


Q ss_pred             -cCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCC
Q 042593          113 -MNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGF  167 (352)
Q Consensus       113 -~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~  167 (352)
                       .++.++|...|++. ...|   +...+..+-..|..    .++.++|...++...+.|.
T Consensus        73 ~~~d~~~A~~~~~~A-a~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           73 VKKDLRKAAQYYSKA-CGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             SCCCHHHHHHHHHHH-HHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             CCccHHHHHHHHHHH-HcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence             77888888888888 4333   45566777777777    7788888888888777764

>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=96.91  E-value=0.0021  Score=57.18  Aligned_cols=97  Identities=10%  Similarity=-0.065  Sum_probs=73.4

Q ss_pred             HHHHHHhhCChHHHHHHHHHhccC--------CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhH
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVD--------RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEG  248 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~--------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a  248 (352)
                      .+.-+.+.|++++|+..+++....        .| ...+++.|..+|...|++++|+.++++.++-              
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i--------------  358 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEP--------------  358 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------------
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHh--------------
Confidence            355566889999999999886543        22 2477999999999999999999999987752              


Q ss_pred             HHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCC
Q 042593          249 LKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPS  293 (352)
Q Consensus       249 ~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  293 (352)
                         +++...  ...| ...+++.|...|...|++++|+.++++...
T Consensus       359 ---~~~~lg--~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          359 ---YRIFFP--GSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             ---HHHHSC--SSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---HHHHcC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence               222111  2223 356789999999999999999998887643

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.90  E-value=0.024  Score=54.66  Aligned_cols=129  Identities=10%  Similarity=-0.018  Sum_probs=86.2

Q ss_pred             HHHHhcCChhHHHH-HhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHH
Q 042593           67 DMYVSLGFLKDSSK-LFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPA  145 (352)
Q Consensus        67 ~~~~~~g~~~~a~~-~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~  145 (352)
                      ......+++++|.+ ++..++  +...          ...++..+.+.|.++.|+++.++- .            .-...
T Consensus       607 ~~~~~~~~~~~a~~~~l~~i~--~~~~----------~~~~~~~l~~~~~~~~a~~~~~~~-~------------~~f~~  661 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPNVE--GKDS----------LTKIARFLEGQEYYEEALNISPDQ-D------------QKFEL  661 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGGCC--CHHH----------HHHHHHHHHHTTCHHHHHHHCCCH-H------------HHHHH
T ss_pred             hHHHHhCCHHHHHHHHHhcCC--chHH----------HHHHHHHHHhCCChHHheecCCCc-c------------hheeh
Confidence            33446788888888 665543  1112          455666778888888888765322 1            11233


Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHH
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAV  225 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~  225 (352)
                      ....|+++.|.++.+.+      . +...|..+.+.+.+.|+++.|+++|..+..       |..+...+...|+.+...
T Consensus       662 ~l~~~~~~~A~~~~~~~------~-~~~~W~~la~~al~~~~~~~A~~~y~~~~d-------~~~l~~l~~~~~~~~~~~  727 (814)
T 3mkq_A          662 ALKVGQLTLARDLLTDE------S-AEMKWRALGDASLQRFNFKLAIEAFTNAHD-------LESLFLLHSSFNNKEGLV  727 (814)
T ss_dssp             HHHHTCHHHHHHHHTTC------C-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC-------HHHHHHHHHHTTCHHHHH
T ss_pred             hhhcCCHHHHHHHHHhh------C-cHhHHHHHHHHHHHcCCHHHHHHHHHHccC-------hhhhHHHHHHcCCHHHHH
Confidence            45678999998886543      2 678899999999999999999999998742       555555566677776666


Q ss_pred             HHHHHHHhc
Q 042593          226 ENFERMQKV  234 (352)
Q Consensus       226 ~~~~~m~~~  234 (352)
                      .+.+.....
T Consensus       728 ~~~~~a~~~  736 (814)
T 3mkq_A          728 TLAKDAETT  736 (814)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHc
Confidence            555554443

>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=96.90  E-value=0.0042  Score=55.18  Aligned_cols=93  Identities=12%  Similarity=0.023  Sum_probs=73.6

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcC---CCC---CchhhHHHHHHHHHhhCChHHHHHHHHHhccC--------CCC-H
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRG---FNA---FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD--------RKN-L  205 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--------~~~-~  205 (352)
                      ..+..+.+.|++++|...+++..+..   +.+   ....+++.+..+|...|++++|+.++++....        .|+ .
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a  371 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRG  371 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHH
Confidence            34555678899999999999887542   111   13568899999999999999999999876432        444 4


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+++.|...|...|++++|..++++..+
T Consensus       372 ~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          372 VQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            6799999999999999999999998765

>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=96.87  E-value=0.0027  Score=47.50  Aligned_cols=114  Identities=6%  Similarity=-0.037  Sum_probs=84.9

Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCCh----------hhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEV----------RNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      .+.+.+++|.+.+++.....  +-+...|..+..++...+++          ++|...+++..+....  ....|..+..
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~--P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~--~~~A~~~LG~   88 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK--KDEAVWCIGN   88 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC--cHHHHHHHHH
Confidence            45567889999999884433  23566788888888887765          5999999999988655  7889999999


Q ss_pred             HHHhhC-----------ChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          181 TYAKCG-----------CIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       181 ~~~~~g-----------~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +|...|           ++++|.+.|++.....|+-..|...+..      .++|.+++-++...
T Consensus        89 ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al~~------~~ka~el~~~~~~~  147 (158)
T 1zu2_A           89 AYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEM------TAKAPQLHAEAYKQ  147 (158)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH------HHTHHHHHHHHHHS
T ss_pred             HHHHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHHHH------HHhCHhccCccccc
Confidence            998875           8999999999988778887666555542      34455555555444

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.69  E-value=0.053  Score=52.18  Aligned_cols=157  Identities=8%  Similarity=0.001  Sum_probs=84.3

Q ss_pred             HHHHhcCCcchHHH-HHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHH
Q 042593           32 RTCVTLSYPNLGTQ-LHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGY  110 (352)
Q Consensus        32 ~~~~~~g~~~~a~~-~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~  110 (352)
                      ......+++++|.+ ++..     ++ +......++..+.+.|..++|.++.+.-   .. -              ....
T Consensus       607 ~~~~~~~~~~~a~~~~l~~-----i~-~~~~~~~~~~~l~~~~~~~~a~~~~~~~---~~-~--------------f~~~  662 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPN-----VE-GKDSLTKIARFLEGQEYYEEALNISPDQ---DQ-K--------------FELA  662 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGG-----CC-CHHHHHHHHHHHHHTTCHHHHHHHCCCH---HH-H--------------HHHH
T ss_pred             hHHHHhCCHHHHHHHHHhc-----CC-chHHHHHHHHHHHhCCChHHheecCCCc---ch-h--------------eehh
Confidence            44456777777766 4411     11 0112256666777777777777665421   10 0              1223


Q ss_pred             HhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH
Q 042593          111 SRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS  190 (352)
Q Consensus       111 ~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  190 (352)
                      ...|+++.|+++.+.+       .+...|..+...+.+.++++.|++.|..+..          |..+...|...|+.+.
T Consensus       663 l~~~~~~~A~~~~~~~-------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d----------~~~l~~l~~~~~~~~~  725 (814)
T 3mkq_A          663 LKVGQLTLARDLLTDE-------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD----------LESLFLLHSSFNNKEG  725 (814)
T ss_dssp             HHHTCHHHHHHHHTTC-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC----------HHHHHHHHHHTTCHHH
T ss_pred             hhcCCHHHHHHHHHhh-------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC----------hhhhHHHHHHcCCHHH
Confidence            4567777777776555       3456777777777777777777777775532          2344444444555554


Q ss_pred             HHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          191 ASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       191 a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      ..++-+......    -++....+|.+.|++++|.+++.++.+
T Consensus       726 ~~~~~~~a~~~~----~~~~A~~~~~~~g~~~~a~~~~~~~~~  764 (814)
T 3mkq_A          726 LVTLAKDAETTG----KFNLAFNAYWIAGDIQGAKDLLIKSQR  764 (814)
T ss_dssp             HHHHHHHHHHTT----CHHHHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcC----chHHHHHHHHHcCCHHHHHHHHHHcCC
Confidence            444433322111    123333344555666666666555443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.17  Score=38.43  Aligned_cols=24  Identities=13%  Similarity=0.295  Sum_probs=12.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      |..|.......|+++-|.+.|.+.
T Consensus        37 Wk~Lg~~AL~~gn~~lAe~cy~~~   60 (177)
T 3mkq_B           37 WERLIQEALAQGNASLAEMIYQTQ   60 (177)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHh
Confidence            555555555555555555555554

>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=96.42  E-value=0.066  Score=45.97  Aligned_cols=140  Identities=8%  Similarity=-0.094  Sum_probs=93.1

Q ss_pred             CCChhhHHHHHHHHHh--CC---ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh---hC-----Ch---HHHHHHHH
Q 042593          133 EPSEITILAVLPAIWK--NG---EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK---CG-----CI---FSASKLFE  196 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~~--~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~---~g-----~~---~~a~~~~~  196 (352)
                      +.+...|...+++...  .+   +..+|..+|++..+..+.  ....|..+.-+|.-   .+     ..   ..+.+-..
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~--~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~  268 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPE--FTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIV  268 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHH
Confidence            4566778887777543  22   347788999998887554  55556554444431   11     11   11222111


Q ss_pred             HhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHH
Q 042593          197 DTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILE  276 (352)
Q Consensus       197 ~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~  276 (352)
                      .+...+.+..+|..+...+...|++++|...+++....                         +  |+...|..+...+.
T Consensus       269 a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~L-------------------------n--~s~~a~~llG~~~~  321 (372)
T 3ly7_A          269 TLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDL-------------------------E--MSWLNYVLLGKVYE  321 (372)
T ss_dssp             TCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-------------------------C--CCHHHHHHHHHHHH
T ss_pred             hcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc-------------------------C--CCHHHHHHHHHHHH
Confidence            22222567888888877777789999999999998875                         2  56677778888889


Q ss_pred             HcCChhHHHHHHhcCCCCCCCchhh
Q 042593          277 RAGRLEQAEEVASGIPSQITNVVVW  301 (352)
Q Consensus       277 ~~g~~~~A~~~~~~m~~~~~~~~~~  301 (352)
                      -.|+.++|.+.+++.....|...+|
T Consensus       322 ~~G~~~eA~e~~~~AlrL~P~~~t~  346 (372)
T 3ly7_A          322 MKGMNREAADAYLTAFNLRPGANTL  346 (372)
T ss_dssp             HTTCHHHHHHHHHHHHHHSCSHHHH
T ss_pred             HCCCHHHHHHHHHHHHhcCCCcChH
Confidence            9999999999998776555555543

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.36  E-value=0.0036  Score=42.50  Aligned_cols=50  Identities=12%  Similarity=0.020  Sum_probs=20.6

Q ss_pred             HhCCChhhHHHHHHHHHhcCCCCCchh-hHHHHHHHHHhhCChHHHHHHHHHh
Q 042593          147 WKNGEVRNCQLIHGYGEKRGFNAFDIH-VSNCLIDTYAKCGCIFSASKLFEDT  198 (352)
Q Consensus       147 ~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~li~~~~~~g~~~~a~~~~~~~  198 (352)
                      .+.|++++|...++...+....  +.. .+..+..+|...|++++|.+.|++.
T Consensus        11 ~~~~~~~~A~~~~~~al~~~p~--~~~~~~~~lg~~~~~~~~~~~A~~~~~~a   61 (99)
T 2kc7_A           11 INQGDIENALQALEEFLQTEPV--GKDEAYYLMGNAYRKLGDWQKALNNYQSA   61 (99)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCSS--THHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHCCC--cHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3344444444444444433221  233 3444444444444444444444443

>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=96.27  E-value=0.026  Score=48.48  Aligned_cols=148  Identities=10%  Similarity=-0.071  Sum_probs=79.5

Q ss_pred             CCCCchhhHHHHHHHHHh--cC---ChhHHHHHhccCCC--CCc-hhHHHHHHHHHhHHHHHHHHHhcCCHHHHHH---H
Q 042593           54 GFQSHVYVNTALGDMYVS--LG---FLKDSSKLFDELPE--RNL-VTWNVIITGLVKWTGIIDGYSRMNRSNEALA---L  122 (352)
Q Consensus        54 ~~~~~~~~~~~li~~~~~--~g---~~~~a~~~~~~m~~--~~~-~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~---~  122 (352)
                      +.+.+...|...+.+...  .+   +..+|..+|++..+  |+- ..+..+.-+   |. +...+. .........   -
T Consensus       189 ~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a---~~-~~~~~~-~~~~~~~~~l~~a  263 (372)
T 3ly7_A          189 ILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALV---DI-VRHSQH-PLDEKQLAALNTE  263 (372)
T ss_dssp             HSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH---HH-HHHHHS-CCCHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHH---HH-HHhccC-CCchhhHHHHHHH
Confidence            346677888887766553  23   35788999999875  543 222111100   11 111111 001111111   1


Q ss_pred             HHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC
Q 042593          123 FRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR  202 (352)
Q Consensus       123 ~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  202 (352)
                      +.........+.+..+|..+...+...|++++|...+++....+  | +...|..+...+.-.|+.++|.+.|++.....
T Consensus       264 ~~a~~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~-s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~  340 (372)
T 3ly7_A          264 IDNIVTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--M-SWLNYVLLGKVYEMKGMNREAADAYLTAFNLR  340 (372)
T ss_dssp             HHHHHTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--C-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--C-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            11110111223455566666655666677777777777777765  4 55666666777777777777777777665556


Q ss_pred             CCHhhHH
Q 042593          203 KNLVSWT  209 (352)
Q Consensus       203 ~~~~~~~  209 (352)
                      |...+|.
T Consensus       341 P~~~t~~  347 (372)
T 3ly7_A          341 PGANTLY  347 (372)
T ss_dssp             CSHHHHH
T ss_pred             CCcChHH
Confidence            6665544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.17  E-value=0.045  Score=36.83  Aligned_cols=68  Identities=4%  Similarity=-0.119  Sum_probs=37.0

Q ss_pred             ChhhHHHHHHHHHhCCC---hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          135 SEITILAVLPAIWKNGE---VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       135 ~~~t~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      |...+..+..++...++   .++|..++++..+....  +......+...+.+.|++++|...|+.+....|+
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~--~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY--NEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            33444455555443333   45666666666655433  5555555666666666666666666665554443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.16  E-value=0.22  Score=35.81  Aligned_cols=137  Identities=10%  Similarity=0.015  Sum_probs=94.1

Q ss_pred             hcCChhHHHHHhccCCCC-CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC
Q 042593           71 SLGFLKDSSKLFDELPER-NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN  149 (352)
Q Consensus        71 ~~g~~~~a~~~~~~m~~~-~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~  149 (352)
                      -.|.+++..++..+..++ +..-          ||.+|-.....-+-+-..++++.+ ..   -.|..          ..
T Consensus        19 ldG~v~qGveii~k~~~ssni~E----------~NW~ICNiiD~a~C~y~v~vLd~I-Gk---iFDis----------~C   74 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKSSTKSE----------YNWFICNLLESIDCRYMFQVLDKI-GS---YFDLD----------KC   74 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHHSCHHH----------HTHHHHHHHHHCCHHHHHHHHHHH-GG---GSCGG----------GC
T ss_pred             HhhhHHHHHHHHHHHcCCCCccc----------cceeeeecchhhchhHHHHHHHHH-hh---hcCcH----------hh
Confidence            457888888888877653 3344          555555555566666666666666 21   22322          23


Q ss_pred             CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHh-ccCCCCHhhHHHHHHHHHcCCCHHHHHHHH
Q 042593          150 GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDT-SVDRKNLVSWTTIISGFAMHGMGKEAVENF  228 (352)
Q Consensus       150 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~-~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  228 (352)
                      |++..+...+-.+   |.   +....+..++.+...|+-+.-.++..++ ...+|++...-.+..+|.+.|+..+|.+++
T Consensus        75 ~NlKrVi~C~~~~---n~---~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl  148 (172)
T 1wy6_A           75 QNLKSVVECGVIN---NT---LNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLL  148 (172)
T ss_dssp             SCTHHHHHHHHHT---TC---CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hcHHHHHHHHHHh---cc---hHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHH
Confidence            4443333333322   21   4566778889999999999999999995 444789999999999999999999999999


Q ss_pred             HHHHhcCCC
Q 042593          229 ERMQKVGLK  237 (352)
Q Consensus       229 ~~m~~~~~~  237 (352)
                      .+.-+.|++
T Consensus       149 ~~AC~kG~k  157 (172)
T 1wy6_A          149 IEACKKGEK  157 (172)
T ss_dssp             HHHHHTTCH
T ss_pred             HHHHHhhhH
Confidence            999888764

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.06  E-value=1e-05  Score=70.96  Aligned_cols=214  Identities=13%  Similarity=0.061  Sum_probs=147.9

Q ss_pred             CChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCCh
Q 042593           73 GFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEV  152 (352)
Q Consensus        73 g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~  152 (352)
                      +++++|.+.-++..+|.+            |+.|.++..+.++..+|++-|-+.       -|...|..++.++.+.|.+
T Consensus        39 ~~ldRa~eyA~~~n~p~V------------Ws~LgkAqL~~~~v~eAIdsyIkA-------~Dps~y~eVi~~A~~~~~~   99 (624)
T 3lvg_A           39 GNLDRAYEFAERCNEPAV------------WSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNW   99 (624)
T ss_dssp             CCSTTTTTSSSSCCCCCC------------SSSHHHHTTTSSSCTTTTTSSCCC-------SCCCSSSHHHHHTTTSSCC
T ss_pred             cccHHHHHHHHHhCCccH------------HHHHHHHHHccCchHHHHHHHHhC-------CChHHHHHHHHHHHhCCCH
Confidence            456666666666655554            888889999998888877655444       3556788999999999999


Q ss_pred             hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042593          153 RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       153 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      ++-...+....+..-   ++.+=+.|+-+|++.+++.+-++++.     .||+.-...+-+-|...|.++.|.-+|..+-
T Consensus       100 edLv~yL~MaRk~~k---e~~IDteLi~ayAk~~rL~elEefl~-----~~N~A~iq~VGDrcf~e~lYeAAKilys~is  171 (624)
T 3lvg_A          100 EELVKYLQMARKKAR---ESYVETELIFALAKTNRLAELEEFIN-----GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS  171 (624)
T ss_dssp             TTHHHHHHTTSTTCC---STTTTHHHHHHHHTSCSSSTTTSTTS-----CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSC
T ss_pred             HHHHHHHHHHHHHhc---ccccHHHHHHHHHhhCcHHHHHHHHc-----CCCcccHHHHHHHHHHccCHHHHHHHHHhCc
Confidence            999999998877643   44556699999999999766444332     6777777888888888898888888877654


Q ss_pred             hcCCCCCcchhh----hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHH
Q 042593          233 KVGLKPNRSWRI----GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRL  308 (352)
Q Consensus       233 ~~~~~p~~~~~~----~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~  308 (352)
                      .-.  -=..|+.    +..|.+.   .    .-.-++.||-.+-.+|...+.+..|...--.+.-   ...-...++..|
T Consensus       172 N~a--kLAstLV~L~~yq~AVda---A----rKAns~ktWKeV~~ACvd~~EfrLAqicGLniIv---hadeL~elv~~Y  239 (624)
T 3lvg_A          172 NFG--RLASTLVHLGEYQAAVDG---A----RKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVV---HADELEELINYY  239 (624)
T ss_dssp             CCT--TTSSSSSSCSGGGSSTTT---T----TTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHC---CSSCCSGGGSSS
T ss_pred             cHH--HHHHHHHHHHHHHHHHHH---H----HhcCChhHHHHHHHHHhCchHHHHHHHhcchhcc---cHHHHHHHHHHH
Confidence            321  0011111    1111110   0    1124778999999999999998877544222211   122234577888


Q ss_pred             HhcccccCcccccccch
Q 042593          309 LINSYFFSPITLNSQRL  325 (352)
Q Consensus       309 ~~~g~~~~a~~~~~~~~  325 (352)
                      -..|.+++-+++++..+
T Consensus       240 E~~G~f~ELIsLlEagl  256 (624)
T 3lvg_A          240 QDRGYFEELITMLEAAL  256 (624)
T ss_dssp             STTCCCTTSTTTHHHHT
T ss_pred             HhCCCHHHHHHHHHHHh
Confidence            99999999999988774

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.86  E-value=0.02  Score=38.62  Aligned_cols=57  Identities=14%  Similarity=0.144  Sum_probs=49.7

Q ss_pred             HHHHHHhhCChHHHHHHHHHhccCCC-CHh-hHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          178 LIDTYAKCGCIFSASKLFEDTSVDRK-NLV-SWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       178 li~~~~~~g~~~~a~~~~~~~~~~~~-~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ....+.+.|++++|.+.|++.....| +.. .+..+..+|...|++++|...|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            45678899999999999999876655 567 8899999999999999999999998875

>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=95.46  E-value=0.085  Score=43.54  Aligned_cols=86  Identities=15%  Similarity=0.056  Sum_probs=69.3

