Citrus Sinensis ID: 042756

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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-------360-------370-------380-------390-------400-------410-------420-----
Protein Sequence
MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT
Secondary Structure (PSIPRED)
ccccccccccccHHHHccccccccHHHHHHHHHHHHHHcHHHHHHHHHHccccHHHHHHHHHHHccccccEEEHHHHHHHHccccccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccEEEHHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccHHHHHHHHHHHHcccccccEEHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccHccccccEEHcHHHHHHHHHHHHHHHHHHHcccccccEEHHHHHHcccccHHHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccEEEEHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHHHHHHHHHHHccccccEEEEHHHccHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccEEEEHHHHHHHHcccccHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
misslhmripppwnsrccrlrQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALShllspdtthprlsslafPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFckhdskrgfdDTYARLNQLVNSSSSVYVKRQALKSMISGlcemgqpheaENLIEEMRVkglepsgfeyKCIIYGYGRLGLLEDMERIVNQMesdgtrvdtVCSNMVlssygdhneLSRMVLWLQKmkdsgipfsvRTYNSVLNSCSTIMSMLQdlnsndfplSILELTEVLNEEEVSVVKEledssvldeamkwdsgetkldlhgmHLGSAYFIILQWMDEMRNRFnnekhvipaeitvvcgsgkhstvrgESSVKAMVKKMMVRT
Flexible Loop (DISEMBL)
misslhmripppwnsrccrLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVkeledssvldeAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEItvvcgsgkhstvrgessvkaMVKKMMVRT
Low Complexity Region (SEG)
MISSLHMRIPPPWNSrccrlrqqrltlvqcltARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSIleltevlneeevsvvkeledssvlDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT
Disordered region (IsUnstruct)
***********PWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY**************************************LIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGS***********************
Disordered Region (DISOPRED)
************WNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVR*
Disordered Region (DISEMBL)
MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCG***********SVKAMVKKMMVRT
Disordered Region (DISPRO)
MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKM****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT
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	425	2.2.26 [Sep-21-2011]
Q8GWA9	505	Pentatricopeptide repeat-	yes	no	0.915	0.770	0.602	1e-134
Q9LKU8	766	Pentatricopeptide repeat-	no	no	0.352	0.195	0.259	9e-12
Q9FMQ1	816	Pentatricopeptide repeat-	no	no	0.458	0.238	0.251	1e-11
Q9M316	766	Pentatricopeptide repeat-	no	no	0.272	0.151	0.290	1e-11
Q9LR67	660	Pentatricopeptide repeat-	no	no	0.454	0.292	0.247	2e-11
Q0WVK7	741	Pentatricopeptide repeat-	no	no	0.442	0.253	0.274	4e-11
Q9FKC3	508	Pentatricopeptide repeat-	no	no	0.501	0.419	0.231	6e-11
Q9SCP4	447	Pentatricopeptide repeat-	no	no	0.477	0.454	0.236	1e-10
Q9T0D6	566	Pentatricopeptide repeat-	no	no	0.451	0.339	0.253	2e-09
Q9FMF6	730	Pentatricopeptide repeat-	no	no	0.357	0.208	0.267	2e-09

>sp|Q8GWA9|PP157_ARATH Pentatricopeptide repeat-containing protein At2g17033 OS=Arabidopsis thaliana GN=At2g17033 PE=2 SV=1

 Score =  478 bits (1229), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 236/392 (60%), Positives = 298/392 (76%), Gaps = 3/392 (0%)

Query: 35  LTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL 93
           L K G RFLSSL+  A+  D  A +R I KFVA+SP+ +ALN LSHLLS  T+HP LS  
Sbjct: 89  LMKHGDRFLSSLSSPALAGDPSAINRHIKKFVAASPKSVALNVLSHLLSDQTSHPHLSFF 148

Query: 94  AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
           A  LY  ITE SWF WNPKL+AE+IA L+KQ + +E+ETL+   +S+L S ER+  LF C
Sbjct: 149 ALSLYSEITEASWFDWNPKLIAELIALLNKQERFDESETLLSTAVSRLKSNERDFTLFLC 208

Query: 154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
           NL++S  K  S +GF +   RL +++  SSSVYVK QA KSM+SGLC M QPH+AE +IE
Sbjct: 209 NLVESNSKQGSIQGFSEASFRLREIIQRSSSVYVKTQAYKSMVSGLCNMDQPHDAERVIE 268