Q ss_pred             hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh-----CChHHHHHHHHHhccCCC--CHhhHHHHHHHHHcC-CCHHH
Q 042593          152 VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC-----GCIFSASKLFEDTSVDRK--NLVSWTTIISGFAMH-GMGKE  223 (352)
Q Consensus       152 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~~~~~~~--~~~~~~~li~~~~~~-~~~~~  223 (352)
                      ...|...+++..+......+...|..+...|.+.     |+.++|.+.|++.....|  +..++....+.+++. |+.++
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~  258 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAG  258 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHH
Confidence            4567777777777754432467899999999994     999999999999877777  378888888888885 99999


Q ss_pred             HHHHHHHHHhcCCC
Q 042593          224 AVENFERMQKVGLK  237 (352)
Q Consensus       224 a~~~~~~m~~~~~~  237 (352)
                      +.+.+++.+.....
T Consensus       259 a~~~L~kAL~a~p~  272 (301)
T 3u64_A          259 FDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHcCCCC
Confidence            99999999987555

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.45  E-value=0.46  Score=34.16  Aligned_cols=140  Identities=13%  Similarity=0.050  Sum_probs=79.6

Q ss_pred             cccHHHHHHHH--HhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-CCchh---HHHHH
Q 042593           24 SFTYSFLIRTC--VTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-RNLVT---WNVII   97 (352)
Q Consensus        24 ~~~~~~ll~~~--~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~---~~~~i   97 (352)
                      ..+...++.+-  .-.|.+++..++........   +..-||-+|.-....-+-+-..+.++.+-+ -|...   .-.++
T Consensus         5 ~el~kkLmeAK~~ildG~v~qGveii~k~~~ss---ni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi   81 (172)
T 1wy6_A            5 SEIIRKLMDAKKFLLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVV   81 (172)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHcCCC---CccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHH
Confidence            34455555443  34688899999988877654   344455555444444444444444443322 01100   00011


Q ss_pred             HHHH-------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC
Q 042593           98 TGLV-------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus        98 ~~~~-------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  168 (352)
                      .+++       ..+..++.....|+-+...+++.++..  +.+|+......+..||.+.|+..++.+++.+..+.|+.
T Consensus        82 ~C~~~~n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~--n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           82 ECGVINNTLNEHVNKALDILVIQGKRDKLEEIGREILK--NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC----CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhcchHHHHHHHHHHHHHhccHhHHHHHHHHHhc--cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            1111       155666777777777777777777423  34566777777777777888877777777777777764

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.42  E-value=0.11  Score=34.91  Aligned_cols=65  Identities=12%  Similarity=-0.039  Sum_probs=54.8

Q ss_pred             chhhHHHHHHHHHhhCC---hHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          171 DIHVSNCLIDTYAKCGC---IFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      ++..+..+..++...++   .++|..++++.....| ++.....+...+.+.|++++|...|+++.+..
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            77788888888876555   7999999999876655 67888888889999999999999999999864

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.28  E-value=0.072  Score=39.38  Aligned_cols=69  Identities=10%  Similarity=-0.073  Sum_probs=29.5

Q ss_pred             CChhhHHHHHHHHHhCC---ChhhHHHHHHHHHhcC-CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          134 PSEITILAVLPAIWKNG---EVRNCQLIHGYGEKRG-FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~~---~~~~a~~~~~~~~~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      ++..+...+.-++++.+   +.+++..+++...+.. ... ....+-.+.-+|.+.|++++|.+.++.+.+..|
T Consensus        30 ~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~-~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~ieP  102 (152)
T 1pc2_A           30 VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEE-QRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEP  102 (152)
T ss_dssp             CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHH-HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccc-hHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence            34444444444444444   3344555555444443 101 122222333344455555555555554443333

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.10  E-value=0.0057  Score=54.10  Aligned_cols=236  Identities=9%  Similarity=0.002  Sum_probs=146.1

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI  137 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  137 (352)
                      .+..|+.|..++.+.+++.+|++-|-+..  |+..          |..++.+..+.|.+++-...+... ++....|.. 
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIkA~--Dps~----------y~eVi~~A~~~~~~edLv~yL~Ma-Rk~~ke~~I-  118 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIKAD--DPSS----------YMEVVQAANTSGNWEELVKYLQMA-RKKARESYV-  118 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCCCS--CCCS----------SSHHHHHTTTSSCCTTHHHHHHTT-STTCCSTTT-
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHhCC--ChHH----------HHHHHHHHHhCCCHHHHHHHHHHH-HHHhccccc-
Confidence            45678888888888888888887776554  4444          777888888888888888776665 544434433 


Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC----------------
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD----------------  201 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----------------  201 (352)
                       =+.++-+|++.+++.+.++++.       .| +..-...+.+=|...|.++.|.-+|..+...                
T Consensus       119 -DteLi~ayAk~~rL~elEefl~-------~~-N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~A  189 (624)
T 3lvg_A          119 -ETELIFALAKTNRLAELEEFIN-------GP-NNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAA  189 (624)
T ss_dssp             -THHHHHHHHTSCSSSTTTSTTS-------CC-SSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSS
T ss_pred             -HHHHHHHHHhhCcHHHHHHHHc-------CC-CcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence             3478888888888777655443       23 4444456666677777777777666654321                


Q ss_pred             ------CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcch-hh-----hHhHHHHHHHHHHhcCCCCChhhHH
Q 042593          202 ------RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSW-RI-----GEEGLKFFDKMVEECEVLPDIKHYG  269 (352)
Q Consensus       202 ------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~-~~-----~~~a~~~~~~m~~~~~~~p~~~~~~  269 (352)
                            ..++.||--+-.+|...+.+.-|.-.--.++-..-..+... +.     +++.+.+++.-..  --....-.|+
T Consensus       190 VdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvhadeL~elv~~YE~~G~f~ELIsLlEaglg--lErAHmGmFT  267 (624)
T 3lvg_A          190 VDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALG--LERAHMGMFT  267 (624)
T ss_dssp             TTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCCSSCCSGGGSSSSTTCCCTTSTTTHHHHTT--STTCCHHHHH
T ss_pred             HHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhcccHHHHHHHHHHHHhCCCHHHHHHHHHHHhC--CCchhHHHHH
Confidence                  24678899999999999888877666555553322221111 11     5555555554331  1123555667


Q ss_pred             HHHHHHHHcCChhHHHHHHhcCCCC---------CCCchhhHHHHHHHHhcccccCccc
Q 042593          270 CLIDILERAGRLEQAEEVASGIPSQ---------ITNVVVWRTGFLRLLINSYFFSPIT  319 (352)
Q Consensus       270 ~li~~~~~~g~~~~A~~~~~~m~~~---------~~~~~~~~~li~~~~~~g~~~~a~~  319 (352)
                      -|.-.|+|- +.++..+-++..-.+         -.....|.-++--|..-.+++.|..
T Consensus       268 ELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~l  325 (624)
T 3lvg_A          268 ELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII  325 (624)
T ss_dssp             HHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHH
Confidence            776666665 344444444433222         1234567777777777777665543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.07  E-value=0.11  Score=35.68  Aligned_cols=66  Identities=9%  Similarity=-0.055  Sum_probs=33.4

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcC-----CCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRG-----FNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                      -+..+...+.+.|+++.|...++...+.-     ..+....++..+..+|.+.|+++.|...+++.....|
T Consensus         7 dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P   77 (104)
T 2v5f_A            7 DCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP   77 (104)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence            34445555555555555555555544321     0111445555666666666666666666665543333

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.06  E-value=0.077  Score=39.22  Aligned_cols=85  Identities=9%  Similarity=-0.041  Sum_probs=66.4

Q ss_pred             ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhC---ChHHHHHHHHHhccCC-C--CHhhHHHHHHHHHcCCCHHHH
Q 042593          151 EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCG---CIFSASKLFEDTSVDR-K--NLVSWTTIISGFAMHGMGKEA  224 (352)
Q Consensus       151 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~-~--~~~~~~~li~~~~~~~~~~~a  224 (352)
                      .+..+++-|.+..+.|. + +..+.-.+..++++++   +.+++..+|++..+.. |  +...+-.|.-+|.+.|++++|
T Consensus        13 ~l~~~~~~y~~e~~~~~-~-~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A   90 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAGS-V-SKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHHHTTC-C-CHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHccCC-C-cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHH
Confidence            44566677777666665 3 7777778888999988   6779999999887665 5  356666777788999999999


Q ss_pred             HHHHHHHHhcCCCCC
Q 042593          225 VENFERMQKVGLKPN  239 (352)
Q Consensus       225 ~~~~~~m~~~~~~p~  239 (352)
                      .+.++.+.+.  .|+
T Consensus        91 ~~y~~~lL~i--eP~  103 (152)
T 1pc2_A           91 LKYVRGLLQT--EPQ  103 (152)
T ss_dssp             HHHHHHHHHH--CTT
T ss_pred             HHHHHHHHhc--CCC
Confidence            9999999984  454

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.04  E-value=0.064  Score=44.26  Aligned_cols=141  Identities=11%  Similarity=-0.017  Sum_probs=92.6

Q ss_pred             cCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHH-HHHhc--C------CHHHHHHHHHHhHhccCCCCC---hhhH
Q 042593           72 LGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIID-GYSRM--N------RSNEALALFRRMAACEYTEPS---EITI  139 (352)
Q Consensus        72 ~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~-~~~~~--~------~~~~a~~~~~~m~~~~~~~p~---~~t~  139 (352)
                      .++..+-.+.+.+....++..   ++     |..++. ++...  |      ....|...+++...   +.|+   ...|
T Consensus       134 ~~~~~~~~~~l~~~~~~dve~---L~-----W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAle---LDP~~~~GsA~  202 (301)
T 3u64_A          134 SGDEQRLHKVLSRCTRVDVGT---LY-----WVGTGYVAAFALTPLGSALPDTVHAAVMMLERACD---LWPSYQEGAVW  202 (301)
T ss_dssp             SSCHHHHHHHHTTCCGGGHHH---HH-----HHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHH---HCTTHHHHHHH
T ss_pred             hcchhhHHHHHHHcCccccHH---HH-----HHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHH---hCCCcccCHHH
Confidence            344455556666665433322   22     555554 33332  3      24566666666634   4566   4578


Q ss_pred             HHHHHHHHhC-----CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhh-CChHHHHHHHHHhccCC----CCHhhHH
Q 042593          140 LAVLPAIWKN-----GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKC-GCIFSASKLFEDTSVDR----KNLVSWT  209 (352)
Q Consensus       140 ~~ll~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~----~~~~~~~  209 (352)
                      ..+...|.+.     |+.++|...|++..+.+..- +..++....+.+++. |+.+.+.+.+++.....    |+....|
T Consensus       203 ~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~-~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          203 NVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAH-DPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             HHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTT-CSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHH
T ss_pred             HHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCC-CchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHH
Confidence            8888889885     99999999999999987754 577888889999985 99999999999987654    4444444


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHH
Q 042593          210 TIISGFAMHGMGKEAVENFERMQ  232 (352)
Q Consensus       210 ~li~~~~~~~~~~~a~~~~~~m~  232 (352)
                      .+-        -++|..+++++.
T Consensus       282 ~~~--------q~eA~~LL~~~~  296 (301)
T 3u64_A          282 ILS--------QKRARWLKAHVQ  296 (301)
T ss_dssp             HHH--------HHHHHHHHHTHH
T ss_pred             HHH--------HHHHHHHHHHhH
Confidence            332        345555555443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.51  E-value=1.1  Score=33.86  Aligned_cols=101  Identities=14%  Similarity=0.099  Sum_probs=64.0

Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCCh
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCI  188 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  188 (352)
                      .....|+++.|.++.+++       -+...|..+.....+.|+++-|++.|+....          +..+.-.|...|+.
T Consensus        14 LAL~lg~l~~A~e~a~~l-------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D----------~~~L~~Ly~~tg~~   76 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL-------NDSITWERLIQEALAQGNASLAEMIYQTQHS----------FDKLSFLYLVTGDV   76 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC----------HHHHHHHHHHHTCH
T ss_pred             HHHhcCCHHHHHHHHHHh-------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC----------HHHHHHHHHHhCCH
Confidence            345678888888887776       3566888888888888888888888875432          34555566666666


Q ss_pred             HHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHH
Q 042593          189 FSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFER  230 (352)
Q Consensus       189 ~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  230 (352)
                      +...++-+......    -++....++...|+++++.+++.+
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            66554443322111    134444445555666666666543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.29  E-value=0.14  Score=35.09  Aligned_cols=69  Identities=14%  Similarity=-0.112  Sum_probs=57.6

Q ss_pred             CCcccHHHHHHHHHhcCCcchHHHHHHHHHHhC------CCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc
Q 042593           22 FDSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVG------FQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL   90 (352)
Q Consensus        22 ~~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~   90 (352)
                      ++...+..+...+.+.|++..|...++...+.-      -.+....+..|..++.+.|+++.|...+++..+  |+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~   79 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEH   79 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCC
Confidence            477778899999999999999999999887642      134567889999999999999999999998764  543

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=94.14  E-value=4.5  Score=40.73  Aligned_cols=149  Identities=9%  Similarity=0.016  Sum_probs=95.8

Q ss_pred             HHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCC---------
Q 042593           64 ALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEP---------  134 (352)
Q Consensus        64 ~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p---------  134 (352)
                      .++..+.+.+..+-+.++..-..+ +...          --.+..++...|++++|.+.|.+. .. |+..         
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~~-~~~~----------~yl~g~~~L~~ge~~~A~~~F~ka-a~-~~~~~~~l~~~~~  883 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLNS-DPIA----------VYLKALIYLKSKEAVKAVRCFKTT-SL-VLYSHTSQFAVLR  883 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSCC-CHHH----------HHHHHHHHHHTTCHHHHHHHHHTC-CC-SCTTCCCSCSSHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccC-CcHH----------HHHHHHHHHhcCCHHHHHHHHHHH-hh-hhcccchhhhhhc
Confidence            455566667777777776555543 3222          233456788899999999999876 21 1111         


Q ss_pred             --------------ChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC-Cc--hhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          135 --------------SEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA-FD--IHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       135 --------------~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~--~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                                    -..-|..++..+.+.+..+.+.++-....+..... ++  ...|..+.+++...|++++|...+-.
T Consensus       884 ~~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~  963 (1139)
T 4fhn_B          884 EFQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMV  963 (1139)
T ss_dssp             HHHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHH
T ss_pred             ccccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHh
Confidence                          01236677777888888888877777665543221 01  12577788888888888888888877


Q ss_pred             hccCCCCHhhHHHHHHHHHcCCCHHHHH
Q 042593          198 TSVDRKNLVSWTTIISGFAMHGMGKEAV  225 (352)
Q Consensus       198 ~~~~~~~~~~~~~li~~~~~~~~~~~a~  225 (352)
                      +.....-......|+..+|.+|..+.-.
T Consensus       964 ~pd~~~r~~cLr~LV~~lce~~~~~~L~  991 (1139)
T 4fhn_B          964 LSTTPLKKSCLLDFVNQLTKQGKINQLL  991 (1139)
T ss_dssp             HHHSSSCHHHHHHHHHHHHHHCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCChhhhh
Confidence            7554444566777777777777655443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=92.90  E-value=0.41  Score=34.02  Aligned_cols=87  Identities=8%  Similarity=-0.156  Sum_probs=40.0

Q ss_pred             CHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhh---HHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHH
Q 042593          115 RSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRN---CQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSA  191 (352)
Q Consensus       115 ~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  191 (352)
                      ++..+.+-|.+. ...|. |+..+-..+.-++.+..+...   +..+++.+.+.+.+.......-.|.-++.+.|++++|
T Consensus        16 ~l~~~~~~y~~e-~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A   93 (126)
T 1nzn_A           16 DLLKFEKKFQSE-KAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKA   93 (126)
T ss_dssp             HHHHHHHHHHHH-HHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHH-hccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHH
Confidence            344444444444 22222 455554455555555554444   5555555554431100222222444455566666666


Q ss_pred             HHHHHHhccCCC
Q 042593          192 SKLFEDTSVDRK  203 (352)
Q Consensus       192 ~~~~~~~~~~~~  203 (352)
                      .+.++.+....|
T Consensus        94 ~~~~~~lL~~eP  105 (126)
T 1nzn_A           94 LKYVRGLLQTEP  105 (126)
T ss_dssp             HHHHHHHHHHCT
T ss_pred             HHHHHHHHHhCC
Confidence            666665544444

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.89  E-value=4.8  Score=35.69  Aligned_cols=249  Identities=10%  Similarity=0.060  Sum_probs=139.7

Q ss_pred             CCcchHHHHHHHHHHh-----CCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCc---hhHHHHHHHHHhHHHHHHH
Q 042593           38 SYPNLGTQLHAVFSKV-----GFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNL---VTWNVIITGLVKWTGIIDG  109 (352)
Q Consensus        38 g~~~~a~~~~~~m~~~-----~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~---~~~~~~i~~~~~~~~li~~  109 (352)
                      |+++.|.+.+-.+.+.     +...+......++..|...|+++...+.+.-+.+...   .....++      +.++.-
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai~~~V------~~~~~~  103 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMI------QKVMEY  103 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHHHHHH------HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHHHHHH------HHHHHH
Confidence            6778888776665542     2344566788899999999999988776665543221   2222222      222222


Q ss_pred             HHhcCCHH--HHHHHHHHhHhc-cC-CCC---ChhhHHHHHHHHHhCCChhhHHHHHHHHHhc--CCCC--CchhhHHHH
Q 042593          110 YSRMNRSN--EALALFRRMAAC-EY-TEP---SEITILAVLPAIWKNGEVRNCQLIHGYGEKR--GFNA--FDIHVSNCL  178 (352)
Q Consensus       110 ~~~~~~~~--~a~~~~~~m~~~-~~-~~p---~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~--~~~~--~~~~~~~~l  178 (352)
                      .......+  .-..+.+..... .| +-.   .......+...+...|++.+|..++..+...  |...  .-...+...
T Consensus       104 l~~~~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q  183 (445)
T 4b4t_P          104 LKSSKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQ  183 (445)
T ss_dssp             HHHHCTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHH
T ss_pred             HhcCCchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            22233222  222233322110 11 111   1112346677788889999999999987532  2211  014567778


Q ss_pred             HHHHHhhCChHHHHHHHHHhccC----C--CC--HhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC-CCCCcchhh-----
Q 042593          179 IDTYAKCGCIFSASKLFEDTSVD----R--KN--LVSWTTIISGFAMHGMGKEAVENFERMQKVG-LKPNRSWRI-----  244 (352)
Q Consensus       179 i~~~~~~g~~~~a~~~~~~~~~~----~--~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~-----  244 (352)
                      ++.|...+++..|..++..+...    .  |+  ...|...+..+...+++.+|...|.+..+.- ...+.....     
T Consensus       184 ~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~  263 (445)
T 4b4t_P          184 MELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSH  263 (445)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHH
Confidence            88899999999999888876421    2  22  2345666777788889988888887775421 111111111     


Q ss_pred             ----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHc--CChhHHHHHHhcCCC
Q 042593          245 ----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERA--GRLEQAEEVASGIPS  293 (352)
Q Consensus       245 ----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~--g~~~~A~~~~~~m~~  293 (352)
                                ...-..+....... .-.++...|..++.+|...  .++..+.+.|.....
T Consensus       264 ~v~~~iLa~~~~~~~~ll~~~~~~-~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~  323 (445)
T 4b4t_P          264 IVYFLVLSPYGNLQNDLIHKIQND-NNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLN  323 (445)
T ss_dssp             HHHHHHHSSCSSTTHHHHHSHHHH-SSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTT
T ss_pred             HHHHHHhCCCCchHHHHHHHHhhc-ccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhc
Confidence                      11111222222222 2224566788888888764  457777777765543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.65  E-value=2.2  Score=40.48  Aligned_cols=134  Identities=9%  Similarity=-0.043  Sum_probs=80.8

Q ss_pred             cccHHHHHHHHHhcCC-cchHHHHHHHHHHhCCCCchhh--HHHHHHHHHhcCC-hhHHHHHhccC-----------CCC
Q 042593           24 SFTYSFLIRTCVTLSY-PNLGTQLHAVFSKVGFQSHVYV--NTALGDMYVSLGF-LKDSSKLFDEL-----------PER   88 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~~~~~~--~~~li~~~~~~g~-~~~a~~~~~~m-----------~~~   88 (352)
                      -.....+++.+...|+ .+.|.++++.+....  |...+  ...++..+...++ --+|.+++.+.           ...
T Consensus       248 N~L~~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~  325 (754)
T 4gns_B          248 NYLMYSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPR  325 (754)
T ss_dssp             SHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSC
T ss_pred             HHHHHHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccc
Confidence            3344556666666666 477999999998875  43322  2333433333332 12344444332           222


Q ss_pred             CchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChh-hHHHHHHHHHhCCChhhHHHHHHHH
Q 042593           89 NLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEI-TILAVLPAIWKNGEVRNCQLIHGYG  162 (352)
Q Consensus        89 ~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~  162 (352)
                      +......+-......+.-.+-+.+.|+++-|+.+-++...   ..|+.. +|..|..+|...|+++.|+-.+..+
T Consensus       326 ~~~~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~---~aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          326 DADSARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE---LALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh---cCchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            2211100000000033344566778999999999998843   457765 9999999999999999999888877

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=92.11  E-value=1.2  Score=31.57  Aligned_cols=87  Identities=7%  Similarity=-0.107  Sum_probs=63.6

Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHH---HHHHHHHhccCC-C--CHhhHHHHHHHHHcCC
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFS---ASKLFEDTSVDR-K--NLVSWTTIISGFAMHG  219 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~---a~~~~~~~~~~~-~--~~~~~~~li~~~~~~~  219 (352)
                      -.....+..+.+-|......|. + +..+--.+..+++++....+   ++.+++++.... |  .....-.|.-++.+.|
T Consensus        11 ~~~~~~l~~~~~~y~~e~~~~~-~-s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg   88 (126)
T 1nzn_A           11 LVSVEDLLKFEKKFQSEKAAGS-V-SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLK   88 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSC-C-CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHHHHHHHhccCC-C-cHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhh
Confidence            3334455566666766666555 3 66666677788888887666   899999887664 4  3344556677899999


Q ss_pred             CHHHHHHHHHHHHhc
Q 042593          220 MGKEAVENFERMQKV  234 (352)
Q Consensus       220 ~~~~a~~~~~~m~~~  234 (352)
                      ++++|.+.++.+.+.
T Consensus        89 ~Y~~A~~~~~~lL~~  103 (126)
T 1nzn_A           89 EYEKALKYVRGLLQT  103 (126)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHh
Confidence            999999999999984

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=91.99  E-value=11  Score=37.88  Aligned_cols=198  Identities=12%  Similarity=0.050  Sum_probs=120.9

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC---C------CchhHHHH
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE---R------NLVTWNVI   96 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~------~~~~~~~~   96 (352)
                      ....++..+...+..+.+.++....     +.|+...=.+..+|...|++++|.+.|++...   .      ....+..+
T Consensus       814 ~~~~l~~~l~~~~~~~~~~~l~~~~-----~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~  888 (1139)
T 4fhn_B          814 LVTELVEKLFLFKQYNACMQLIGWL-----NSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEI  888 (1139)
T ss_dssp             HHHHHHHHHHHHSCTTHHHHHHHHS-----CCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHH
T ss_pred             hHHHHHHHHHHhhhHHHHHHHhhhc-----cCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccc
Confidence            3445566666777777766654332     33444434567788899999999999988742   0      00111111


Q ss_pred             H---------HHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-h--hhHHHHHHHHHhCCChhhHHHHHHHHHh
Q 042593           97 I---------TGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-E--ITILAVLPAIWKNGEVRNCQLIHGYGEK  164 (352)
Q Consensus        97 i---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~  164 (352)
                      .         ..|  |..++..+-+.+.++.+.++-.......+..++ .  ..|..+.+++...|++++|...+-.+..
T Consensus       889 ~~~~~~~~~l~~Y--Y~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd  966 (1139)
T 4fhn_B          889 AEKYHHQNLLSCY--YLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLST  966 (1139)
T ss_dssp             HHTTTSCCSSHHH--HHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHH
T ss_pred             cccccccccHHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCC
Confidence            1         011  778888999999999998887766333322221 1  2578899999999999999999987765


Q ss_pred             cCCCCCchhhHHHHHHHHHhhCChHHH------------HHHHHHhccC----CCCHhhHHHHHHHHHcCCCHHH-HHHH
Q 042593          165 RGFNAFDIHVSNCLIDTYAKCGCIFSA------------SKLFEDTSVD----RKNLVSWTTIISGFAMHGMGKE-AVEN  227 (352)
Q Consensus       165 ~~~~~~~~~~~~~li~~~~~~g~~~~a------------~~~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~-a~~~  227 (352)
                      ...   -......|+...|..|..+.-            .+++...-+.    ...+.-|..|=.-+..+|++.+ |.-+
T Consensus       967 ~~~---r~~cLr~LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vm 1043 (1139)
T 4fhn_B          967 TPL---KKSCLLDFVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAII 1043 (1139)
T ss_dssp             SSS---CHHHHHHHHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHH
T ss_pred             HHH---HHHHHHHHHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHH
Confidence            543   345667778878877765443            3333221111    1111234555555666777744 4555


Q ss_pred             HHHHHh
Q 042593          228 FERMQK  233 (352)
Q Consensus       228 ~~~m~~  233 (352)
                      |+...+
T Consensus      1044 Ye~~~R 1049 (1139)
T 4fhn_B         1044 YEKLSR 1049 (1139)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555544

>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=91.52  E-value=0.77  Score=40.01  Aligned_cols=79  Identities=13%  Similarity=0.315  Sum_probs=61.7

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh-----cCCCCCcchhhhH
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK-----VGLKPNRSWRIGE  246 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~~~  246 (352)
                      .+...++.++...|+.++|...+..+....| +...|..+|.++.+.|+..+|.+.|++..+     .|+.|..      
T Consensus       172 ~a~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~------  245 (388)
T 2ff4_A          172 LAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP------  245 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCH------
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCH------
Confidence            3455678888999999999998888765544 788999999999999999999999998754     4777753      


Q ss_pred             hHHHHHHHHHH
Q 042593          247 EGLKFFDKMVE  257 (352)
Q Consensus       247 ~a~~~~~~m~~  257 (352)
                      +..++++.+..
T Consensus       246 ~l~~l~~~il~  256 (388)
T 2ff4_A          246 TLRALNERILR  256 (388)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHc
Confidence            34455555554

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=90.76  E-value=2.3  Score=31.77  Aligned_cols=103  Identities=10%  Similarity=0.054  Sum_probs=64.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-------hhHHHHHHHHHhCCChhhHHHHHHHHHhcCC--C-C---
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE-------ITILAVLPAIWKNGEVRNCQLIHGYGEKRGF--N-A---  169 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~-~---  169 (352)
                      +-.-++.+...+.++.|.-+.+.+....+..|+.       .++..+.+++...+++..|...|++..+..-  . .   
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~  102 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKV  102 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC------
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            3344566777888888888877763333333442       2677888889999999999999998643211  0 0   


Q ss_pred             -----------------CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          170 -----------------FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       170 -----------------~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                                       .+...--.+-.+|.+.++.++|+.+++.+.....++
T Consensus       103 ~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k~Rt~  155 (167)
T 3ffl_A          103 RPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSRQRTP  155 (167)
T ss_dssp             --------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGGGCCH
T ss_pred             cccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCchhcCH
Confidence                             011222345666667777777777777664443333

>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=90.21  E-value=1.8  Score=29.15  Aligned_cols=61  Identities=7%  Similarity=-0.003  Sum_probs=40.4

Q ss_pred             ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHH
Q 042593          151 EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTII  212 (352)
Q Consensus       151 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li  212 (352)
                      |.-++.+-++.+-...+.| ++.+..+.+++|.+.+++..|.++|+.++.+ .....+|..++
T Consensus        25 D~~e~rrglN~l~~~DlVP-~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~l   86 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVP-EPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   86 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCC-CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHH
Confidence            3445666666666777777 7777888888888888888888888776544 22333455544

>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=89.84  E-value=2.8  Score=30.79  Aligned_cols=63  Identities=11%  Similarity=0.154  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      +|.++|.++|+.+... .-.- ...|.....-=.+.|+++.|.+++......+..|  .......|+
T Consensus        74 ~D~d~aR~vy~~a~~~-hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~--~~~le~a~~  136 (161)
T 4h7y_A           74 QEPDDARDYFQMARAN-CKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP--LEMLEIALR  136 (161)
T ss_dssp             HCGGGCHHHHHHHHHH-CTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC--HHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHH-hHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc--HHHHHHHHH
Confidence            7888888888888433 2222 4455555555567889999999998888877664  444444443

>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=89.76  E-value=3  Score=30.61  Aligned_cols=55  Identities=13%  Similarity=0.021  Sum_probs=37.7

Q ss_pred             hhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC
Q 042593          184 KCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKP  238 (352)
Q Consensus       184 ~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p  238 (352)
                      ..++.++|.++|+.+.+.. .=...|-...+-=.++|+..+|.+++.+....+.+|
T Consensus        72 ei~D~d~aR~vy~~a~~~hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           72 AIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             HHHCGGGCHHHHHHHHHHCTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             HhcCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            3478888888888774431 114555555555678888888888888888765554

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=89.73  E-value=2.5  Score=40.13  Aligned_cols=127  Identities=12%  Similarity=0.003  Sum_probs=79.1

Q ss_pred             HHHHHHHHHhCCC-hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC-hHHHHHHHHHhcc-------C--CCCH--
Q 042593          139 ILAVLPAIWKNGE-VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC-IFSASKLFEDTSV-------D--RKNL--  205 (352)
Q Consensus       139 ~~~ll~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~~~~-------~--~~~~--  205 (352)
                      ...++..+...++ .+.|..+++.+.+..... +......++..+.+.++ --+|.+++.+..+       .  ..+.  
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~-~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKDPIH-DIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGG-HHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhCCch-hHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            3455666666666 577999999988875433 33333334444333332 2234444443221       1  1111  


Q ss_pred             --------hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH
Q 042593          206 --------VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILER  277 (352)
Q Consensus       206 --------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  277 (352)
                              ...+.-..-|...|+++-|..+-++....                          .+-+-.+|..|..+|.+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~--------------------------aPseF~tW~~La~vYi~  383 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTEL--------------------------ALDSFESWYNLARCHIK  383 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------------------------CSSCHHHHHHHHHHHHH
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhc--------------------------CchhhHHHHHHHHHHHH
Confidence                    11222234466788999999999987752                          22367899999999999


Q ss_pred             cCChhHHHHHHhcCC
Q 042593          278 AGRLEQAEEVASGIP  292 (352)
Q Consensus       278 ~g~~~~A~~~~~~m~  292 (352)
                      .|+++.|+-.++.+.
T Consensus       384 l~d~e~ALLtLNScP  398 (754)
T 4gns_B          384 KEEYEKALFAINSMP  398 (754)
T ss_dssp             TTCHHHHHHHHHHSC
T ss_pred             hccHHHHHHHHhcCC
Confidence            999999999999886

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.41  E-value=12  Score=33.74  Aligned_cols=64  Identities=8%  Similarity=-0.042  Sum_probs=45.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHhccCCCCCc-hhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHh
Q 042593           60 YVNTALGDMYVSLGFLKDSSKLFDELPERNL-VTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus        60 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~-~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                      ..+|.+++.|...+.++.|..+.++..-|.. ...+-..+-   +.-+...+.-.+++.+|.+.+...
T Consensus       232 ~l~nllLRnYL~~~~y~qA~~lvsk~~fP~~~~sn~q~~rY---~YY~GRI~a~q~~Y~eA~~~L~~A  296 (523)
T 4b4t_S          232 MLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARY---FFYLSKINAIQLDYSTANEYIIAA  296 (523)
T ss_dssp             HHHHHHHHHHHHSSCSTTHHHHHHHHCSCTTTSCHHHHHHH---HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCcHHHHHHHHhcCcCCcccCCHHHHHHH---HHHHHHHHHHhccHHHHHHHHHHH
Confidence            4578888999999999999999998876643 222222221   334455666788999999888887

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.86  E-value=12  Score=33.12  Aligned_cols=166  Identities=5%  Similarity=-0.053  Sum_probs=105.1

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHh--CCCCc---hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKV--GFQSH---VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVII   97 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~--~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i   97 (352)
                      ..+.+.+-..|++.+|.+++..+...  |....   ...+...+..|...+++..|..++.++..     +.......-+
T Consensus       141 ~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~  220 (445)
T 4b4t_P          141 KDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEY  220 (445)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHH
Confidence            45778888999999999999988642  32121   35677888999999999999998888642     1111111111


Q ss_pred             HHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhH----HHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchh
Q 042593           98 TGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITI----LAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus        98 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~----~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                           |...+..+...+++.+|.+.|.+........-|...+    ..++.+..-.+....-..+.....+....+ +..
T Consensus       221 -----~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~~~~-~l~  294 (445)
T 4b4t_P          221 -----YNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDNNLK-KLE  294 (445)
T ss_dssp             -----HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHSSCH-HHH
T ss_pred             -----HHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhccccc-ccH
Confidence                 7777788888999999999888874333232333222    222222233333333344444444333334 778


Q ss_pred             hHHHHHHHHHhh--CChHHHHHHHHHhc
Q 042593          174 VSNCLIDTYAKC--GCIFSASKLFEDTS  199 (352)
Q Consensus       174 ~~~~li~~~~~~--g~~~~a~~~~~~~~  199 (352)
                      .|..++.+|...  .+++.+.+.|....
T Consensus       295 ~~~~L~k~f~~~~L~~~~~~~~~~~~~L  322 (445)
T 4b4t_P          295 SQESLVKLFTTNELMRWPIVQKTYEPVL  322 (445)
T ss_dssp             HHHHHHHHHHHCCSSSHHHHHHHTCSST
T ss_pred             HHHHHHHHHHhchHhhhHHHHHHHHHHh
Confidence            889999999765  35677777776543

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=86.38  E-value=3.9  Score=29.28  Aligned_cols=61  Identities=7%  Similarity=-0.003  Sum_probs=42.8

Q ss_pred             ChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHH
Q 042593          151 EVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTII  212 (352)
Q Consensus       151 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li  212 (352)
                      |.-+..+-++.+....+.| ++.+..+.+++|.+.+|+.-|.++|+.++.+ .+...+|..++
T Consensus        68 D~wElrrglN~l~~~DlVP-eP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~l  129 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVP-EPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI  129 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCC-CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHH
Confidence            3344566666666777777 8888888888888888888888888887654 33344455554

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=86.33  E-value=11  Score=30.30  Aligned_cols=186  Identities=11%  Similarity=0.002  Sum_probs=96.4

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchh---hHHHHHHHHHhcCChhHHHHHhccCCCCC---chhHHHHHHHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVY---VNTALGDMYVSLGFLKDSSKLFDELPERN---LVTWNVIITGLV  101 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~~i~~~~  101 (352)
                      ++.+...++.|+.+.    ++.+.+.|..++..   .-...+...+..|+.+-+..+++.-..++   ..-         
T Consensus         6 ~~~L~~A~~~g~~~~----v~~Ll~~g~~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~~g~~~~~~~~~g---------   72 (285)
T 1wdy_A            6 NHLLIKAVQNEDVDL----VQQLLEGGANVNFQEEEGGWTPLHNAVQMSREDIVELLLRHGADPVLRKKNG---------   72 (285)
T ss_dssp             HHHHHHHHHTTCHHH----HHHHHHTTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHHTTCCTTCCCTTC---------
T ss_pred             chHHHHHHHcCCHHH----HHHHHHcCCCcccccCCCCCcHHHHHHHcCCHHHHHHHHHcCCCCcccCCCC---------
Confidence            345667777888754    44455566544422   12245666778899888888877643322   221         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh---hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchh-----
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSE---ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIH-----  173 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~---~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----  173 (352)
                       ++ .+...+..|+.+-+..+++     .|..++.   .-. +.+...+..|+.+-+.    .+.+.|..+ +..     
T Consensus        73 -~t-~L~~A~~~~~~~~v~~Ll~-----~g~~~~~~~~~g~-t~L~~A~~~~~~~~~~----~Ll~~g~~~-~~~~~~~~  139 (285)
T 1wdy_A           73 -AT-PFLLAAIAGSVKLLKLFLS-----KGADVNECDFYGF-TAFMEAAVYGKVKALK----FLYKRGANV-NLRRKTKE  139 (285)
T ss_dssp             -CC-HHHHHHHHTCHHHHHHHHH-----TTCCTTCBCTTCC-BHHHHHHHTTCHHHHH----HHHHTTCCT-TCCCCCCH
T ss_pred             -CC-HHHHHHHcCCHHHHHHHHH-----cCCCCCccCcccC-CHHHHHHHhCCHHHHH----HHHHhCCCc-ccccccHH
Confidence             11 2233445566654443333     3333332   222 2344455667765444    444444433 211     


Q ss_pred             -------hHHHHHHHHHhhCChHHHHHHHHHhccC--CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCc
Q 042593          174 -------VSNCLIDTYAKCGCIFSASKLFEDTSVD--RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNR  240 (352)
Q Consensus       174 -------~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  240 (352)
                             .-...+...+..|+.+-+..+++.....  ..|....+.+.. .+..++.....++.+.+.+.|..++.
T Consensus       140 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~~~~~~~~~~~~g~t~l~~-a~~~~~~~~~~~i~~~Ll~~g~~~~~  214 (285)
T 1wdy_A          140 DQERLRKGGATALMDAAEKGHVEVLKILLDEMGADVNACDNMGRNALIH-ALLSSDDSDVEAITHLLLDHGADVNV  214 (285)
T ss_dssp             HHHHTTCCCCCHHHHHHHHTCHHHHHHHHHTSCCCTTCCCTTSCCHHHH-HHHCSCTTTHHHHHHHHHHTTCCSSC
T ss_pred             HHHhhccCCCcHHHHHHHcCCHHHHHHHHHhcCCCCCccCCCCCCHHHH-HHHccccchHHHHHHHHHHcCCCCCC
Confidence                   0113455566788888777777653221  223333333333 34455655566777777777766653

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=86.15  E-value=8.8  Score=32.06  Aligned_cols=158  Identities=11%  Similarity=-0.047  Sum_probs=94.6

Q ss_pred             hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHH----
Q 042593          152 VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVEN----  227 (352)
Q Consensus       152 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~----  227 (352)
                      ++....-++.-.+.|---.-.+.|.++..=|.+.+++++|.+++..-             ...+.+.|+...|.++    
T Consensus        13 ~~r~l~rl~~~I~~G~yYEAhQ~~Rtl~~Ry~~~~~~~eAidlL~~g-------------a~~ll~~~Q~~sa~DLa~ll   79 (312)
T 2wpv_A           13 LAKTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQG-------------ALSFLKAKQGGSGTDLIFYL   79 (312)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-------------HHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH-------------HHHHHHCCCcchHHHHHHHH
Confidence            34444444444444422213456778888888889999998887654             3456677887776665    


Q ss_pred             HHHHHhcCCCCCcchhh------------hHhHHHHHHHHHH----hcC-CCCChhhHHHHHHHHHHcCChhHHHHHHhc
Q 042593          228 FERMQKVGLKPNRSWRI------------GEEGLKFFDKMVE----ECE-VLPDIKHYGCLIDILERAGRLEQAEEVASG  290 (352)
Q Consensus       228 ~~~m~~~~~~p~~~~~~------------~~~a~~~~~~m~~----~~~-~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  290 (352)
                      .+-..+.+++++..+..            ...-.++.+++++    ..+ ..-|+.....+...|.+.|++.+|+.-|-.
T Consensus        80 vev~~~~~~~~~~~~~~rl~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~  159 (312)
T 2wpv_A           80 LEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFML  159 (312)
T ss_dssp             HHHHHHTTCCCSHHHHHHHHHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHT
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHh
Confidence            44455567887765544            1112233333332    211 122667778888999999999999987763


Q ss_pred             CCCCCCCchhhHHHHHHHHhc---ccccCcccccccc
Q 042593          291 IPSQITNVVVWRTGFLRLLIN---SYFFSPITLNSQR  324 (352)
Q Consensus       291 m~~~~~~~~~~~~li~~~~~~---g~~~~a~~~~~~~  324 (352)
                      -...  +...+..++.-+...   |...++--+..+.
T Consensus       160 ~~~~--s~~~~a~~l~~w~~~~~~~~~~e~dlf~~Ra  194 (312)
T 2wpv_A          160 GTHD--SMIKYVDLLWDWLCQVDDIEDSTVAEFFSRL  194 (312)
T ss_dssp             SCHH--HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHH
T ss_pred             CCCc--cHHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Confidence            3322  466677766666665   5555544444444

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=85.67  E-value=11  Score=36.87  Aligned_cols=162  Identities=12%  Similarity=0.049  Sum_probs=91.2

Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH--HHhhCChHHHHHHHHHhccC-CCCHhhHH---HHHHHHHc
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT--YAKCGCIFSASKLFEDTSVD-RKNLVSWT---TIISGFAM  217 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~--~~~~g~~~~a~~~~~~~~~~-~~~~~~~~---~li~~~~~  217 (352)
                      ..+.-.|+-+....++..+.+..    +..+...+.-+  +.-.|+.+.+..+.+.+... .|.+ -|.   ++.-+|+.
T Consensus       498 li~vGTgn~~ai~~LL~~~~e~~----~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~~dp~v-Rygaa~alglAyaG  572 (963)
T 4ady_A          498 LCMLGTGKPEAIHDMFTYSQETQ----HGNITRGLAVGLALINYGRQELADDLITKMLASDESLL-RYGGAFTIALAYAG  572 (963)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHHCS----CHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHCSCHHH-HHHHHHHHHHHTTT
T ss_pred             hhhcccCCHHHHHHHHHHHhccC----cHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhCCCHHH-HHHHHHHHHHHhcC
Confidence            33456677777788888776542    22333334444  44678888888888887644 2332 233   33446788


Q ss_pred             CCCHHHHHHHHHHHHhcCCCCCcchhh-------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCCh-hH
Q 042593          218 HGMGKEAVENFERMQKVGLKPNRSWRI-------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRL-EQ  283 (352)
Q Consensus       218 ~~~~~~a~~~~~~m~~~~~~p~~~~~~-------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~-~~  283 (352)
                      .|+......++..+.+..   +.....             .+.+.++++.+.+  ...|.+.--..+.-+....|+. .+
T Consensus       573 TGn~~aIq~LL~~~~~d~---~d~VRraAViaLGlI~~g~~e~v~rlv~~L~~--~~d~~VR~gAalALGli~aGn~~~~  647 (963)
T 4ady_A          573 TGNNSAVKRLLHVAVSDS---NDDVRRAAVIALGFVLLRDYTTVPRIVQLLSK--SHNAHVRCGTAFALGIACAGKGLQS  647 (963)
T ss_dssp             SCCHHHHHHHHHHHHHCS---CHHHHHHHHHHHHHHTSSSCSSHHHHTTTGGG--CSCHHHHHHHHHHHHHHTSSSCCHH
T ss_pred             CCCHHHHHHHHHHhccCC---cHHHHHHHHHHHHhhccCCHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHhccCCCcHH
Confidence            889888888988887642   111111             2333444443333  2345555555555555556654 56