Query: 214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN 273
           EMR++ ++P  FEYK ++YGYGRLGL +DM R+V++M ++G ++DTVCSNMVLSSYG H+
Sbjct: 269 EMRMEKIKPGLFEYKSVLYGYGRLGLFDDMNRVVHRMGTEGHKIDTVCSNMVLSSYGAHD 328

Query: 274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEE 333
            L +M  WLQK+K   +PFS+RTYNSVLNSC TI+SML+DL+S   P+S+ EL   LNE+
Sbjct: 329 ALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIISMLKDLDS--CPVSLSELRTFLNED 386

Query: 334 EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIP 393
           E  +V EL  SSVLDEA++W++ E KLDLHGMHL S+Y I+LQWMDE R RF+ EK VIP
Sbjct: 387 EALLVHELTQSSVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQWMDETRLRFSEEKCVIP 446

Query: 394 AEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           AEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct: 447 AEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 478

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LKU8|PP401_ARATH Pentatricopeptide repeat-containing protein At5g28460 OS=Arabidopsis thaliana GN=At5g28460 PE=2 SV=1

 Score = 72.0 bits (175), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 82/158 (51%), Gaps = 8/158 (5%)

Query: 155 LIDSFCKHDSKRGFDDTYARLNQL----VNSSSSVYVKRQALKSMISGLCEMGQPHEAEN 210
           LI++ CK    R  D+      Q+     +  + +        ++I GLC++G+  EAE 
Sbjct: 335 LINTLCK---SRRVDEALEVFEQMRGKRTDDGNVIKADSIHFNTLIDGLCKVGRLKEAEE 391

Query: 211 LIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY 269
           L+  M+++    P+   Y C+I GY R G LE  + +V++M+ D  + + V  N ++   
Sbjct: 392 LLVRMKLEERCVPNAVTYNCLIDGYCRAGKLETAKEVVSRMKEDEIKPNVVTVNTIVGGM 451

Query: 270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI 307
             H+ L+  V++   M+  G+  +V TY +++++C ++
Sbjct: 452 CRHHGLNMAVVFFMDMEKEGVKGNVVTYMTLIHACCSV 489

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMQ1|PP376_ARATH Pentatricopeptide repeat-containing protein At5g12100, mitochondrial OS=Arabidopsis thaliana GN=At5g12100 PE=2 SV=1

 Score = 71.6 bits (174), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/203 (25%), Positives = 97/203 (47%), Gaps = 8/203 (3%)

Query: 104 ESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHD 163
           +S  + N    + ++  L K+G+ E+AE ++   ++K G    E++  Y  +ID +C+  
Sbjct: 347 DSGVKMNAYTCSILLNALCKEGKIEKAEEILGREMAK-GLVPNEVI--YNTMIDGYCRKG 403

Query: 164 SKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS 223
              G     AR+         +     A   +I   CE+G+   AE  + +M++KG+ PS
Sbjct: 404 DLVG-----ARMKIEAMEKQGMKPDHLAYNCLIRRFCELGEMENAEKEVNKMKLKGVSPS 458

Query: 224 GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQ 283
              Y  +I GYGR    +    I+ +ME +GT  + V    +++     ++L    +  +
Sbjct: 459 VETYNILIGGYGRKYEFDKCFDILKEMEDNGTMPNVVSYGTLINCLCKGSKLLEAQIVKR 518

Query: 284 KMKDSGIPFSVRTYNSVLNSCST 306
            M+D G+   VR YN +++ C +
Sbjct: 519 DMEDRGVSPKVRIYNMLIDGCCS 541

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M316|PP292_ARATH Pentatricopeptide repeat-containing protein At3g61520, mitochondrial OS=Arabidopsis thaliana GN=At3g61520 PE=2 SV=1

 Score = 71.2 bits (173), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 68/117 (58%), Gaps = 1/117 (0%)

Query: 192 LKSMISGLCEMGQPHEAENLIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQM 250
             ++I GLC++G+  EAE L+  M+++    P+   Y C+I GY R G LE  + +V++M
Sbjct: 373 FNTLIDGLCKVGRLKEAEELLVRMKLEERCAPNAVTYNCLIDGYCRAGKLETAKEVVSRM 432