Q ss_pred             HHHHHhcCCCCCCCchhhHH--HHHHHHhcccccC
Q 042593          284 AEEVASGIPSQITNVVVWRT--GFLRLLINSYFFS  316 (352)
Q Consensus       284 A~~~~~~m~~~~~~~~~~~~--li~~~~~~g~~~~  316 (352)
                      |..++..+... ++..+-..  +..|.+-.|..+.
T Consensus       648 aid~L~~L~~D-~d~~Vrq~Ai~ALG~Ig~gtnna  681 (963)
T 4ady_A          648 AIDVLDPLTKD-PVDFVRQAAMIALSMILIQQTEK  681 (963)
T ss_dssp             HHHHHHHHHTC-SSHHHHHHHHHHHHHHSTTCCTT
T ss_pred             HHHHHHHHccC-CCHHHHHHHHHHHHHHhcCCccc
Confidence            77788877655 33333322  3345555555554

>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=85.32  E-value=18  Score=31.40  Aligned_cols=168  Identities=13%  Similarity=-0.064  Sum_probs=91.1

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHh-CCCC---chhhHHHHHHHHHhcC-ChhHHHHHhccCCC---CCchhH-HH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKV-GFQS---HVYVNTALGDMYVSLG-FLKDSSKLFDELPE---RNLVTW-NV   95 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~~---~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~---~~~~~~-~~   95 (352)
                      .....+...+.+.|+.++..+++...... +.-|   .......|++.+.... ..+.-.++..+..+   .+-.+| ..
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~r~flr~   99 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQ   99 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566777777888877777776655431 1112   2334556666666543 23333333333221   111121 00


Q ss_pred             HHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC----hhhHHHHHHHHHhCCChhhHHHHHHHHHhcC--CCC
Q 042593           96 IITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS----EITILAVLPAIWKNGEVRNCQLIHGYGEKRG--FNA  169 (352)
Q Consensus        96 ~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~  169 (352)
                      -+     =..+...|...|++.+|.+++.++.+......|    ...+..-+..|...++..++...+.......  +.+
T Consensus       100 ~l-----~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~  174 (394)
T 3txn_A          100 SL-----EARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYC  174 (394)
T ss_dssp             HH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HH-----HHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCC
Confidence            00     225677888888999988888888443221111    1246666777888888888888887775432  212


Q ss_pred             CchhhHHH----HHHHHH-hhCChHHHHHHHHHh
Q 042593          170 FDIHVSNC----LIDTYA-KCGCIFSASKLFEDT  198 (352)
Q Consensus       170 ~~~~~~~~----li~~~~-~~g~~~~a~~~~~~~  198 (352)
                       ++.+...    -.-.+. ..+++..|...|-+.
T Consensus       175 -~p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~ea  207 (394)
T 3txn_A          175 -PPKVQGALDLQSGILHAADERDFKTAFSYFYEA  207 (394)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHhhHHHHHhccCHHHHHHHHHHH
Confidence             2222211    122234 677888887776554

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.83  E-value=6.9  Score=26.27  Aligned_cols=85  Identities=7%  Similarity=0.031  Sum_probs=57.7

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHH
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNE  118 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~  118 (352)
                      .-++|..+-+.+...+-  ....--+-+..+.+.|++++|..+.+.+.-||...          |-+|.  -.+.|..++
T Consensus        21 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlep----------w~ALc--e~rlGl~s~   86 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEP----------WFALC--EWHLGLGAA   86 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHH----------HHHHH--HHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHH----------HHHHH--HHhcccHHH
Confidence            45677778888877663  22222233445668899999999999998899988          44443  347788888


Q ss_pred             HHHHHHHhHhccCCCCChhhH
Q 042593          119 ALALFRRMAACEYTEPSEITI  139 (352)
Q Consensus       119 a~~~~~~m~~~~~~~p~~~t~  139 (352)
                      +..-+.++ ...| .|....|
T Consensus        87 le~rL~~l-a~sg-~p~~q~F  105 (115)
T 2uwj_G           87 LDRRLAGL-GGSS-DPALADF  105 (115)
T ss_dssp             HHHHHHHH-HTCS-SHHHHHH
T ss_pred             HHHHHHHH-HhCC-CHHHHHH
Confidence            88888788 5554 3444343

>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=84.35  E-value=7.4  Score=30.50  Aligned_cols=190  Identities=9%  Similarity=-0.019  Sum_probs=98.9

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCchhh--HHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYV--NTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGII  107 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li  107 (352)
                      .+...++.|+.+.+..+++.+.+.|..++...  -...+...+..|+.+-+..+++.-..++.....        -...+
T Consensus        12 ~L~~A~~~g~~~~v~~Ll~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~g~~~~~~~~~--------g~t~l   83 (241)
T 1k1a_A           12 PLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRH--------GQTAA   83 (241)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTCCSCCCCTTSCCHHHHHHHTTCHHHHHHHHHTTCCTTCCCTT--------SCCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCcccccCCCHHHHHHHcCCHHHHHHHHHcCCCccccCCC--------CCCHH
Confidence            35667788999988888888877776554321  223456667788888888777754332221100        11122


Q ss_pred             HHHHhcCCHHHHHHHHHHhHhccCCCCC---hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCch---hhHHHHHHH
Q 042593          108 DGYSRMNRSNEALALFRRMAACEYTEPS---EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDI---HVSNCLIDT  181 (352)
Q Consensus       108 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~li~~  181 (352)
                      ...+..|+.+-+..+++.. ...++.++   ..-. +.+...+..|+.+-+    +.+.+.|..+ +.   ..-...+..
T Consensus        84 ~~A~~~~~~~~~~~Ll~~~-~~~~~~~~~~~~~g~-t~L~~A~~~~~~~~~----~~Ll~~g~~~-~~~~~~~g~t~L~~  156 (241)
T 1k1a_A           84 HLACEHRSPTCLRALLDSA-APGTLDLEARNYDGL-TALHVAVNTECQETV----QLLLERGADI-DAVDIKSGRSPLIH  156 (241)
T ss_dssp             HHHHHTTCHHHHHHHHHHS-CTTSCCTTCCCTTSC-CHHHHHHHHTCHHHH----HHHHHTTCCT-TCCCTTTCCCHHHH
T ss_pred             HHHHHcCCHHHHHHHHHcC-CCccccccccCcCCC-cHHHHHHHcCCHHHH----HHHHHcCCCc-ccccccCCCcHHHH
Confidence            3345677777666666654 32222222   2222 233344455665444    4444455443 22   112234555


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN  239 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~  239 (352)
                      .++.|+.+-+.-+++.-... ..|..-.+. +...+..|+.+    +.+.+.+.|..++
T Consensus       157 A~~~~~~~~v~~Ll~~g~~~~~~~~~g~t~-L~~A~~~~~~~----~v~~Ll~~ga~~~  210 (241)
T 1k1a_A          157 AVENNSLSMVQLLLQHGANVNAQMYSGSSA-LHSASGRGLLP----LVRTLVRSGADSS  210 (241)
T ss_dssp             HHHTTCHHHHHHHHHTTCCTTCBCTTSCBH-HHHHHHHTCHH----HHHHHHHTTCCTT
T ss_pred             HHHcCCHHHHHHHHHcCCCCCCcCCCCCCH-HHHHHHcCCHH----HHHHHHhcCCCCC
Confidence            66778877777666642111 122222222 33334556654    4445555666555

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=84.35  E-value=7.4  Score=26.19  Aligned_cols=85  Identities=14%  Similarity=0.137  Sum_probs=57.0

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHH
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNE  118 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~  118 (352)
                      .-++|..+-+.+...+-  ....--+-+..+.+.|++++|..+.+.+.-||...          |-+|..  .+.|..++
T Consensus        22 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlep----------w~ALce--~rlGl~s~   87 (116)
T 2p58_C           22 YHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEP----------WLALCE--YRLGLGSA   87 (116)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHH----------HHHHHH--HHHTCHHH
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHH----------HHHHHH--HhcccHHH
Confidence            45677778888877663  22222233445668899999999999998899988          444433  46788888


Q ss_pred             HHHHHHHhHhccCCCCChhhH
Q 042593          119 ALALFRRMAACEYTEPSEITI  139 (352)
Q Consensus       119 a~~~~~~m~~~~~~~p~~~t~  139 (352)
                      +..-+.++ ...| .|....|
T Consensus        88 le~rL~~l-a~sg-~p~~q~F  106 (116)
T 2p58_C           88 LESRLNRL-ARSQ-DPRIQTF  106 (116)
T ss_dssp             HHHHHHHH-TTCC-CHHHHHH
T ss_pred             HHHHHHHH-HhCC-CHHHHHH
Confidence            88877777 5554 3443333

>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=83.96  E-value=3  Score=36.20  Aligned_cols=96  Identities=9%  Similarity=-0.139  Sum_probs=67.7

Q ss_pred             HHHHHHHH---HhcCCHHHHHHHHHHhHhcc-C-CCCCh------h------------hHHHHHHHHHhCCChhhHHHHH
Q 042593          103 WTGIIDGY---SRMNRSNEALALFRRMAACE-Y-TEPSE------I------------TILAVLPAIWKNGEVRNCQLIH  159 (352)
Q Consensus       103 ~~~li~~~---~~~~~~~~a~~~~~~m~~~~-~-~~p~~------~------------t~~~ll~~~~~~~~~~~a~~~~  159 (352)
                      |..++...   ...|+.+.|.+.+.+..... | .-++.      .            +...++.++...|+.+++...+
T Consensus       115 f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~w~~~~r~~l~~~~~~a~~~~~~~~l~~g~~~~a~~~l  194 (388)
T 2ff4_A          115 FVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAEL  194 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            44444432   34578888888888774432 2 11221      0            1224456667889999999999


Q ss_pred             HHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhcc
Q 042593          160 GYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  200 (352)
                      ..+.....  .+...+..+|.++.+.|+..+|++.|+.+..
T Consensus       195 ~~~~~~~P--~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~  233 (388)
T 2ff4_A          195 EALTFEHP--YREPLWTQLITAYYLSDRQSDALGAYRRVKT  233 (388)
T ss_dssp             HHHHHHST--TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            88877643  3888999999999999999999999998643

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=83.64  E-value=9.9  Score=27.12  Aligned_cols=71  Identities=13%  Similarity=-0.078  Sum_probs=41.9

Q ss_pred             CCChhhHHHHHHHHHhCCC---hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          133 EPSEITILAVLPAIWKNGE---VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      .|+..|--...-++.+..+   ...+..+++.+.+.+... .....-.|.-++.+.|+++.|.+..+.+....|+
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~-~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~  110 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESR-RRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  110 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGG-HHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcch-hHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCC
Confidence            4555554445555555543   345666666666655322 3344445666777777777777777777666554

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=83.11  E-value=12  Score=27.82  Aligned_cols=116  Identities=12%  Similarity=-0.042  Sum_probs=64.7

Q ss_pred             HHHHHHHhhCChHHHHHHHHHhccC---CCCH-------hhHHHHHHHHHcCCCHHHHHHHHHHHHhcC-CCCCcchhhh
Q 042593          177 CLIDTYAKCGCIFSASKLFEDTSVD---RKNL-------VSWTTIISGFAMHGMGKEAVENFERMQKVG-LKPNRSWRIG  245 (352)
Q Consensus       177 ~li~~~~~~g~~~~a~~~~~~~~~~---~~~~-------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~  245 (352)
                      .-++.+...|.++.|+-+.+.+...   .|++       .++..+.+++...|++.+|...|++.++.. .-+...+...
T Consensus        25 dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~~~  104 (167)
T 3ffl_A           25 DHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKVRP  104 (167)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC--------
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCccc
Confidence            3456666677777776666553322   3432       345666778888999999999998864421 1111000000


Q ss_pred             HhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          246 EEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       246 ~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                        ....-..-.......++...--.+..+|.+.|++++|..+++.+..+
T Consensus       105 --~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A          105 --STGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             --------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGG
T ss_pred             --cccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCch
Confidence              00000000000012223344446889999999999999999998776

>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=82.53  E-value=9  Score=25.86  Aligned_cols=62  Identities=13%  Similarity=0.026  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHH
Q 042593          116 SNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLID  180 (352)
Q Consensus       116 ~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  180 (352)
                      .=++.+-++.+ -...+.|+.....+.++||.|.+++..|.++++-++..- .. ...+|..+++
T Consensus        26 ~~e~rrglN~l-~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~-~~~iY~~~lq   87 (109)
T 1v54_E           26 AWELRKGMNTL-VGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GP-HKEIYPYVIQ   87 (109)
T ss_dssp             HHHHHHHHHHH-TTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TT-CTTHHHHHHH
T ss_pred             HHHHHHHHHHH-hccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cC-chhhHHHHHH
Confidence            33555666666 556678999999999999999999999999999887543 22 4456777754

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=82.09  E-value=22  Score=29.98  Aligned_cols=59  Identities=10%  Similarity=-0.044  Sum_probs=37.3

Q ss_pred             ChhhHHHHHHHHHHcCChhHHHHHHhcCCCCCCCchhhHHHHHHHHhcccccCcccccccc
Q 042593          264 DIKHYGCLIDILERAGRLEQAEEVASGIPSQITNVVVWRTGFLRLLINSYFFSPITLNSQR  324 (352)
Q Consensus       264 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  324 (352)
                      |+..-..+...|.+.|++.+|+.-|-. ... +....+..++.-+...+...++--+..+.
T Consensus       135 dp~LH~~ig~~~~~e~~~~~Ae~H~il-g~~-~s~~~~a~mL~ew~~~~~~~e~dlfiaRa  193 (336)
T 3lpz_A          135 DPELHHVVGTLYVEEGEFEAAEKHLVL-GTK-ESPEVLARMEYEWYKQDESHTAPLYCARA  193 (336)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHTT-SCT-THHHHHHHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHh-cCC-chHHHHHHHHHHHHHhcCCccHHHHHHHH
Confidence            667777889999999999999988842 222 22356666555555555444443333343

>3eiq_C Programmed cell death protein 4; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Mus musculus}

Probab=80.69  E-value=10  Score=32.41  Aligned_cols=61  Identities=13%  Similarity=0.067  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC--hHHHHHHHHHhcc
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC--IFSASKLFEDTSV  200 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~--~~~a~~~~~~~~~  200 (352)
                      ....++.-|...|+.++|.+.++++..-...  ...+...+..++-+.++  .+.+.+++..+..
T Consensus       219 ki~~lL~EY~~s~D~~EA~~ci~EL~~p~fh--he~V~~av~~aLE~~~~~~re~~~~LL~~L~~  281 (358)
T 3eiq_C          219 EIDMLLKEYLLSGDISEAEHCLKELEVPHFH--HELVYEAIVMVLESTGESAFKMILDLLKSLWK  281 (358)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHCCTTCH--HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCHHHHHHHHHHccCCcch--HHHHHHHHHHHHccCchHHHHHHHHHHHHHHH
Confidence            4678899999999999999999988643221  34455566666665543  4557777777643

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=80.45  E-value=9.6  Score=30.97  Aligned_cols=117  Identities=5%  Similarity=-0.025  Sum_probs=75.9

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHHHHHHhHHHHHH
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVIITGLVKWTGIID  108 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i~~~~~~~~li~  108 (352)
                      +....+.|+++++++....-++.. |-|...-..|+..+|-.|++++|.+-++...+  |+... .+.+     |-.+|.
T Consensus         4 ~~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~-~a~~-----yr~lI~   76 (273)
T 1zbp_A            4 WKNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLP-GASQ-----LRHLVK   76 (273)
T ss_dssp             HHHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHH-HHHH-----HHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhH-HHHH-----HHHHHH
Confidence            345678899999999988888876 67888888999999999999999988887764  33221 0000     444443


Q ss_pred             HHHhcCCHHHHHHHHHHhHhccCCCC-----ChhhHHHHHHHHH--hCCChhhHHHHHHHHHhc
Q 042593          109 GYSRMNRSNEALALFRRMAACEYTEP-----SEITILAVLPAIW--KNGEVRNCQLIHGYGEKR  165 (352)
Q Consensus       109 ~~~~~~~~~~a~~~~~~m~~~~~~~p-----~~~t~~~ll~~~~--~~~~~~~a~~~~~~~~~~  165 (352)
                      +          +..=.+. -..+-.|     ...-...++.+..  ..|+.++|..+-.++.+.
T Consensus        77 a----------E~~R~~v-faG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~  129 (273)
T 1zbp_A           77 A----------AQARKDF-AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  129 (273)
T ss_dssp             H----------HHHHHHH-TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             H----------HHHHHHH-HcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhc
Confidence            3          1111222 2222222     2224555666554  458999999888888665

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=80.40  E-value=3.7  Score=33.37  Aligned_cols=58  Identities=10%  Similarity=0.019  Sum_probs=39.5

Q ss_pred             HHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          145 AIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       145 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      ...+.|+++++......-++....  |...-..++..+|-.|++++|.+-++...+..|+
T Consensus         6 ~ll~~g~L~~al~~~~~~VR~~P~--da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~   63 (273)
T 1zbp_A            6 NALSEGQLQQALELLIEAIKASPK--DASLRSSFIELLCIDGDFERADEQLMQSIKLFPE   63 (273)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCCc--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCch
Confidence            345667777777777766666543  6777777777888888888877777765444443

---

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	352
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.79
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.72
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.59
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.43
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.14
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.09
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.04
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.02
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.02
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.9
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.88
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.84
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.74
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.71
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.68
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.66
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.51
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.42
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.41
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.32
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.31
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.27
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.22
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.2
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.13
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.1
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.03
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.01
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.93
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.85
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.8
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.8
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.79
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.77
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.71
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.7
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.68
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.64
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.63
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.51
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.49
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.48
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.48
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.38
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.26
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.17
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.07
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.04
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.03
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.02
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.86
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.7
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.39
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.23
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.17
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	91.94
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	90.95
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	90.83
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.93
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	89.47
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	83.59

>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=99.79  E-value=2.7e-17  Score=142.77  Aligned_cols=301  Identities=10%  Similarity=0.048  Sum_probs=209.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCch-hHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLV-TWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~-~~~~~i~~   99 (352)
                      +...+..+...+.+.|++++|...++...+.. +-+..++..+..+|.+.|++++|...+....+  +... ........
T Consensus        32 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  110 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAA  110 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccccccccccccccccccccccccccc
Confidence            56778888899999999999999999998876 55678899999999999999999999988764  2111 11111100


Q ss_pred             HH------------------------hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhH
Q 042593          100 LV------------------------KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNC  155 (352)
Q Consensus       100 ~~------------------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a  155 (352)
                      ..                        ............+....+...+.+... .. +-+...+..+...+...|+.++|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~l~~~~~~~~~~~~A  188 (388)
T d1w3ba_         111 LVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIE-TQ-PNFAVAWSNLGCVFNAQGEIWLA  188 (388)
T ss_dssp             HHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhc-cC-cchhHHHHhhcccccccCcHHHH
Confidence            00                        122333344444555555555555422 11 12334566666677777777777


Q ss_pred             HHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          156 QLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ...++...+....  +...+..+..++...|++++|...++..... ..+...+..+...+.+.|++++|...|++..+.
T Consensus       189 ~~~~~~al~~~p~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  266 (388)
T d1w3ba_         189 IHHFEKAVTLDPN--FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL  266 (388)
T ss_dssp             HHHHHHHHHHCTT--CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCcc--cHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            7777777665433  5666777777777777777777777765543 345566666777777777777777777776663


Q ss_pred             CCCCCcchhh------------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhh
Q 042593          235 GLKPNRSWRI------------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVW  301 (352)
Q Consensus       235 ~~~p~~~~~~------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~  301 (352)
                        .|+.....            .++|...++.....  .+.+...+..+...+.+.|++++|.+.+++.... +.+..+|
T Consensus       267 --~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~  342 (388)
T d1w3ba_         267 --QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAH  342 (388)
T ss_dssp             --CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHH
T ss_pred             --CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc--CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHH
Confidence              33332211            66677777666653  3456778888999999999999999999988776 5567789


Q ss_pred             HHHHHHHHhcccccCcccccccchhhhhhHH
Q 042593          302 RTGFLRLLINSYFFSPITLNSQRLFFFPAAL  332 (352)
Q Consensus       302 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  332 (352)
                      ..+...|...|++++|+..+.+.+...|..-
T Consensus       343 ~~la~~~~~~g~~~~A~~~~~~al~l~P~~~  373 (388)
T d1w3ba_         343 SNLASVLQQQGKLQEALMHYKEAIRISPTFA  373 (388)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTCTTCH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCH
Confidence            9999999999999999999999887666543

>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=99.72  E-value=2.9e-16  Score=136.18  Aligned_cols=285  Identities=12%  Similarity=0.001  Sum_probs=220.6

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCc-hhHHHHHHHHHhHHHH
Q 042593           30 LIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNL-VTWNVIITGLVKWTGI  106 (352)
Q Consensus        30 ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~~i~~~~~~~~l  106 (352)
                      +...+.+.|++++|.+.++.+.+.. |-++..+..+..+|.+.|++++|...|++..+  |+. .+          |..+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~a----------~~~l   73 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEA----------YSNL   73 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH----------HHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH----------HHHH
Confidence            4466778999999999999998875 44678899999999999999999999999865  432 33          8889


Q ss_pred             HHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHH----------------------------------HHHHHHHhCCCh
Q 042593          107 IDGYSRMNRSNEALALFRRMAACEYTEPSEITIL----------------------------------AVLPAIWKNGEV  152 (352)
Q Consensus       107 i~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~----------------------------------~ll~~~~~~~~~  152 (352)
                      ...+.+.|++++|+..+........  .+.....                                  .........+..
T Consensus        74 ~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (388)
T d1w3ba_          74 GNVYKERGQLQEAIEHYRHALRLKP--DFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRL  151 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCH
T ss_pred             HHHhhhhcccccccccccccccccc--ccccccccccccccccccccccccccccccccccccccccccccccccccchh
Confidence            9999999999999999998843222  1111111                                  222223333444


Q ss_pred             hhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 042593          153 RNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERM  231 (352)
Q Consensus       153 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m  231 (352)
                      ..+...+.........  +...+..+...+...|+++.|...++......| +...|..+...+...|++++|...+++.
T Consensus       152 ~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  229 (388)
T d1w3ba_         152 EEAKACYLKAIETQPN--FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRA  229 (388)
T ss_dssp             HHHHHHHHHHHHHCTT--CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             hhhHHHHHHhhccCcc--hhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHh
Confidence            4455555555444332  677888899999999999999999998765554 5778999999999999999999999998


Q ss_pred             HhcCCCCCcchhh----------hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchh
Q 042593          232 QKVGLKPNRSWRI----------GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVV  300 (352)
Q Consensus       232 ~~~~~~p~~~~~~----------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~  300 (352)
                      ...........+.          .++|...+++..+.  .+-+..++..+..++...|++++|.+.++..... +.+...
T Consensus       230 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  307 (388)
T d1w3ba_         230 LSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADS  307 (388)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchh
Confidence            8865433222221          88999999998864  2235678889999999999999999999887666 667789


Q ss_pred             hHHHHHHHHhcccccCcccccccchhhhhhH
Q 042593          301 WRTGFLRLLINSYFFSPITLNSQRLFFFPAA  331 (352)
Q Consensus       301 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  331 (352)
                      +..+...+...|++++|+..+.+.+...|..
T Consensus       308 ~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~  338 (388)
T d1w3ba_         308 LNNLANIKREQGNIEEAVRLYRKALEVFPEF  338 (388)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHTTSCTTC
T ss_pred             hhHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            9999999999999999999999987755543

>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=99.59  E-value=6.1e-14  Score=118.93  Aligned_cols=261  Identities=12%  Similarity=0.002  Sum_probs=196.8

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHHhHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLVKWT  104 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~~~~  104 (352)
                      -.....+.+.|++++|...|+.+.+.. |-+..+|..+..+|...|++++|...|++..+  |+ ...          |.
T Consensus        23 ~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~----------~~   91 (323)
T d1fcha_          23 FEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTA----------LM   91 (323)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH----------HH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccc----------cc
Confidence            345667889999999999999999876 55678999999999999999999999998764  43 333          88


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCCh-------------hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSE-------------ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD  171 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-------------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  171 (352)
                      .+...|...|++++|.+.+++......-.+..             ......+..+...+...++...+....+......+
T Consensus        92 ~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~  171 (323)
T d1fcha_          92 ALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSID  171 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCC
T ss_pred             cccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccc
Confidence            88899999999999999999984322111100             01112223334456677888888887776554436


Q ss_pred             hhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHH
Q 042593          172 IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLK  250 (352)
Q Consensus       172 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~  250 (352)
                      ..++..+...+...|++++|...|++.....| +...|..+..+|...|++++|.+.|++..+.  .|+           
T Consensus       172 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~-----------  238 (323)
T d1fcha_         172 PDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPG-----------  238 (323)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------
T ss_pred             cccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHH--hhc-----------
Confidence            77888899999999999999999999765554 5788999999999999999999999998863  222           


Q ss_pred             HHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCCC------------CCCchhhHHHHHHHHhcccccCcc
Q 042593          251 FFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPSQ------------ITNVVVWRTGFLRLLINSYFFSPI  318 (352)
Q Consensus       251 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------------~~~~~~~~~li~~~~~~g~~~~a~  318 (352)
                                   +...+..+..+|.+.|++++|.+.|++....            ......|..+-.++...|+.+.+.
T Consensus       239 -------------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~  305 (323)
T d1fcha_         239 -------------YIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  305 (323)
T ss_dssp             -------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             -------------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence                         5678889999999999999999999865432            112235666666777777776655


Q ss_pred             cccccch
Q 042593          319 TLNSQRL  325 (352)
Q Consensus       319 ~~~~~~~  325 (352)
                      ....+.+
T Consensus       306 ~~~~~~l  312 (323)
T d1fcha_         306 AADARDL  312 (323)
T ss_dssp             HHHTTCH
T ss_pred             HHHHhCH
Confidence            5555544

>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=99.43  E-value=7.4e-12  Score=105.77  Aligned_cols=248  Identities=13%  Similarity=-0.027  Sum_probs=179.7

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchh---HHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVT---WNVII   97 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~---~~~~i   97 (352)
                      +..+|..+..++...|+++.|...++...+.. +-+...+..+..+|...|++++|.+.+++...  |+...   .....
T Consensus        52 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  130 (323)
T d1fcha_          52 HMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEG  130 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC-----
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhh
Confidence            56789999999999999999999999998875 44678899999999999999999999988643  21100   00000


Q ss_pred             H---HHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhh
Q 042593           98 T---GLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHV  174 (352)
Q Consensus        98 ~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  174 (352)
                      .   ........+..+...+...+|...|.+......-.++..++..+...+...|++++|...++...+....  +...
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~--~~~~  208 (323)
T d1fcha_         131 AGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPN--DYLL  208 (323)
T ss_dssp             ----------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHH
T ss_pred             hhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccc--cccc
Confidence            0   0000222233445566788899999887554444456678888899999999999999999999887644  7889


Q ss_pred             HHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHH
Q 042593          175 SNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFD  253 (352)
Q Consensus       175 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~  253 (352)
                      |..+..+|.+.|++++|.+.|++..+..| +...|..+..+|.+.|++++|.+.|++.++.  .|+....          
T Consensus       209 ~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~----------  276 (323)
T d1fcha_         209 WNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNM--QRKSRGP----------  276 (323)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HHTC-------------
T ss_pred             hhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCcChhh----------
Confidence            99999999999999999999998766554 6788999999999999999999999998763  1221100          


Q ss_pred             HHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHH
Q 042593          254 KMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA  288 (352)
Q Consensus       254 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~  288 (352)
                        ... ........|..+-.++...|+.+.+....
T Consensus       277 --~~~-~~~~~~~~~~~l~~al~~~~~~d~~~~~~  308 (323)
T d1fcha_         277 --RGE-GGAMSENIWSTLRLALSMLGQSDAYGAAD  308 (323)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHHTCGGGHHHHH
T ss_pred             --hhh-hHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence              000 11123345666666777777776665443

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=5.3e-09  Score=87.62  Aligned_cols=198  Identities=9%  Similarity=-0.057  Sum_probs=155.0

Q ss_pred             cccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcC-ChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           24 SFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLG-FLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        24 ~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      ...|+.+-..+.+.+..++|+++++.+++.. |-+...|+....++...| ++++|+..+++..+-++..+.+       
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a-------  114 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQV-------  114 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHH-------
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhH-------
Confidence            4456677777888999999999999999976 556678899998888876 5899999999987533322233       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+.+...+.+.|++++|+..++++.+..  +-+...|..+...+.+.|++++|...++.+.+.++.  +...|+.+..++
T Consensus       115 ~~~~~~~~~~l~~~~eAl~~~~kal~~d--p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~--n~~a~~~r~~~l  190 (315)
T d2h6fa1         115 WHHRRVLVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR--NNSVWNQRYFVI  190 (315)
T ss_dssp             HHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHHHhHHHHhhccHHHHHHHHhhhhhhh--hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc--cHHHHHHHHHHH
Confidence            8888899999999999999999995432  235678999999999999999999999999998655  788888887777


Q ss_pred             HhhCC------hHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          183 AKCGC------IFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       183 ~~~g~------~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .+.+.      +++|.+.+.......| +...|+.+...+.. ...+++.+.++...+.
T Consensus       191 ~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l  248 (315)
T d2h6fa1         191 SNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQD-RGLSKYPNLLNQLLDL  248 (315)
T ss_dssp             HHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHH
T ss_pred             HHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHh-cChHHHHHHHHHHHHh
Confidence            77665      5678888877655544 67778777665544 4467788888877764

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.09  E-value=8.3e-10  Score=93.51  Aligned_cols=273  Identities=10%  Similarity=-0.050  Sum_probs=190.4

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCc-----hhhHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSH-----VYVNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWN   94 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~   94 (352)
                      .........+...|++++|..+++...+.. +.+     ...+..+..+|...|++++|.+.|++..+     ++...  
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~-~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~--   89 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEEL-PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHY--   89 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH--
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhC-cCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHH--
Confidence            344445566789999999999999988754 222     24677788999999999999999998754     22111  


Q ss_pred             HHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhc---cCCCCC--h-hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC
Q 042593           95 VIITGLVKWTGIIDGYSRMNRSNEALALFRRMAAC---EYTEPS--E-ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus        95 ~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~p~--~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  168 (352)
                       .+.+   +..+...+...|++..+...+.+....   .+....  . ..+..+...+...|+++.+...+.........
T Consensus        90 -~~~~---~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~  165 (366)
T d1hz4a_          90 -ALWS---LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSS  165 (366)
T ss_dssp             -HHHH---HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT
T ss_pred             -HHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhh
Confidence             1111   677778899999999999998876321   111111  1 24556677888999999999999888765332


Q ss_pred             C---CchhhHHHHHHHHHhhCChHHHHHHHHHhccC----CC----CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCC
Q 042593          169 A---FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD----RK----NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLK  237 (352)
Q Consensus       169 ~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  237 (352)
                      .   .....+......+...++...+...+.+....    ..    ....+..+...+...|+.++|...+.+..+....
T Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~  245 (366)
T d1hz4a_         166 YQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFA  245 (366)
T ss_dssp             SCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCT
T ss_pred             hhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccc
Confidence            1   13445566677788899999988887764322    11    2344666777889999999999999886653221


Q ss_pred             CCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHhcCCC------C-CCCchhhHHHHHHHHh
Q 042593          238 PNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVASGIPS------Q-ITNVVVWRTGFLRLLI  310 (352)
Q Consensus       238 p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~------~-~~~~~~~~~li~~~~~  310 (352)
                                            ........+..+..++...|++++|...++....      . +....++..+...|..
T Consensus       246 ----------------------~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  303 (366)
T d1hz4a_         246 ----------------------NNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQ  303 (366)
T ss_dssp             ----------------------TCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             ----------------------cchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHH
Confidence                                  1122344556678888888999988888876532      1 2234567778888889


Q ss_pred             cccccCcccccccchh
Q 042593          311 NSYFFSPITLNSQRLF  326 (352)
Q Consensus       311 ~g~~~~a~~~~~~~~~  326 (352)
                      .|++++|++.+.+.+.
T Consensus       304 ~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         304 AGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999988888887754

>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=99.04  E-value=1e-08  Score=85.61  Aligned_cols=186  Identities=9%  Similarity=0.013  Sum_probs=140.0

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHH
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNE  118 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~  118 (352)
                      ..++|..+|+...+...+.+...|...+....+.|+++.|..+|+++.+.+......+      |...+....+.|+.++
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~------w~~~~~~~~~~~~~~~  152 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLV------YIQYMKFARRAEGIKS  152 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHH------HHHHHHHHHHHHCHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHH------HHHHHHHHHHcCChHH
Confidence            3467788888887665455667788888899999999999999998765222211111      7788888889999999


Q ss_pred             HHHHHHHhHhccCCCCChhhHHHHHHH-HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHH
Q 042593          119 ALALFRRMAACEYTEPSEITILAVLPA-IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFED  197 (352)
Q Consensus       119 a~~~~~~m~~~~~~~p~~~t~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  197 (352)
                      |.++|+++.+...  .+...|...... +...|+.+.|..+++.+.+....  +...|...++.+.+.|+.+.|..+|++
T Consensus       153 ar~i~~~al~~~~--~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~--~~~~w~~y~~~~~~~g~~~~aR~~fe~  228 (308)
T d2onda1         153 GRMIFKKAREDAR--TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGD--IPEYVLAYIDYLSHLNEDNNTRVLFER  228 (308)
T ss_dssp             HHHHHHHHHTSTT--CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTT--CHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCC--CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            9999999844332  233334333332 34568899999999999887433  788999999999999999999999998


Q ss_pred             hccCC---C--CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          198 TSVDR---K--NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       198 ~~~~~---~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .....   |  ....|...+..-...|+.+.+..+++++.+.
T Consensus       229 ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         229 VLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            75542   2  2457888888888889999999999988763

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.02  E-value=1.2e-08  Score=85.37  Aligned_cols=163  Identities=9%  Similarity=-0.081  Sum_probs=132.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcC-CHHHHHHHHHHhHhccCCCCC-h
Q 042593           59 VYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMN-RSNEALALFRRMAACEYTEPS-E  136 (352)
Q Consensus        59 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~p~-~  136 (352)
                      ...++.+...+.+.+..++|+++++++.+-++..+++       |+....++...| ++++|+..+++..+.   .|+ .
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a-------~~~r~~~l~~l~~~~~eal~~~~~al~~---~p~~~  112 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTV-------WHFRRVLLKSLQKDLHEEMNYITAIIEE---QPKNY  112 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHH-------HHHHHHHHHHTTCCHHHHHHHHHHHHHH---CTTCH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHH-------HHHHHHHHHHhCcCHHHHHHHHHHHHHH---HHhhh
Confidence            4567777888889999999999999998744444444       888888888876 599999999998442   344 5


Q ss_pred             hhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHH
Q 042593          137 ITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGF  215 (352)
Q Consensus       137 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~  215 (352)
                      .+|..+...+.+.|+.++|...++.+.+....  +...|..+..++.+.|++++|++.++......| +...|+.+...+
T Consensus       113 ~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp~--n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l  190 (315)
T d2h6fa1         113 QVWHHRRVLVEWLRDPSQELEFIADILNQDAK--NYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVI  190 (315)
T ss_dssp             HHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHhHHHHhhccHHHHHHHHhhhhhhhhc--chHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHH
Confidence            68999999999999999999999999987654  899999999999999999999999999876654 678888777666


Q ss_pred             HcCCC------HHHHHHHHHHHHh
Q 042593          216 AMHGM------GKEAVENFERMQK  233 (352)
Q Consensus       216 ~~~~~------~~~a~~~~~~m~~  233 (352)
                      .+.+.      +++|.+.+.+..+
T Consensus       191 ~~~~~~~~~~~~~~ai~~~~~al~  214 (315)
T d2h6fa1         191 SNTTGYNDRAVLEREVQYTLEMIK  214 (315)
T ss_dssp             HHTTCSCSHHHHHHHHHHHHHHHH
T ss_pred             HHccccchhhhhHHhHHHHHHHHH
Confidence            66554      4667777776665

>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=99.02  E-value=2.4e-08  Score=83.32  Aligned_cols=216  Identities=11%  Similarity=0.044  Sum_probs=154.5

Q ss_pred             chHHHHHHHHHHhCCCCchhhHHHHHHHHHh--------------cCChhHHHHHhccCCC---C-CchhHHHHHHHHHh
Q 042593           41 NLGTQLHAVFSKVGFQSHVYVNTALGDMYVS--------------LGFLKDSSKLFDELPE---R-NLVTWNVIITGLVK  102 (352)
Q Consensus        41 ~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~--------------~g~~~~a~~~~~~m~~---~-~~~~~~~~i~~~~~  102 (352)
                      +.+..+|+.+...- +.++..|-.-+..+-+              .+..++|..+|++..+   | +...          
T Consensus        33 ~Rv~~vyerAl~~~-~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l----------  101 (308)
T d2onda1          33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLL----------  101 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHH----------
T ss_pred             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHH----------
Confidence            34566777777653 4455555554443322              2345778888887543   2 2223          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH-
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT-  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~-  181 (352)
                      |...+....+.|+.++|..+|+++.. .........|...+....+.|+.+.|..+++.+.+.+..  +...|...... 
T Consensus       102 ~~~ya~~~~~~~~~~~a~~i~~~~l~-~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~--~~~~~~~~a~~e  178 (308)
T d2onda1         102 YFAYADYEESRMKYEKVHSIYNRLLA-IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART--RHHVYVTAALME  178 (308)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHT-SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTC--CTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHH-HhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC--cHHHHHHHHHHH
Confidence            77777888899999999999999843 222222346888899999999999999999999887654  44555444433 


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcC
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECE  260 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~  260 (352)
                      +...|+.+.|.++|+.+... +.+...|...+..+.+.|+.++|..+|++..+..                        +
T Consensus       179 ~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~------------------------~  234 (308)
T d2onda1         179 YYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG------------------------S  234 (308)
T ss_dssp             HHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSS------------------------S
T ss_pred             HHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC------------------------C
Confidence            34468899999999988766 4467889999999999999999999999987642                        2


Q ss_pred             CCC--ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          261 VLP--DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       261 ~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      ..|  ....|...+..-...|+.+.+.++.+++...
T Consensus       235 ~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         235 LPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             SCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            223  2457888888888899999999998876544

>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=98.90  E-value=2.9e-08  Score=80.30  Aligned_cols=187  Identities=7%  Similarity=-0.159  Sum_probs=127.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      |..+...|.+.|++++|...|++....   .|+ ..+|..+..++.+.|++++|...+++..+....  +..++..+..+
T Consensus        40 ~~~~G~~y~~~g~~~~A~~~~~~al~l---~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~--~~~a~~~lg~~  114 (259)
T d1xnfa_          40 LYERGVLYDSLGLRALARNDFSQALAI---RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT--YNYAHLNRGIA  114 (259)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CTHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHhhcc---CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhh--hhhhHHHHHHH
Confidence            777888999999999999999998553   344 568999999999999999999999999987654  67788899999


Q ss_pred             HHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh-----hHhHHHHHHHH
Q 042593          182 YAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRI-----GEEGLKFFDKM  255 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-----~~~a~~~~~~m  255 (352)
                      |...|++++|.+.|+...+..| +......+..++.+.+..+.+..+..........+......     .......+...
T Consensus       115 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (259)
T d1xnfa_         115 LYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERL  194 (259)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHHHHHHTTSSCHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHhhccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998765544 44444444455566666666666666555532222111111     00011112222


Q ss_pred             HHhcC----CCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC
Q 042593          256 VEECE----VLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       256 ~~~~~----~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  294 (352)
                      .....    ..| ...+|..+...|...|++++|.+.|+.....
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  238 (259)
T d1xnfa_         195 KADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  238 (259)
T ss_dssp             HHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            21100    111 2345666788888888888888888877665

>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=98.88  E-value=6.7e-09  Score=84.15  Aligned_cols=195  Identities=11%  Similarity=-0.079  Sum_probs=132.5

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITG   99 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~   99 (352)
                      ...+|..+..++.+.|++++|.+.|+...+.. +-++.+|..+..+|.+.|++++|++.|++..+  |+ ..+       
T Consensus        36 ~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a-------  107 (259)
T d1xnfa_          36 RAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYA-------  107 (259)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHH-------
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhh-------
Confidence            34577778889999999999999999999876 55788999999999999999999999999875  43 334       


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          100 LVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       100 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                         |..+..++...|++++|...|++..+..  +.+......+..+..+.+..+....+..........+   ..+ .++
T Consensus       108 ---~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~  178 (259)
T d1xnfa_         108 ---HLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQ---WGW-NIV  178 (259)
T ss_dssp             ---HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCS---THH-HHH
T ss_pred             ---HHHHHHHHHHHhhHHHHHHHHHHHHhhc--cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhh---hhh-hHH
Confidence               7788888999999999999999984432  1234444444445556666555555555555443222   122 222


Q ss_pred             HHHHhhCChHHHHHHHHHhccC----CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          180 DTYAKCGCIFSASKLFEDTSVD----RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ..+...........-.......    .| ...+|..+...|...|++++|...|+..+..
T Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  238 (259)
T d1xnfa_         179 EFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  238 (259)
T ss_dssp             HHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            3322222222222211111111    22 3356777889999999999999999998864

>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=98.84  E-value=1.1e-09  Score=92.75  Aligned_cols=191  Identities=8%  Similarity=-0.071  Sum_probs=116.5

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHhCCCCch-hhHHHHHHH----------HHhcCChhHHHHHhccCCCCCchhHHHH
Q 042593           28 SFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHV-YVNTALGDM----------YVSLGFLKDSSKLFDELPERNLVTWNVI   96 (352)
Q Consensus        28 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~li~~----------~~~~g~~~~a~~~~~~m~~~~~~~~~~~   96 (352)
                      ..++.........++|+++++...+..  |+. ..|+..-..          +...|++++|+.+++...+.++..+.. 
T Consensus        33 ~~~~~~~~~~~~~~~al~~~~~~l~~~--P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~-  109 (334)
T d1dcea1          33 QAVFQKRQAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGT-  109 (334)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHH-
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHH-
Confidence            333333333444578999999888755  544 344332222          223345778888888876522222222 