Query: 251 ESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI 307
           + D  + + V  N ++     H+ L+  V++   M+  G+  +V TY +++++C ++
Sbjct: 433 KEDEIKPNVVTVNTIVGGMCRHHGLNMAVVFFMDMEKEGVKGNVVTYMTLIHACCSV 489

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LR67|PPR9_ARATH Pentatricopeptide repeat-containing protein At1g03560, mitochondrial OS=Arabidopsis thaliana GN=At1g03560 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/202 (24%), Positives = 97/202 (48%), Gaps = 9/202 (4%)

Query: 103 EESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH 162
           +E   Q  P   + +I  L K+G+  E  T + E + + GS+    V  Y  LID + K 
Sbjct: 319 DEKGIQVPPHAFSLVIGGLCKEGKLNEGYT-VFENMIRKGSKPN--VAIYTVLIDGYAKS 375

Query: 163 DSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP 222
            S    +D    L+++++      V   ++  +++GLC+ G+  EA +     R  GL  
Sbjct: 376 GS---VEDAIRLLHRMIDEGFKPDVVTYSV--VVNGLCKNGRVEEALDYFHTCRFDGLAI 430

Query: 223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWL 282
           +   Y  +I G G+ G +++ ER+  +M   G   D+ C N ++ ++  H ++   +   
Sbjct: 431 NSMFYSSLIDGLGKAGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHRKVDEAIALF 490

Query: 283 QKM-KDSGIPFSVRTYNSVLNS 303
           ++M ++ G   +V TY  +L+ 
Sbjct: 491 KRMEEEEGCDQTVYTYTILLSG 512

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WVK7|PPR12_ARATH Pentatricopeptide repeat-containing protein At1g05670, mitochondrial OS=Arabidopsis thaliana GN=At1g05670 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 93/197 (47%), Gaps = 9/197 (4%)

Query: 117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN 176
           II+   + G   EA  L  E   K    E + V F   LI+ +CK    +   D +   N
Sbjct: 392 IISGFCQIGDMVEAGKLFHEMFCK--GLEPDSVTF-TELINGYCKAGHMK---DAFRVHN 445

Query: 177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR 236
            ++ +  S  V      ++I GLC+ G    A  L+ EM   GL+P+ F Y  I+ G  +
Sbjct: 446 HMIQAGCSPNV--VTYTTLIDGLCKEGDLDSANELLHEMWKIGLQPNIFTYNSIVNGLCK 503

Query: 237 LGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT 296
            G +E+  ++V + E+ G   DTV    ++ +Y    E+ +    L++M   G+  ++ T
Sbjct: 504 SGNIEEAVKLVGEFEAAGLNADTVTYTTLMDAYCKSGEMDKAQEILKEMLGKGLQPTIVT 563

Query: 297 YNSVLNSCSTIMSMLQD 313
           +N ++N    +  ML+D
Sbjct: 564 FNVLMNG-FCLHGMLED 579

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKC3|PP424_ARATH Pentatricopeptide repeat-containing protein At5g48730, chloroplastic OS=Arabidopsis thaliana GN=At5g48730 PE=2 SV=2

 Score = 69.3 bits (168), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 52/225 (23%), Positives = 109/225 (48%), Gaps = 12/225 (5%)

Query: 84  DTTHPRLSSL----AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLS 139
           ++ H R+++L    A  ++  + E+ W++ N  +  ++I  L K  Q E+A  L  E ++
Sbjct: 119 ESLHERITALRWESAIQVFELLREQLWYKPNVGIYVKLIVMLGKCKQPEKAHELFQEMIN 178

Query: 140 KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGL 199
           +      E+   Y  L+ ++ +      FD  +  L ++  SS +          +I   
Sbjct: 179 EGCVVNHEV---YTALVSAYSRSGR---FDAAFTLLERM-KSSHNCQPDVHTYSILIKSF 231

Query: 200 CEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQM-ESDGTRVD 258
            ++    + ++L+ +MR +G+ P+   Y  +I  YG+  +  +ME  + QM   D  + D
Sbjct: 232 LQVFAFDKVQDLLSDMRRQGIRPNTITYNTLIDAYGKAKMFVEMESTLIQMLGEDDCKPD 291