Q ss_pred             HHHHHhHHHHHHHHHhcC--CHHHHHHHHHHhHhccCCCCChhhHH-HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchh
Q 042593           97 ITGLVKWTGIIDGYSRMN--RSNEALALFRRMAACEYTEPSEITIL-AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIH  173 (352)
Q Consensus        97 i~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~~p~~~t~~-~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  173 (352)
                            |..+..++...+  ++++|...++++....  +++...+. .....+...+..+.|...++.+.+....  +..
T Consensus       110 ------~~~~~~~~~~~~~~~~~~a~~~~~~al~~~--~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~--~~~  179 (334)
T d1dcea1         110 ------WHHRCWLLSRLPEPNWARELELCARFLEAD--ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS--NYS  179 (334)
T ss_dssp             ------HHHHHHHHHTCSSCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC--CHH
T ss_pred             ------HHHhhHHHHHhccccHHHHHHHHHHHHhhC--chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCC--CHH
Confidence                  666666665555  5788888888884422  23344443 4446677788899999998888877654  788


Q ss_pred             hHHHHHHHHHhhCChHHHHHHHHHhccCCCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          174 VSNCLIDTYAKCGCIFSASKLFEDTSVDRKNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       174 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .|+.+..++.+.|++++|...++......|+.   ......+...+..+++...+......
T Consensus       180 a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~a~~~~~~~l~~  237 (334)
T d1dcea1         180 SWHYRSCLLPQLHPQPDSGPQGRLPENVLLKE---LELVQNAFFTDPNDQSAWFYHRWLLG  237 (334)
T ss_dssp             HHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHH---HHHHHHHHHHCSSCSHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhHHhHHHH---HHHHHHHHHhcchhHHHHHHHHHHHh
Confidence            88888889999998887766555443222221   12223344556666777777766654

>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=98.74  E-value=1.6e-06  Score=71.25  Aligned_cols=207  Identities=9%  Similarity=-0.081  Sum_probs=138.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHhccCCC-----CCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           61 VNTALGDMYVSLGFLKDSSKLFDELPE-----RNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        61 ~~~~li~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      .|......|...+++++|.+.|.+..+     .+....   ..   +|+.+..+|.+.|++++|...+++......-..+
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~---a~---~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~  112 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEA---GN---TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQ  112 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHH---HH---HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHH---HH---HHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhccc
Confidence            466677888889999999999887753     222111   11   1888899999999999999999976322111111


Q ss_pred             ----hhhHHHHHHHHH-hCCChhhHHHHHHHHHhc----CCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCCH-
Q 042593          136 ----EITILAVLPAIW-KNGEVRNCQLIHGYGEKR----GFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKNL-  205 (352)
Q Consensus       136 ----~~t~~~ll~~~~-~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-  205 (352)
                          ..++..+...+. ..|++++|...+++..+.    +..+....++..+...|.+.|++++|.+.|++.....++. 
T Consensus       113 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~  192 (290)
T d1qqea_         113 FRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNR  192 (290)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCT
T ss_pred             chhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccch
Confidence                235666666664 469999999999887542    2222124567889999999999999999999875542221 


Q ss_pred             -------hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH-
Q 042593          206 -------VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILER-  277 (352)
Q Consensus       206 -------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~-  277 (352)
                             ..+...+..+...|+++.|...+++..+.....                     ...........++.++.. 
T Consensus       193 ~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~---------------------~~sre~~~l~~l~~a~~~~  251 (290)
T d1qqea_         193 LSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNF---------------------ADSRESNFLKSLIDAVNEG  251 (290)
T ss_dssp             TTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC------------------------------HHHHHHHHHHHHTT
T ss_pred             hhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCc---------------------cchHHHHHHHHHHHHHHhc
Confidence                   223455556778899999999999887642110                     001123345666776654 


Q ss_pred             -cCChhHHHHHHhcCCCC
Q 042593          278 -AGRLEQAEEVASGIPSQ  294 (352)
Q Consensus       278 -~g~~~~A~~~~~~m~~~  294 (352)
                       .+.+++|..-|+.+.+.
T Consensus       252 d~e~~~eai~~y~~~~~l  269 (290)
T d1qqea_         252 DSEQLSEHCKEFDNFMRL  269 (290)
T ss_dssp             CTTTHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHHHHHHHhhc
Confidence             34588888888887765

>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=98.71  E-value=5.6e-07  Score=75.48  Aligned_cols=271  Identities=11%  Similarity=0.006  Sum_probs=184.7

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCC--C---CchhhHHHHHHHHHhcCChhHHHHHhccCCC-------CCchh
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGF--Q---SHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------RNLVT   92 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~~~~~   92 (352)
                      ..+..+..++...|++++|...++...+...  .   .....+..+...+...|++..+...+.+...       +....
T Consensus        52 ~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~  131 (366)
T d1hz4a_          52 VATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPM  131 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhH
Confidence            4677788899999999999999998875321  1   1234567777888899999999888876542       11111


Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccC---CCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC-
Q 042593           93 WNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEY---TEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN-  168 (352)
Q Consensus        93 ~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-  168 (352)
                       ...+     +..+...+...|+++.+...+........   ......++......+...++...+...+.+....... 
T Consensus       132 -~~~~-----~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~  205 (366)
T d1hz4a_         132 -HEFL-----VRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNG  205 (366)
T ss_dssp             -HHHH-----HHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS
T ss_pred             -HHHH-----HHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHh
Confidence             1111     66677888999999999999988733221   1112335566667777889998888887766543211 


Q ss_pred             ---C-CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-----CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCC
Q 042593          169 ---A-FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-----NLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPN  239 (352)
Q Consensus       169 ---~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~  239 (352)
                         + .....+..+...+...|+.+.|...++......+     ....+..+..++...|++++|...+++.....    
T Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~----  281 (366)
T d1hz4a_         206 KYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENA----  281 (366)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH----
T ss_pred             cccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH----
Confidence               1 0234566777888999999999999998765422     23556678889999999999999999876521    


Q ss_pred             cchhhhHhHHHHHHHHHHhcCCCC-ChhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CC---------CchhhHHHHHHH
Q 042593          240 RSWRIGEEGLKFFDKMVEECEVLP-DIKHYGCLIDILERAGRLEQAEEVASGIPSQ-IT---------NVVVWRTGFLRL  308 (352)
Q Consensus       240 ~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~---------~~~~~~~li~~~  308 (352)
                                      ... +..| ....+..+..+|.+.|++++|.+.+++.... .+         .......++..+
T Consensus       282 ----------------~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~~~~~~~~~~~~~l  344 (366)
T d1hz4a_         282 ----------------RSL-RLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMAQQLRQL  344 (366)
T ss_dssp             ----------------HHT-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHHHHHHHHHH
T ss_pred             ----------------hhc-ccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHHHHHHHHHHHHHHH
Confidence                            111 3333 3457888899999999999999999876433 11         112334455556


Q ss_pred             HhcccccCcccccc
Q 042593          309 LINSYFFSPITLNS  322 (352)
Q Consensus       309 ~~~g~~~~a~~~~~  322 (352)
                      ...++..++.+-..
T Consensus       345 ~~~~~l~e~e~~~a  358 (366)
T d1hz4a_         345 IQLNTLPELEQHRA  358 (366)
T ss_dssp             HHTTCSCHHHHHHH
T ss_pred             HhcCCChHHHHHHH
Confidence            66677666654333

>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=98.68  E-value=7.6e-07  Score=68.35  Aligned_cols=125  Identities=12%  Similarity=-0.041  Sum_probs=104.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+. ...+...|++++|++.|.++     .+|+..+|..+..++...|++++|...|++..+....  ....|..+..+|
T Consensus         9 ~~~-g~~~~~~~d~~~Al~~~~~i-----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~--~~~a~~~~g~~~   80 (192)
T d1hh8a_           9 WNE-GVLAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH--LAVAYFQRGMLY   80 (192)
T ss_dssp             HHH-HHHHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHH
T ss_pred             HHH-HHHHHHCCCHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh--hhhhHHHHHHHH
Confidence            665 55678899999999999987     3577888999999999999999999999999988654  788999999999


Q ss_pred             HhhCChHHHHHHHHHhccC-CC----------------CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          183 AKCGCIFSASKLFEDTSVD-RK----------------NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~-~~----------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      .+.|++++|.+.|++.... +.                ...++..+..++.+.|++++|.+.+....+..
T Consensus        81 ~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          81 YQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            9999999999999885432 11                12556677888999999999999999887643

>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=98.66  E-value=5.9e-07  Score=73.91  Aligned_cols=205  Identities=7%  Similarity=-0.095  Sum_probs=142.1

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHh----CCCC-chhhHHHHHHHHHhcCChhHHHHHhccCCC--CCchhHHHHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKV----GFQS-HVYVNTALGDMYVSLGFLKDSSKLFDELPE--RNLVTWNVII   97 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~~i   97 (352)
                      ..|......|...|++++|.+.|+...+.    +-++ -..+|..+..+|.+.|++++|.+.+++..+  ++........
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  117 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHH
Confidence            35888889999999999999999988763    2122 236789999999999999999999987653  1111111111


Q ss_pred             HHHHhHHHHHHHHH-hcCCHHHHHHHHHHhHhc---cCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCc-
Q 042593           98 TGLVKWTGIIDGYS-RMNRSNEALALFRRMAAC---EYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFD-  171 (352)
Q Consensus        98 ~~~~~~~~li~~~~-~~~~~~~a~~~~~~m~~~---~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-  171 (352)
                      ..   +..+...|- ..|++++|+..|++....   .+..+. ..++..+...+...|++++|...++++.......+. 
T Consensus       118 ~~---~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~  194 (290)
T d1qqea_         118 NF---KFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLS  194 (290)
T ss_dssp             HH---HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTT
T ss_pred             HH---HHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhh
Confidence            11   667777774 469999999999987332   221121 236888899999999999999999998876433201 


Q ss_pred             ----hhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC------HhhHHHHHHHHHcC--CCHHHHHHHHHHHH
Q 042593          172 ----IHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN------LVSWTTIISGFAMH--GMGKEAVENFERMQ  232 (352)
Q Consensus       172 ----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~------~~~~~~li~~~~~~--~~~~~a~~~~~~m~  232 (352)
                          ...+...+.++...|+.+.|.+.++......|+      ......++.++-..  +.+++|...|+++.
T Consensus       195 ~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         195 QWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             hhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence                123445566777899999999999998766442      23456667776553  45788888776544

>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=98.51  E-value=4e-06  Score=64.17  Aligned_cols=127  Identities=12%  Similarity=-0.021  Sum_probs=92.3

Q ss_pred             HHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHH
Q 042593           66 GDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPA  145 (352)
Q Consensus        66 i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~  145 (352)
                      ...+...|+++.|++.|+++..++..+          |..+..+|...|++++|++.|++..+..  +-+...|..+..+
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~~~~~~----------~~nlG~~~~~~g~~~~A~~~~~kAl~ld--p~~~~a~~~~g~~   79 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQDPHSRI----------CFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYFQRGML   79 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSSCCHHH----------HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCCCCHHH----------HHHHHHHHHHcCCchhHHHHHHHHHHHh--hhhhhhHHHHHHH
Confidence            445567788888888888877776665          6777888888888888888888874422  1234577788888


Q ss_pred             HHhCCChhhHHHHHHHHHhcCCC--------------CCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFN--------------AFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~--------------~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      +.+.|++++|...++...+....              .....++..+..++.+.|++++|.+.|+......|+
T Consensus        80 ~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          80 YYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            88888888888887776543111              101345667788899999999999999987766555

>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=98.42  E-value=1.2e-07  Score=79.90  Aligned_cols=232  Identities=7%  Similarity=-0.080  Sum_probs=160.8

Q ss_pred             cCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCC--hhHHHHHhccCCCCCchhHHHHHHHHHhHH-HHHHHHHhc
Q 042593           37 LSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGF--LKDSSKLFDELPERNLVTWNVIITGLVKWT-GIIDGYSRM  113 (352)
Q Consensus        37 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~--~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~-~li~~~~~~  113 (352)
                      .|++++|+.+++...+.. +-+...|..+..++...++  .++|...++++.+.+...+..       |. .....+...
T Consensus        86 ~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~-------~~~~~~~~~~~~  157 (334)
T d1dcea1          86 AALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHC-------WDYRRFVAAQAA  157 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHH-------HHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhh-------hhhHHHHHHHhc
Confidence            345678888899888765 5567778888777777664  789999999876533222222       33 344677778


Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHH
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASK  193 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  193 (352)
                      +..++|+..+++... .. +-+...|+.+...+.+.|++++|...++...+..     .. .......+...+..+.+..
T Consensus       158 ~~~~~Al~~~~~~i~-~~-p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~-----~~-~~~~~~~~~~l~~~~~a~~  229 (334)
T d1dcea1         158 VAPAEELAFTDSLIT-RN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVL-----LK-ELELVQNAFFTDPNDQSAW  229 (334)
T ss_dssp             CCHHHHHHHHHTTTT-TT-CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHH-----HH-HHHHHHHHHHHCSSCSHHH
T ss_pred             cccHHHHHHHHHHHH-cC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhH-----HH-HHHHHHHHHHhcchhHHHH
Confidence            999999999999833 22 1345678889999999999988876665544431     11 1223444566777788888


Q ss_pred             HHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHH
Q 042593          194 LFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLI  272 (352)
Q Consensus       194 ~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li  272 (352)
                      .+...... +++...+..+...+...++.++|...+.+.....                          +-+...+..+.
T Consensus       230 ~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------------------p~~~~~~~~l~  283 (334)
T d1dcea1         230 FYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPEN--------------------------KWCLLTIILLM  283 (334)
T ss_dssp             HHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC--------------------------HHHHHHHHHHH
T ss_pred             HHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC--------------------------chHHHHHHHHH
Confidence            77765444 4456666777777788888888888888766531                          12556778888


Q ss_pred             HHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHh
Q 042593          273 DILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLI  310 (352)
Q Consensus       273 ~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~  310 (352)
                      .+|.+.|+.++|.+.++..... |.+..-|+.|...+..
T Consensus       284 ~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~~~L~~~~~~  322 (334)
T d1dcea1         284 RALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLL  322 (334)
T ss_dssp             HHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHCcccHHHHHHHHHHHhH
Confidence            8999999999999999988766 3344566666655554

>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=98.41  E-value=2.6e-06  Score=65.55  Aligned_cols=98  Identities=11%  Similarity=-0.100  Sum_probs=84.1

Q ss_pred             CChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHH
Q 042593          134 PSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTII  212 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li  212 (352)
                      |+...+....+.+.+.|++++|...|+...+....  +...|..+..+|.+.|++++|...|+......| ++.+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~--~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL--VAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHH
Confidence            66677777888899999999999999988887543  788899999999999999999999999877655 578888999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHh
Q 042593          213 SGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+|.+.|++++|...|++..+
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999998765

>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=2.2e-06  Score=65.89  Aligned_cols=98  Identities=8%  Similarity=-0.153  Sum_probs=85.8

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      +...+......+.+.|++++|+..|+...... |.++..|..+..+|.+.|++++|+..|++..+-++....+       
T Consensus         3 ~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a-------   74 (201)
T d2c2la1           3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKA-------   74 (201)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHH-------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHH-------
Confidence            88889999999999999999999999999886 6678899999999999999999999999988733322222       


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHh
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAA  128 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~  128 (352)
                      |..+..+|.+.|++++|+..|++...
T Consensus        75 ~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          75 HFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            88899999999999999999998743

>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=98.31  E-value=6.2e-06  Score=57.47  Aligned_cols=88  Identities=14%  Similarity=-0.045  Sum_probs=51.5

Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHH
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~  222 (352)
                      +.+.+.|++++|...|.+..+....  +...|..+..+|.+.|++++|++.++..... +.+...|..+..++...|+++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~p~--~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLDPH--NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCc--chhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHH
Confidence            4455556666666666666555433  5556666666666666666666666655433 335555666666666666666


Q ss_pred             HHHHHHHHHHh
Q 042593          223 EAVENFERMQK  233 (352)
Q Consensus       223 ~a~~~~~~m~~  233 (352)
                      +|...|++..+
T Consensus        89 ~A~~~~~~a~~   99 (117)
T d1elwa_          89 EAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            66666666554

>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=98.27  E-value=1e-05  Score=56.25  Aligned_cols=97  Identities=8%  Similarity=-0.085  Sum_probs=83.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh
Q 042593          105 GIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK  184 (352)
Q Consensus       105 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  184 (352)
                      .-.+.+.+.|++++|+..|++..+..  +-+...|..+..++.+.|++++|...+....+.+..  +...|..+..++..
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~--~~~~~~~~g~~~~~   83 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD--WGKGYSRKAAALEF   83 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC--CcchhhhhcccccccccccccccchhhhhHHHhccc--hhhHHHHHHHHHHH
Confidence            34567889999999999999995532  234568999999999999999999999999988654  88899999999999


Q ss_pred             hCChHHHHHHHHHhccCCCCH
Q 042593          185 CGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       185 ~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .|++++|...|+......|+-
T Consensus        84 ~~~~~~A~~~~~~a~~~~p~~  104 (117)
T d1elwa_          84 LNRFEEAKRTYEEGLKHEANN  104 (117)
T ss_dssp             TTCHHHHHHHHHHHHTTCTTC
T ss_pred             ccCHHHHHHHHHHHHHhCCCC
Confidence            999999999999988776653

>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=98.22  E-value=3.2e-06  Score=62.56  Aligned_cols=55  Identities=4%  Similarity=-0.159  Sum_probs=25.5

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCC
Q 042593           31 IRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELP   86 (352)
Q Consensus        31 l~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~   86 (352)
                      ...+.+.|++++|...|+...+.. +-+...|..+..+|...|++++|+..|++..
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal   71 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAI   71 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHH
Confidence            334444455555555555444443 3334444444444444444444444444443

>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=98.20  E-value=1.3e-05  Score=59.06  Aligned_cols=89  Identities=12%  Similarity=0.016  Sum_probs=57.5

Q ss_pred             HHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHH
Q 042593          144 PAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGK  222 (352)
Q Consensus       144 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~  222 (352)
                      +.+.+.|++++|...|++..+....  +...|..+..+|...|++++|.+.|+...+..| +...|..+..++...|+++
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~p~--~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~~   95 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELNPS--NAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   95 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHhhhccccchh--hhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCHH
Confidence            4455666666666666666665433  666666666677777777777777766554433 4566666666777777777


Q ss_pred             HHHHHHHHHHhc
Q 042593          223 EAVENFERMQKV  234 (352)
Q Consensus       223 ~a~~~~~~m~~~  234 (352)
                      +|...+++..+.
T Consensus        96 eA~~~~~~a~~~  107 (159)
T d1a17a_          96 AALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc
Confidence            777776666653

>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=98.13  E-value=6.8e-06  Score=56.75  Aligned_cols=90  Identities=8%  Similarity=-0.090  Sum_probs=69.1

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCC
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHG  219 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~  219 (352)
                      .....+.+.|++++|...+++..+....  +...|..+..++.+.|++++|+..|+......| +...|..+..+|...|
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~p~--~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g   98 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKEPE--REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEH   98 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccccc--cchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCC
Confidence            4556677788888888888888777543  677888888888888888888888887655544 5777888888888888


Q ss_pred             CHHHHHHHHHHHH
Q 042593          220 MGKEAVENFERMQ  232 (352)
Q Consensus       220 ~~~~a~~~~~~m~  232 (352)
                      ++++|.+.+++.+
T Consensus        99 ~~~~A~~~l~~~l  111 (112)
T d1hxia_          99 NANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHh
Confidence            8888888887653

>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=98.10  E-value=1e-05  Score=56.71  Aligned_cols=91  Identities=10%  Similarity=-0.063  Sum_probs=53.5

Q ss_pred             HHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCC---hHHHHHHHHHhccCCCCH---hhHHHHHHH
Q 042593          141 AVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGC---IFSASKLFEDTSVDRKNL---VSWTTIISG  214 (352)
Q Consensus       141 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~---~~~~~li~~  214 (352)
                      .+++.+...+++++|++.|+...+.+..  +..++..+..++.++++   +++|.++|++.....|+.   .+|..+..+
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~--~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAGSV--SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSCC--CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhCCC--CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            4555666666666666666666665433  55566666666655443   334666666655443322   245556666


Q ss_pred             HHcCCCHHHHHHHHHHHHh
Q 042593          215 FAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~  233 (352)
                      |.+.|++++|.+.|++.++
T Consensus        82 y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHH
Confidence            6666666666666666665

>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=98.03  E-value=5.6e-06  Score=57.21  Aligned_cols=91  Identities=9%  Similarity=-0.093  Sum_probs=78.1

Q ss_pred             ccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC--CC-chhHHHHHHHHH
Q 042593           25 FTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE--RN-LVTWNVIITGLV  101 (352)
Q Consensus        25 ~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~~i~~~~  101 (352)
                      ...-.....+.+.|++++|...++...+.. +-++.+|..+..++.+.|++++|+..|++..+  |+ ...         
T Consensus        17 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a---------   86 (112)
T d1hxia_          17 ENPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAV---------   86 (112)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH---------
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccccccc---------
Confidence            344456678889999999999999999876 45788999999999999999999999999875  43 333         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHh
Q 042593          102 KWTGIIDGYSRMNRSNEALALFRRM  126 (352)
Q Consensus       102 ~~~~li~~~~~~~~~~~a~~~~~~m  126 (352)
                       |..+..+|...|++++|++.+++.
T Consensus        87 -~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          87 -HAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -hHHHHHHHHHCCCHHHHHHHHHHH
Confidence             888999999999999999999875

>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=98.01  E-value=1.7e-05  Score=55.51  Aligned_cols=101  Identities=9%  Similarity=-0.072  Sum_probs=79.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCC---hhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGE---VRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                      ...+++.+...+++++|.+.|++.....  +.+..++..+..++.+.++   .++|..+++.+.+.+..+....++..+.
T Consensus         2 ~~~l~n~~~~~~~l~~Ae~~Y~~aL~~~--p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg   79 (122)
T d1nzna_           2 MEAVLNELVSVEDLLKFEKKFQSEKAAG--SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLA   79 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHH
Confidence            3567788889999999999999995432  2466788888888887654   4569999999887765441245778899


Q ss_pred             HHHHhhCChHHHHHHHHHhccCCCCH
Q 042593          180 DTYAKCGCIFSASKLFEDTSVDRKNL  205 (352)
Q Consensus       180 ~~~~~~g~~~~a~~~~~~~~~~~~~~  205 (352)
                      .+|.+.|++++|.+.|++..+..|+-
T Consensus        80 ~~y~~~g~~~~A~~~~~~aL~~~P~~  105 (122)
T d1nzna_          80 VGNYRLKEYEKALKYVRGLLQTEPQN  105 (122)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHhhhHHHHHHHHHHHHhCcCC
Confidence            99999999999999999987766753

>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=97.93  E-value=0.00018  Score=53.39  Aligned_cols=106  Identities=11%  Similarity=-0.086  Sum_probs=68.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-------------hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-------------EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-------------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  169 (352)
                      +......+.+.|++++|+..|.+........+.             ..+|+.+..+|.+.|++++|...++...+..+. 
T Consensus        16 l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~-   94 (170)
T d1p5qa1          16 VKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN-   94 (170)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcccc-
Confidence            556667889999999999999988443222121             123445566666777777777777777666433 


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-CHhhHHH
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-NLVSWTT  210 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~  210 (352)
                       ++..+..+..+|...|++++|...|+...+..| |......
T Consensus        95 -~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~  135 (170)
T d1p5qa1          95 -NEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQ  135 (170)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             -chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHH
Confidence             666666777777777777777777776655444 3333333

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.85  E-value=0.0014  Score=53.89  Aligned_cols=146  Identities=11%  Similarity=-0.032  Sum_probs=91.9

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHh
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVK  102 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~  102 (352)
                      |..--..+...|-+.|.++.|..+|..+         .-|..++..+.+.++++.|.+++.+..  +..+          
T Consensus        13 n~~d~~~i~~~c~~~~lye~A~~lY~~~---------~d~~rl~~~~v~l~~~~~avd~~~k~~--~~~~----------   71 (336)
T d1b89a_          13 NNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN--STRT----------   71 (336)
T ss_dssp             ----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHH----------
T ss_pred             CcCCHHHHHHHHHHCCCHHHHHHHHHhC---------CCHHHHHHHHHhhccHHHHHHHHHHcC--CHHH----------
Confidence            7777788888898999999999998744         345667888888999999988887653  3445          


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |..+...+.+..+..-|     .+ ...+...+......++..|-..|..++...+++...... .. +...++-++.+|
T Consensus        72 ~k~~~~~l~~~~e~~la-----~i-~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~-~~~~~~~L~~ly  143 (336)
T d1b89a_          72 WKEVCFACVDGKEFRLA-----QM-CGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RA-HMGMFTELAILY  143 (336)
T ss_dssp             HHHHHHHHHHTTCHHHH-----HH-TTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TC-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcHHHHH-----HH-HHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-cc-chHHHHHHHHHH
Confidence            77777777777666543     22 222234555666788999999999999999998775432 23 777888999999


Q ss_pred             HhhCChHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDT  198 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~  198 (352)
                      ++.+ .++..+.+...
T Consensus       144 ak~~-~~kl~e~l~~~  158 (336)
T d1b89a_         144 SKFK-PQKMREHLELF  158 (336)
T ss_dssp             HTTC-HHHHHHHHHHH
T ss_pred             HHhC-hHHHHHHHHhc
Confidence            8875 34555555544

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.80  E-value=0.0038  Score=51.27  Aligned_cols=186  Identities=13%  Similarity=0.060  Sum_probs=117.1

Q ss_pred             CCchhhHHHHHHHHHhcCChhHHHHHhccCCCCCchhHHHHHHHHHhHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC
Q 042593           56 QSHVYVNTALGDMYVSLGFLKDSSKLFDELPERNLVTWNVIITGLVKWTGIIDGYSRMNRSNEALALFRRMAACEYTEPS  135 (352)
Q Consensus        56 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~i~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~  135 (352)
                      .||..--..+.+.|-+.|.++.|..+|..+..               |..++..+.+.+++..|.+.+.+.       -+
T Consensus        11 ~~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------------~~rl~~~~v~l~~~~~avd~~~k~-------~~   68 (336)
T d1b89a_          11 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------------FGRLASTLVHLGEYQAAVDGARKA-------NS   68 (336)
T ss_dssp             CC----------------CTTTHHHHHHHTTC---------------HHHHHHHHHTTTCHHHHHHHHHHH-------TC
T ss_pred             CCCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------------HHHHHHHHHhhccHHHHHHHHHHc-------CC
Confidence            36666677788888899999999999998864               888889999999999999988777       35


Q ss_pred             hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHH
Q 042593          136 EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISG  214 (352)
Q Consensus       136 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~  214 (352)
                      ..+|..+..++.+......+     .+....... .+.....++..|-..|..++...+++..... .++...++-++..
T Consensus        69 ~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~-~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~l  142 (336)
T d1b89a_          69 TRTWKEVCFACVDGKEFRLA-----QMCGLHIVV-HADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAIL  142 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH-----HHTTTTTTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHH-----HHHHHHhhc-CHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHH
Confidence            56888999999887665443     222333333 5566678999999999999999999986544 6778889999999


Q ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHH
Q 042593          215 FAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVA  288 (352)
Q Consensus       215 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~  288 (352)
                      |++.+ .++..+.++..   +-.     +..+.+.++.    +      ....|.-++-.|.+.|++++|..+.
T Consensus       143 yak~~-~~kl~e~l~~~---s~~-----y~~~k~~~~c----~------~~~l~~elv~Ly~~~~~~~~A~~~~  197 (336)
T d1b89a_         143 YSKFK-PQKMREHLELF---WSR-----VNIPKVLRAA----E------QAHLWAELVFLYDKYEEYDNAIITM  197 (336)
T ss_dssp             HHTTC-HHHHHHHHHHH---STT-----SCHHHHHHHH----H------TTTCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHhC-hHHHHHHHHhc---ccc-----CCHHHHHHHH----H------HcCChHHHHHHHHhcCCHHHHHHHH
Confidence            99875 34444443332   111     1112222111    1      1123455677777777777776554

>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=97.80  E-value=5.9e-05  Score=53.17  Aligned_cols=98  Identities=11%  Similarity=0.118  Sum_probs=79.7

Q ss_pred             cHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC---CCchhHHHHHHHHHh
Q 042593           26 TYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE---RNLVTWNVIITGLVK  102 (352)
Q Consensus        26 ~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~~i~~~~~  102 (352)
                      .+..+...+.+.|++++|+..|+..++.+ +.+...+..+..+|.+.|++++|+..+++..+   .+...+..+-.+   
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~---   81 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKA---   81 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHH---
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHH---
Confidence            35567788999999999999999999986 56788999999999999999999999999765   233333332222   


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMA  127 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~  127 (352)
                      |..+...+...+++++|+..|++..
T Consensus        82 ~~~lg~~~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          82 YARIGNSYFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            7788888899999999999998873

>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=97.79  E-value=0.00044  Score=51.63  Aligned_cols=121  Identities=10%  Similarity=0.084  Sum_probs=84.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      ...........|++++|.+.|.+......-.+-           ......+-+...-..+...     ....+..+..++
T Consensus        14 ~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l-----------~~~~~~~w~~~~r~~l~~~-----~~~a~~~la~~~   77 (179)
T d2ff4a2          14 EKTAGVHAAAAGRFEQASRHLSAALREWRGPVL-----------DDLRDFQFVEPFATALVED-----KVLAHTAKAEAE   77 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTT-----------GGGTTSTTHHHHHHHHHHH-----HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCccccc-----------ccCcchHHHHHHHHHHHHH-----HHHHHHHHHHHH
Confidence            445556778899999999999998443211110           0011111122222222221     456788899999


Q ss_pred             HhhCChHHHHHHHHHhccCCC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHh-----cCCCCC
Q 042593          183 AKCGCIFSASKLFEDTSVDRK-NLVSWTTIISGFAMHGMGKEAVENFERMQK-----VGLKPN  239 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~  239 (352)
                      .+.|++++|...++......| +...|..++.+|.+.|+..+|.+.|++..+     .|+.|.
T Consensus        78 ~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~  140 (179)
T d2ff4a2          78 IACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPG  140 (179)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             HHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcC
Confidence            999999999999999876654 789999999999999999999999999754     455554

>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=97.77  E-value=0.00026  Score=52.45  Aligned_cols=97  Identities=9%  Similarity=-0.101  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCC-------------chhhHHHHHHHHHhhCChHHHHHHHHHhccCCC-
Q 042593          138 TILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAF-------------DIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK-  203 (352)
Q Consensus       138 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-  203 (352)
                      .+....+.+.+.|++++|...|.+..+.-....             ...+|+.+..+|.+.|++++|++.++......| 
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~   94 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN   94 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcccc
Confidence            344556678899999999999998876532210             135677788899999999999999999776655 


Q ss_pred             CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          204 NLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       204 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      ++..|..+..+|...|++++|...|++..+.
T Consensus        95 ~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          95 NEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             chhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999874

>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=97.71  E-value=0.0005  Score=49.84  Aligned_cols=109  Identities=14%  Similarity=0.029  Sum_probs=57.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +..-...+.+.|++.+|+..|.+........++..               +..  .......    . ...+|+.+..+|
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~---------------~~~--~~~~~~~----~-~~~~~~Nla~~~   77 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWD---------------DQI--LLDKKKN----I-EISCNLNLATCY   77 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCC---------------CHH--HHHHHHH----H-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhh---------------hHH--HHHhhhh----H-HHHHHhhHHHHH
Confidence            55566778889999999999998743221111000               000  0000000    0 223444555555


Q ss_pred             HhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          183 AKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+.|++++|++.++...... .++.+|..+..++...|++++|...|++..+
T Consensus        78 ~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          78 NKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            55566666655555544332 2455555555556666666666666655555

>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=97.70  E-value=7.1e-05  Score=52.74  Aligned_cols=90  Identities=9%  Similarity=0.050  Sum_probs=44.6

Q ss_pred             HHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCC---CC-----HhhHHHHHH
Q 042593          142 VLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDR---KN-----LVSWTTIIS  213 (352)
Q Consensus       142 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~---~~-----~~~~~~li~  213 (352)
                      +.+.+.+.|++++|...|.+..+.+..  +...+..+..+|.+.|++++|.+.+++.....   +.     ..+|..+-.
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~p~--~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~   87 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELDPT--NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGN   87 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCcc--cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence            334455555555555555555554322  45555555555555555555555555543221   11     123444445


Q ss_pred             HHHcCCCHHHHHHHHHHHHh
Q 042593          214 GFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       214 ~~~~~~~~~~a~~~~~~m~~  233 (352)
                      .+...+++++|.+.|+....
T Consensus        88 ~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          88 SYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHh
Confidence            55555566666666655443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=6.5e-06  Score=72.95  Aligned_cols=49  Identities=8%  Similarity=-0.219  Sum_probs=22.6

Q ss_pred             hhhHHHHHHHHHHcCChhHHHHHHhcCCCC-CCCchhhHHHHHHHHhccc
Q 042593          265 IKHYGCLIDILERAGRLEQAEEVASGIPSQ-ITNVVVWRTGFLRLLINSY  313 (352)
Q Consensus       265 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~~~~~~~~~li~~~~~~g~  313 (352)
                      ...|+.|...+...|+..+|...|.+.... +|...++..|...+.+..+
T Consensus       186 ~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~~  235 (497)
T d1ya0a1         186 GQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALE  235 (497)
T ss_dssp             SHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhh
Confidence            344455555555555555554444444333 4444444444444444333

>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=97.64  E-value=0.0012  Score=48.57  Aligned_cols=99  Identities=10%  Similarity=-0.125  Sum_probs=65.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-------------hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCC
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-------------EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNA  169 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-------------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  169 (352)
                      +.-....+.+.|++++|...|++........++             ...|+.+..++.+.|++++|...++...+.... 
T Consensus        18 ~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~-   96 (168)
T d1kt1a1          18 VKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA-   96 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcccc-
Confidence            566677888999999999999886332211111             122444556667777777777777777765433 


Q ss_pred             CchhhHHHHHHHHHhhCChHHHHHHHHHhccCCC
Q 042593          170 FDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRK  203 (352)
Q Consensus       170 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  203 (352)
                       +...|..+..+|...|++++|.+.|+......|
T Consensus        97 -~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P  129 (168)
T d1kt1a1          97 -NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP  129 (168)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT
T ss_pred             -hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence             666677777777777777777777777665544

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.63  E-value=0.0075  Score=47.53  Aligned_cols=192  Identities=10%  Similarity=-0.027  Sum_probs=116.4

Q ss_pred             CcccHHHHHHHHHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHh----cCChhHHHHHhccCCCCCchhHHHHHH
Q 042593           23 DSFTYSFLIRTCVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVS----LGFLKDSSKLFDELPERNLVTWNVIIT   98 (352)
Q Consensus        23 ~~~~~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~~i~   98 (352)
                      |+..+..+...+-+.+++++|.+.|+...+.|   +...+-.|...|..    ..+...|...++...+++....     
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a-----   72 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNG-----   72 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH-----
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccch-----
Confidence            34566677778888999999999999998877   45566667777776    5578888888887655433221     


Q ss_pred             HHHhHHHHHHHHH----hcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCC
Q 042593           99 GLVKWTGIIDGYS----RMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAF  170 (352)
Q Consensus        99 ~~~~~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~  170 (352)
                          ...+...+.    ...+.+.|...++.. ...|.   ......+...+..    ......+...+......+    
T Consensus        73 ----~~~l~~~~~~~~~~~~~~~~a~~~~~~a-~~~g~---~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~----  140 (265)
T d1ouva_          73 ----CHLLGNLYYSGQGVSQNTNKALQYYSKA-CDLKY---AEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN----  140 (265)
T ss_dssp             ----HHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHTTC---HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT----
T ss_pred             ----hhccccccccccccchhhHHHHHHHhhh-hhhhh---hhHHHhhcccccCCCcccchhHHHHHHhhhhhccc----
Confidence                223333332    356788898888887 44442   2222233333332    334455555555554433    


Q ss_pred             chhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCCHhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcC
Q 042593          171 DIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKNLVSWTTIISGFAM----HGMGKEAVENFERMQKVG  235 (352)
Q Consensus       171 ~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~  235 (352)
                      +...+..|...|..    ..+...+...++.... ..+......+-..|..    ..+.++|...|++..+.|
T Consensus       141 ~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~-~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g  212 (265)
T d1ouva_         141 DGDGCTILGSLYDAGRGTPKDLKKALASYDKACD-LKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE  212 (265)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT
T ss_pred             ccchhhhhhhhhccCCCcccccccchhhhhcccc-ccccccccchhhhcccCcccccchhhhhhhHhhhhccc
Confidence            55666777777775    3355566666665432 3345554445444443    457777888887776654

>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=97.51  E-value=0.00079  Score=49.63  Aligned_cols=110  Identities=8%  Similarity=0.013  Sum_probs=74.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      +......+...|++++|++.|.+..+.             ...........         ....+.|.....+..+..+|
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~-------------~~~~~~~~~~~---------~~~~~~~~~~~~~~nla~~~   87 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRY-------------VEGSRAAAEDA---------DGAKLQPVALSCVLNIGACK   87 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH-------------HHHHHHHSCHH---------HHGGGHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh-------------hhhhhhhhhhH---------HHHHhChhhHHHHHHHHHHH
Confidence            555667777788888888888776221             00000000000         00111222566777788889


Q ss_pred             HhhCChHHHHHHHHHhccCC-CCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          183 AKCGCIFSASKLFEDTSVDR-KNLVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       183 ~~~g~~~~a~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      .+.|++++|+..++...... .++..|..+..++...|++++|...|++..+.
T Consensus        88 ~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          88 LKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            99999999999998877664 46788888999999999999999999988874

>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=97.49  E-value=0.00032  Score=50.93  Aligned_cols=73  Identities=15%  Similarity=0.038  Sum_probs=56.9

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHH
Q 042593          206 VSWTTIISGFAMHGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAE  285 (352)
Q Consensus       206 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~  285 (352)
                      .+|+.+..+|.+.|++++|++.+++.++..                          +.+..+|..+..++...|++++|.
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~--------------------------p~~~ka~~~~g~~~~~lg~~~~A~  121 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID--------------------------KNNVKALYKLGVANMYFGFLEEAK  121 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--------------------------TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc--------------------------chhhhhhHHhHHHHHHcCCHHHHH
Confidence            467778888999999999999999887632                          236788999999999999999999


Q ss_pred             HHHhcCCCC-CCCchhhHHH
Q 042593          286 EVASGIPSQ-ITNVVVWRTG  304 (352)
Q Consensus       286 ~~~~~m~~~-~~~~~~~~~l  304 (352)
                      ..|+..... |.|..+.+.+
T Consensus       122 ~~~~~al~l~P~n~~~~~~l  141 (153)
T d2fbna1         122 ENLYKAASLNPNNLDIRNSY  141 (153)
T ss_dssp             HHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHH
Confidence            999887765 3344444443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.48  E-value=0.0047  Score=48.81  Aligned_cols=220  Identities=9%  Similarity=-0.076  Sum_probs=130.0

Q ss_pred             chhhHHHHHHHHHhcCChhHHHHHhccCCCC-CchhHHHHHHHHHhHHHHHHHHHh----cCCHHHHHHHHHHhHhccCC
Q 042593           58 HVYVNTALGDMYVSLGFLKDSSKLFDELPER-NLVTWNVIITGLVKWTGIIDGYSR----MNRSNEALALFRRMAACEYT  132 (352)
Q Consensus        58 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~i~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~  132 (352)
                      |+..+..|...+-+.+++++|.+.|++..+. +...          +..|-..|..    ..+...|...+... ...+ 
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~~~A----------~~~Lg~~y~~G~~~~~d~~~a~~~~~~a-~~~~-   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSG----------CFNLGVLYYQGQGVEKNLKKAASFYAKA-CDLN-   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHH----------HHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHTT-
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHH----------HHHHHHHHHcCCCcchhHHHHHHhhccc-cccc-
Confidence            4556677777888889999999999987543 4433          4445555554    56888888888887 4333 


Q ss_pred             CCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh----hCChHHHHHHHHHhccCCCC
Q 042593          133 EPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK----CGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       133 ~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~  204 (352)
                        +......+...+..    ..+.+.|...++...+.|...    ....+...+..    ......+...+.... ...+
T Consensus        69 --~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~----a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~-~~~~  141 (265)
T d1ouva_          69 --YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAE----GCASLGGIYHDGKVVTRDFKKAVEYFTKAC-DLND  141 (265)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHH----HHHHHHHHHHHCSSSCCCHHHHHHHHHHHH-HTTC
T ss_pred             --ccchhhccccccccccccchhhHHHHHHHhhhhhhhhhh----HHHhhcccccCCCcccchhHHHHHHhhhhh-cccc
Confidence              22333333333332    456777888888877776432    22223223332    334555555555442 2445


Q ss_pred             HhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcCCCCCcchhhhHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHH---
Q 042593          205 LVSWTTIISGFAM----HGMGKEAVENFERMQKVGLKPNRSWRIGEEGLKFFDKMVEECEVLPDIKHYGCLIDILER---  277 (352)
Q Consensus       205 ~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~---  277 (352)
                      ...+..|...|..    ..+...+...++...+.|                            +......+...|..   
T Consensus       142 ~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g----------------------------~~~A~~~lg~~y~~g~~  193 (265)
T d1ouva_         142 GDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK----------------------------DSPGCFNAGNMYHHGEG  193 (265)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----------------------------CHHHHHHHHHHHHHTCS
T ss_pred             cchhhhhhhhhccCCCcccccccchhhhhcccccc----------------------------ccccccchhhhcccCcc
Confidence            5666666666654    334555555555554432                            34444445555554   


Q ss_pred             -cCChhHHHHHHhcCCCCCCCchhhHHHHHHHHh----cccccCcccccccch
Q 042593          278 -AGRLEQAEEVASGIPSQITNVVVWRTGFLRLLI----NSYFFSPITLNSQRL  325 (352)
Q Consensus       278 -~g~~~~A~~~~~~m~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~  325 (352)
                       ..+.++|...|+..... .++..+..|...|..    ..+.++|.+.++++.
T Consensus       194 ~~~d~~~A~~~~~~aa~~-g~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa  245 (265)
T d1ouva_         194 ATKNFKEALARYSKACEL-ENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGC  245 (265)
T ss_dssp             SCCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHH
T ss_pred             cccchhhhhhhHhhhhcc-cCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHH
Confidence             55788888888776544 455666666666654    336777777777663