Query: 259 TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS 303
           +   N  L ++G + ++  M    +K + SGI  ++RT+N +L+S
Sbjct: 292 SWTMNSTLRAFGGNGQIEMMENCYEKFQSSGIEPNIRTFNILLDS 336

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SCP4|PP279_ARATH Pentatricopeptide repeat-containing protein At3g53170 OS=Arabidopsis thaliana GN=At3g53170 PE=2 SV=1

 Score = 68.6 bits (166), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/211 (23%), Positives = 101/211 (47%), Gaps = 8/211 (3%)

Query: 94  AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
           A  ++  + ++ W++   K   ++   L    Q ++A +L+ E +  L    +  +  Y 
Sbjct: 77  ALKIFNLLRKQHWYEPRCKTYTKLFKVLGNCKQPDQA-SLLFEVM--LSEGLKPTIDVYT 133

Query: 154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
           +LI  + K +     D  ++ L + + S S           +IS  C++G+    ++++ 
Sbjct: 134 SLISVYGKSEL---LDKAFSTL-EYMKSVSDCKPDVFTFTVLISCCCKLGRFDLVKSIVL 189

Query: 214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCS-NMVLSSYGDH 272
           EM   G+  S   Y  II GYG+ G+ E+ME ++  M  DG  +  VC+ N ++ SYG+ 
Sbjct: 190 EMSYLGVGCSTVTYNTIIDGYGKAGMFEEMESVLADMIEDGDSLPDVCTLNSIIGSYGNG 249

Query: 273 NELSRMVLWLQKMKDSGIPFSVRTYNSVLNS 303
             + +M  W  + +  G+   + T+N ++ S
Sbjct: 250 RNMRKMESWYSRFQLMGVQPDITTFNILILS 280

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T0D6|PP306_ARATH Pentatricopeptide repeat-containing protein At4g11690 OS=Arabidopsis thaliana GN=At4g11690 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 53/209 (25%), Positives = 103/209 (49%), Gaps = 17/209 (8%)

Query: 94  AFPLYMRITEESWFQWNPKLV--AEIIAFLDKQGQREEAETLILETLSKLG--SRERELV 149
           +F L + +TE   F ++P +V    +I    K+G+ E+A+ L  E + KLG  + ER   
Sbjct: 182 SFDLLIELTE---FGFSPNVVIYTTLIDGCCKKGEIEKAKDLFFE-MGKLGLVANERT-- 235

Query: 150 LFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAE 209
             Y  LI+   K+  K+   + Y ++ +       V+        +++ LC+ G+  +A 
Sbjct: 236 --YTVLINGLFKNGVKKQGFEMYEKMQE-----DGVFPNLYTYNCVMNQLCKDGRTKDAF 288

Query: 210 NLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY 269
            + +EMR +G+  +   Y  +I G  R   L +  ++V+QM+SDG   + +  N ++  +
Sbjct: 289 QVFDEMRERGVSCNIVTYNTLIGGLCREMKLNEANKVVDQMKSDGINPNLITYNTLIDGF 348

Query: 270 GDHNELSRMVLWLQKMKDSGIPFSVRTYN 298
               +L + +   + +K  G+  S+ TYN
Sbjct: 349 CGVGKLGKALSLCRDLKSRGLSPSLVTYN 377

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMF6|PP444_ARATH Pentatricopeptide repeat-containing protein At5g64320, mitochondrial OS=Arabidopsis thaliana GN=At5g64320 PE=2 SV=1

 Score = 63.9 bits (154), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/157 (26%), Positives = 81/157 (51%), Gaps = 5/157 (3%)

Query: 147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH 206
           E+V+F   LI  F  H      DD  A L+ +V +S  +        S+I G  + G   
Sbjct: 352 EIVIFN-TLIHGFVTHGR---LDDAKAVLSDMV-TSYGIVPDVCTYNSLIYGYWKEGLVG 406

Query: 207 EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL 266
            A  ++ +MR KG +P+ + Y  ++ G+ +LG +++   ++N+M +DG + +TV  N ++
Sbjct: 407 LALEVLHDMRNKGCKPNVYSYTILVDGFCKLGKIDEAYNVLNEMSADGLKPNTVGFNCLI 466

Query: 267 SSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS 303
           S++   + +   V   ++M   G    V T+NS+++ 
Sbjct: 467 SAFCKEHRIPEAVEIFREMPRKGCKPDVYTFNSLISG 503