>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=97.48  E-value=0.0011  Score=48.88  Aligned_cols=61  Identities=7%  Similarity=-0.138  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhc
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKR  165 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  165 (352)
                      |+.+..++.+.|++++|+..+++..+..  +-+..+|..+..++.+.|++++|...++...+.
T Consensus        80 ~~nla~~~~~~~~~~~Ai~~~~~al~~~--p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          80 VLNIGACKLKMSDWQGAVDSCLEALEID--PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccchhhhhhhhhhhhh--hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            4445555555555555555555552211  122335555555555555555555555555554

>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=97.38  E-value=0.0019  Score=47.47  Aligned_cols=92  Identities=7%  Similarity=-0.039  Sum_probs=68.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTY  182 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  182 (352)
                      |+.+..+|.+.|++++|+..+++.....  +.+...|..+..++...|++++|...++...+..+.  +..+...+-.+.
T Consensus        67 ~~Nla~~~~~l~~~~~Ai~~~~~al~l~--p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~--n~~~~~~l~~~~  142 (168)
T d1kt1a1          67 FLNLAMCYLKLREYTKAVECCDKALGLD--SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQ--NKAARLQIFMCQ  142 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT--CHHHHHHHHHHH
T ss_pred             HHhHHHHHHHhhhcccchhhhhhhhhcc--cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC--CHHHHHHHHHHH
Confidence            7778889999999999999999985532  245668999999999999999999999999887543  666666665555


Q ss_pred             HhhCChH-HHHHHHHHh
Q 042593          183 AKCGCIF-SASKLFEDT  198 (352)
Q Consensus       183 ~~~g~~~-~a~~~~~~~  198 (352)
                      .+.+... ...++|..|
T Consensus       143 ~~~~~~~e~~kk~~~~~  159 (168)
T d1kt1a1         143 KKAKEHNERDRRTYANM  159 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHH
Confidence            4444332 233444433

>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=97.26  E-value=0.00067  Score=50.59  Aligned_cols=107  Identities=8%  Similarity=-0.039  Sum_probs=74.1

Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcCCCCCcchhh---hHhHHHHHHHHHHhcCCCCChhhHHHHHHHHHHcCChhHHHHHHh
Q 042593          213 SGFAMHGMGKEAVENFERMQKVGLKPNRSWRI---GEEGLKFFDKMVEECEVLPDIKHYGCLIDILERAGRLEQAEEVAS  289 (352)
Q Consensus       213 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~  289 (352)
                      ......|++++|.+.|.+....  .+....-.   ..-+...-..+...     ....+..+..++.+.|++++|...++
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l--~rG~~l~~~~~~~w~~~~r~~l~~~-----~~~a~~~la~~~~~~g~~~~Al~~~~   91 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALRE--WRGPVLDDLRDFQFVEPFATALVED-----KVLAHTAKAEAEIACGRASAVIAELE   91 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTT--CCSSTTGGGTTSTTHHHHHHHHHHH-----HHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhh--CcccccccCcchHHHHHHHHHHHHH-----HHHHHHHHHHHHHHCCCchHHHHHHH
Confidence            4566777777777777776653  11111000   00111111122222     34567788999999999999999999


Q ss_pred             cCCCC-CCCchhhHHHHHHHHhcccccCcccccccchh
Q 042593          290 GIPSQ-ITNVVVWRTGFLRLLINSYFFSPITLNSQRLF  326 (352)
Q Consensus       290 ~m~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  326 (352)
                      .+... +.+...|..++.+|...|+..+|++.+.+...
T Consensus        92 ~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~  129 (179)
T d2ff4a2          92 ALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKT  129 (179)
T ss_dssp             HHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            88777 77889999999999999999999999988653

>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=97.17  E-value=0.00015  Score=57.92  Aligned_cols=53  Identities=6%  Similarity=0.004  Sum_probs=42.8

Q ss_pred             HHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE   87 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~   87 (352)
                      ..+.|++++|+..++..++.. |-|...+..|...++..|++++|.+.|+...+
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456788888888888888776 56778888888888888888888888888765

>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=97.07  E-value=0.00098  Score=53.05  Aligned_cols=122  Identities=7%  Similarity=-0.090  Sum_probs=86.3

Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChH
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIF  189 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  189 (352)
                      ..+.|++++|+..+++..+..  +-|...+..+...++..|++++|...++...+....  +...+..+..++...+..+
T Consensus         6 aL~~G~l~eAl~~l~~al~~~--P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~--~~~~~~~l~~ll~a~~~~~   81 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE--YLPGASQLRHLVKAAQARK   81 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG--GHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--cHHHHHHHHHHHHhccccH
Confidence            456899999999999995532  245678999999999999999999999999987543  5666666665555444444


Q ss_pred             HHHHHHHHhccC-CC-CHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Q 042593          190 SASKLFEDTSVD-RK-NLVSWTTIISGFAMHGMGKEAVENFERMQKVG  235 (352)
Q Consensus       190 ~a~~~~~~~~~~-~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  235 (352)
                      ++..-...-... .| +...+......+...|+.++|.+.+++..+..
T Consensus        82 ~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          82 DFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             HHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            433222211111 23 33445555677889999999999999988753

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.04  E-value=0.00083  Score=48.13  Aligned_cols=73  Identities=4%  Similarity=-0.083  Sum_probs=36.2

Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhC----------CChhhHHHHHHHHHhcCCCCCchhhHHHHH
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKN----------GEVRNCQLIHGYGEKRGFNAFDIHVSNCLI  179 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~----------~~~~~a~~~~~~~~~~~~~~~~~~~~~~li  179 (352)
                      |-+.+.+++|...|+...+..  +-+..++..+..++...          +.+++|...++...+..+.  +..+|..+.
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~--P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~--~~~a~~~lG   82 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK--KDEAVWCIG   82 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC--CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcch--hhHHHhhHH
Confidence            344555666666666663322  12334555555555433          2234455555555554332  455555555


Q ss_pred             HHHHhhC
Q 042593          180 DTYAKCG  186 (352)
Q Consensus       180 ~~~~~~g  186 (352)
                      .+|...|
T Consensus        83 ~~y~~~g   89 (145)
T d1zu2a1          83 NAYTSFA   89 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHcc
Confidence            5555443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.03  E-value=0.0012  Score=57.83  Aligned_cols=107  Identities=4%  Similarity=-0.144  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEYTEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDT  181 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  181 (352)
                      +..+...+.+.|+.++|...+.+...     ++ ..++..+...+...|++++|...|++..+....  +...|+.|...
T Consensus       123 ~~~lg~~~~~~~~~~~A~~~~~~al~-----~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~--~~~~~~~Lg~~  195 (497)
T d1ya0a1         123 SSQLGIISNKQTHTSAIVKPQSSSCS-----YICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPS--NGQPYNQLAIL  195 (497)
T ss_dssp             --------------------CCHHHH-----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--BSHHHHHHHHH
T ss_pred             HHHhHHHHHhCCCHHHHHHHHHHHhC-----CCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC--chHHHHHHHHH
Confidence            44444444455555555544443311     11 124445555555566666666666655555332  55556666666


Q ss_pred             HHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHH
Q 042593          182 YAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFA  216 (352)
Q Consensus       182 ~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~  216 (352)
                      +...|+..+|...|.+.... +|-..++..|...+.
T Consensus       196 ~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         196 ASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence            66666666665555554333 344445555544443

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.02  E-value=0.0015  Score=46.69  Aligned_cols=109  Identities=9%  Similarity=-0.060  Sum_probs=84.5

Q ss_pred             HHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHH----------hhCChHHHHHHHHHhccCCC-CHhhHHHHHHH
Q 042593          146 IWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYA----------KCGCIFSASKLFEDTSVDRK-NLVSWTTIISG  214 (352)
Q Consensus       146 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~----------~~g~~~~a~~~~~~~~~~~~-~~~~~~~li~~  214 (352)
                      |-+.+.+++|...++...+..+.  +..++..+..+|.          ..+.+++|...|++.....| +..+|..+..+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~--~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPL--DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhCCc--chHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHH
Confidence            45667799999999999988654  8888888888876          35679999999999876644 67889888888


Q ss_pred             HHcCC-----------CHHHHHHHHHHHHhcCCCCCcchhh-----hHhHHHHHHHHHHh
Q 042593          215 FAMHG-----------MGKEAVENFERMQKVGLKPNRSWRI-----GEEGLKFFDKMVEE  258 (352)
Q Consensus       215 ~~~~~-----------~~~~a~~~~~~m~~~~~~p~~~~~~-----~~~a~~~~~~m~~~  258 (352)
                      |...|           ++++|.+.|++..+  +.|+...+.     ...+.+++.+..+.
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~~ka~~~~~e~~k~  142 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMTAKAPQLHAEAYKQ  142 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHTHHHHHHHHHHS
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            87654           36888889988887  567777766     66667777776654

>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=96.86  E-value=0.01  Score=42.59  Aligned_cols=61  Identities=13%  Similarity=0.012  Sum_probs=35.2

Q ss_pred             HHHH--HHHHHhcCCHHHHHHHHHHhHhccCCCCC----------hhhHHHHHHHHHhCCChhhHHHHHHHHH
Q 042593          103 WTGI--IDGYSRMNRSNEALALFRRMAACEYTEPS----------EITILAVLPAIWKNGEVRNCQLIHGYGE  163 (352)
Q Consensus       103 ~~~l--i~~~~~~~~~~~a~~~~~~m~~~~~~~p~----------~~t~~~ll~~~~~~~~~~~a~~~~~~~~  163 (352)
                      |..+  ...+.+.|++++|+..|++......-.|+          ...|+.+..++...|++++|...+++..
T Consensus        10 ~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al   82 (156)
T d2hr2a1          10 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL   82 (156)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh
Confidence            5555  44556678889888888887443322233          1245555555555565555555555443

>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=96.70  E-value=0.0043  Score=44.78  Aligned_cols=96  Identities=13%  Similarity=0.055  Sum_probs=72.7

Q ss_pred             hHHHH--HHHHHhCCChhhHHHHHHHHHhcCCCCCc----------hhhHHHHHHHHHhhCChHHHHHHHHHhccC----
Q 042593          138 TILAV--LPAIWKNGEVRNCQLIHGYGEKRGFNAFD----------IHVSNCLIDTYAKCGCIFSASKLFEDTSVD----  201 (352)
Q Consensus       138 t~~~l--l~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----  201 (352)
                      +|..+  ...+.+.|++++|...|++..+.....++          ...|+.+..+|.+.|++++|.+.+++....    
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~   88 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   88 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccccc
Confidence            44444  45566789999999999999864322111          357888999999999999999888875432    


Q ss_pred             ---CCC-----HhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 042593          202 ---RKN-----LVSWTTIISGFAMHGMGKEAVENFERMQK  233 (352)
Q Consensus       202 ---~~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~  233 (352)
                         .++     ...++.+..+|...|++++|...|++..+
T Consensus        89 ~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          89 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence               222     23567788999999999999999999776

>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=96.39  E-value=0.012  Score=38.27  Aligned_cols=28  Identities=18%  Similarity=-0.035  Sum_probs=13.5

Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhcc
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSV  200 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~  200 (352)
                      .+++.+..+|.+.|++++|.+.+++..+
T Consensus        47 ~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          47 SVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            3444445555555555555555544433

>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=96.23  E-value=0.021  Score=36.99  Aligned_cols=74  Identities=5%  Similarity=-0.112  Sum_probs=57.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhHhccC----CCCC-hhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHH
Q 042593          103 WTGIIDGYSRMNRSNEALALFRRMAACEY----TEPS-EITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNC  177 (352)
Q Consensus       103 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~----~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  177 (352)
                      +-.+...+.+.|++++|...|++..+...    ..++ ..++..+..++.+.|++++|...++++.+..+.  +..+++.
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~--~~~a~~N   85 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPE--HQRANGN   85 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT--CHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcC--CHHHHHH
Confidence            45677888999999999999998744321    1223 347889999999999999999999999998654  5666655


Q ss_pred             H
Q 042593          178 L  178 (352)
Q Consensus       178 l  178 (352)
                      +
T Consensus        86 l   86 (95)
T d1tjca_          86 L   86 (95)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=94.17  E-value=0.47  Score=31.88  Aligned_cols=127  Identities=13%  Similarity=0.084  Sum_probs=77.3

Q ss_pred             HHhcCCcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCC-------CCchhHHHHHHHHH-----
Q 042593           34 CVTLSYPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPE-------RNLVTWNVIITGLV-----  101 (352)
Q Consensus        34 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~~~~~~~~~i~~~~-----  101 (352)
                      +.-.|.+++..+++.......   +..-||-.|.-....-+-+-..+.++.+-+       .|..+   ++.+++     
T Consensus        12 ~ildG~ve~Gveii~k~~~ss---~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~---vv~C~~~~n~~   85 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKS---VVECGVINNTL   85 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHH---HHHHHHHTTCC
T ss_pred             HHHhhhHHhHHHHHHHHcccC---CccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHH---HHHHHHHhcch
Confidence            445678888888888777643   344455555555555555555555544432       11110   111111     


Q ss_pred             --hHHHHHHHHHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCC
Q 042593          102 --KWTGIIDGYSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFN  168 (352)
Q Consensus       102 --~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  168 (352)
                        ..+..++...+.|+-+...++++++.+  +-+|++.....+..||.+.|+..++..++.+..+.|+.
T Consensus        86 se~vdlALd~lv~~~kkd~Ld~i~~~l~k--n~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          86 NEHVNKALDILVIQGKRDKLEEIGREILK--NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC----CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence              155666777777777777777777524  23566777777778888888888888888887777764

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=91.94  E-value=1.1  Score=30.02  Aligned_cols=123  Identities=11%  Similarity=0.000  Sum_probs=84.3

Q ss_pred             HHhcCCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhc---------------C--CCCCch
Q 042593          110 YSRMNRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKR---------------G--FNAFDI  172 (352)
Q Consensus       110 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~---------------~--~~~~~~  172 (352)
                      +.-.|..++..+++.+..+..    +..-||-+|.-....-+-+....+++.+-+.               +  ... +.
T Consensus        12 ~ildG~ve~Gveii~k~~~ss----~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n~-~s   86 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSS----TKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNT-LN   86 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS----CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTC-CC
T ss_pred             HHHhhhHHhHHHHHHHHcccC----CccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhcc-hH
Confidence            445677888888888873322    2334444444444444444444444443221               0  011 45


Q ss_pred             hhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHHHHHHHcCCCHHHHHHHHHHHHhcCCC
Q 042593          173 HVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTIISGFAMHGMGKEAVENFERMQKVGLK  237 (352)
Q Consensus       173 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  237 (352)
                      ..++..++.+.++|+-+.-.++.+++.+. .+++...-.+..+|.+-|...++-+++.+.-+.|++
T Consensus        87 e~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          87 EHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            56677888999999999999999885544 789999999999999999999999999999888764

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.95  E-value=0.91  Score=30.41  Aligned_cols=70  Identities=13%  Similarity=-0.072  Sum_probs=34.9

Q ss_pred             CChhhHHHHHHHHHhC---CChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccCCCC
Q 042593          134 PSEITILAVLPAIWKN---GEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVDRKN  204 (352)
Q Consensus       134 p~~~t~~~ll~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  204 (352)
                      |+..|--...-++++.   .+++.+..+++++.+.+... ....+-.|.-+|.+.|++++|.+.++.+.+..|+
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~-~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~  105 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESR-RRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  105 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGG-HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchh-HHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence            3333433333344433   23455666666665543221 1233345555566666666666666666544443

>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=90.83  E-value=1.5  Score=29.49  Aligned_cols=112  Identities=11%  Similarity=0.006  Sum_probs=74.1

Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHhCCChhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHh----hCChH
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWKNGEVRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAK----CGCIF  189 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~  189 (352)
                      .|+++|...|++. ...|   +...+..+.  .....+.++|...++...+.|    ++.....|-..|..    ..+.+
T Consensus         7 kd~~~A~~~~~ka-a~~g---~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g----~~~a~~~Lg~~y~~g~~~~~d~~   76 (133)
T d1klxa_           7 KDLKKAIQYYVKA-CELN---EMFGCLSLV--SNSQINKQKLFQYLSKACELN----SGNGCRFLGDFYENGKYVKKDLR   76 (133)
T ss_dssp             HHHHHHHHHHHHH-HHTT---CTTHHHHHH--TCTTSCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHCSSSCCCHH
T ss_pred             cCHHHHHHHHHHH-HHCC---Chhhhhhhc--cccccCHHHHHHHHhhhhccc----chhhhhhHHHhhhhccccchhhH
Confidence            3678999999998 5444   222233332  234567889999999888876    44445555555654    45789


Q ss_pred             HHHHHHHHhccCCCCHhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcCC
Q 042593          190 SASKLFEDTSVDRKNLVSWTTIISGFAM----HGMGKEAVENFERMQKVGL  236 (352)
Q Consensus       190 ~a~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~  236 (352)
                      +|.+.|+...+. -++.....|-..|..    ..+.++|...|++..+.|.
T Consensus        77 ~A~~~~~~aa~~-g~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          77 KAAQYYSKACGL-NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhhhcc-CcchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            999999987543 344445555555544    4588899999998887764

>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=89.93  E-value=0.97  Score=28.65  Aligned_cols=59  Identities=5%  Similarity=-0.041  Sum_probs=35.7

Q ss_pred             hhhHHHHHHHHHhcCCCCCchhhHHHHHHHHHhhCChHHHHHHHHHhccC-CCCHhhHHHH
Q 042593          152 VRNCQLIHGYGEKRGFNAFDIHVSNCLIDTYAKCGCIFSASKLFEDTSVD-RKNLVSWTTI  211 (352)
Q Consensus       152 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~l  211 (352)
                      .-++.+-+..+......| ++.+..+.+++|.+.+++.-|.++|+.++.+ .++-..|.-+
T Consensus        22 ~we~rrgmN~l~~~DlVP-eP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yi   81 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVP-EPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYV   81 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHH
T ss_pred             HHHHHHHHHHHhccccCC-CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            334555555566666666 7777777777777777777777777766433 2333344443

>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=89.47  E-value=1.1  Score=30.36  Aligned_cols=109  Identities=8%  Similarity=-0.108  Sum_probs=53.1

Q ss_pred             CcchHHHHHHHHHHhCCCCchhhHHHHHHHHHhcCChhHHHHHhccCCCC-CchhHHHHHHHHHhHHHHHHHHHh----c
Q 042593           39 YPNLGTQLHAVFSKVGFQSHVYVNTALGDMYVSLGFLKDSSKLFDELPER-NLVTWNVIITGLVKWTGIIDGYSR----M  113 (352)
Q Consensus        39 ~~~~a~~~~~~m~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~~i~~~~~~~~li~~~~~----~  113 (352)
                      |+++|.+.|+...+.|.   +..+..|.  .....+.++|.+.+++.-+. ++..          +..|-..|..    .
T Consensus         8 d~~~A~~~~~kaa~~g~---~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~~~a----------~~~Lg~~y~~g~~~~   72 (133)
T d1klxa_           8 DLKKAIQYYVKACELNE---MFGCLSLV--SNSQINKQKLFQYLSKACELNSGNG----------CRFLGDFYENGKYVK   72 (133)
T ss_dssp             HHHHHHHHHHHHHHTTC---TTHHHHHH--TCTTSCHHHHHHHHHHHHHTTCHHH----------HHHHHHHHHHCSSSC
T ss_pred             CHHHHHHHHHHHHHCCC---hhhhhhhc--cccccCHHHHHHHHhhhhcccchhh----------hhhHHHhhhhccccc
Confidence            56677778877777662   22222222  12334566666666654432 2222          2223333322    3


Q ss_pred             CCHHHHHHHHHHhHhccCCCCChhhHHHHHHHHHh----CCChhhHHHHHHHHHhcC
Q 042593          114 NRSNEALALFRRMAACEYTEPSEITILAVLPAIWK----NGEVRNCQLIHGYGEKRG  166 (352)
Q Consensus       114 ~~~~~a~~~~~~m~~~~~~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~  166 (352)
                      .+.++|.+.|++. ...|   +......|-..|..    ..+.++|..+++...+.|
T Consensus        73 ~d~~~A~~~~~~a-a~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          73 KDLRKAAQYYSKA-CGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             CCHHHHHHHHHHH-HHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHhhh-hccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            4566666666666 3333   22233333333333    245556666666655554

>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=83.59  E-value=4.1  Score=27.07  Aligned_cols=64  Identities=11%  Similarity=-0.069  Sum_probs=48.0

Q ss_pred             chhhHHHHHHHHHhhC---ChHHHHHHHHHhccCCC-C-HhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 042593          171 DIHVSNCLIDTYAKCG---CIFSASKLFEDTSVDRK-N-LVSWTTIISGFAMHGMGKEAVENFERMQKV  234 (352)
Q Consensus       171 ~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~-~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  234 (352)
                      +..+--...-+++++.   +.+++..+|+++.+..| + ...+.-|..+|.+.|++++|...++.+++.
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            5555555666677664   45689999998865555 3 256667778899999999999999999984