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	425
225428119	435	PREDICTED: pentatricopeptide repeat-cont	0.962	0.940	0.630	1e-146
255560449	460	pentatricopeptide repeat-containing prot	0.941	0.869	0.612	1e-141
224103135	473	predicted protein [Populus trichocarpa]	0.929	0.835	0.621	1e-137
18398289	504	pentatricopeptide repeat-containing prot	0.915	0.771	0.602	1e-132
110738240	501	hypothetical protein [Arabidopsis thalia	0.915	0.776	0.602	1e-132
30679852	505	pentatricopeptide repeat-containing prot	0.915	0.770	0.602	1e-132
297832300	504	pentatricopeptide repeat-containing prot	0.955	0.805	0.572	1e-131
51477396	488	pentatricopeptide (PPR) repeat protein-l	0.931	0.811	0.577	1e-125
449482319	1296	PREDICTED: uncharacterized protein LOC10	0.927	0.304	0.571	1e-123
449447735	1913	PREDICTED: uncharacterized protein LOC10	0.931	0.207	0.572	1e-122

>gi|225428119|ref|XP_002278390.1| PREDICTED: pentatricopeptide repeat-containing protein At2g17033 [Vitis vinifera] gi|297744557|emb|CBI37819.3| unnamed protein product [Vitis vinifera]

 Score =  526 bits (1354), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 268/425 (63%), Positives = 325/425 (76%), Gaps = 16/425 (3%)

Query: 1   MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRL 60
           M+++L +  P PWN R          L+QC    L+KQGQ FLSS+A    RD  A++RL
Sbjct: 1   MLANLQVSRPQPWNHRSP-------LLIQC---ALSKQGQLFLSSVA----RDPSASNRL 46

Query: 61  ISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAF 120
           I KF+ASS + IALNALSHLLSP TTHP LSSLA PLY RI+E SWF WNPKL+A++IA 
Sbjct: 47  ICKFIASSSKSIALNALSHLLSPTTTHPYLSSLALPLYSRISEASWFSWNPKLIADVIAL 106

Query: 121 LDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVN 180
           L KQGQ +EAETL+ ETL KLGSRER+LV FYCNLIDS  KH S +G  D  +RL+++V+
Sbjct: 107 LYKQGQLKEAETLVSETLIKLGSRERDLVSFYCNLIDSHSKHSSNQGVFDVISRLSRIVS 166

Query: 181 SSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLL 240
            SSSVYVK +A KSMIS LC +G P EAENLIEEMRVKGL+PS FE++ ++YGYGR+GL 
Sbjct: 167 ESSSVYVKERAYKSMISSLCAVGLPLEAENLIEEMRVKGLKPSVFEFRSVVYGYGRVGLS 226

Query: 241 EDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV 300
           EDM+RI+ QM ++G  +DTV SNMVLSSYG +N+ S MV WLQ+MK+S IPFS+RTYNSV
Sbjct: 227 EDMQRILLQMGNEGFELDTVVSNMVLSSYGAYNKQSEMVSWLQRMKNSSIPFSIRTYNSV 286

Query: 301 LNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKL 360
           LNSC  IMS+LQDL +  FP +I EL E L  +E  +VKEL  S VL E M+WD  E KL
Sbjct: 287 LNSCPMIMSILQDLKT--FPPTIDELMETLKGDEALLVKELIGSMVLAELMEWDCSEGKL 344

Query: 361 DLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKK 420
           DLHGMHLGSAY I+LQW +E+R R N  ++V+P EITVVCGSGKHS+VRGES VK MV++
Sbjct: 345 DLHGMHLGSAYLIMLQWREELRYRLNAAEYVMPVEITVVCGSGKHSSVRGESPVKRMVRE 404

Query: 421 MMVRT 425
           MM RT
Sbjct: 405 MMTRT 409

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255560449|ref|XP_002521239.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223539507|gb|EEF41095.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  508 bits (1308), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 256/418 (61%), Positives = 317/418 (75%), Gaps = 18/418 (4%)

Query: 9   IPPPWNSRCCRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTR-DSKAASRLISKFVAS 67
           +P  W  RC               A L+KQGQRFLSSLA+A T+ D+ A +RLI KFVA+
Sbjct: 34  LPMKWVFRC---------------AALSKQGQRFLSSLAIATTKGDTVATNRLIKKFVAA 78

Query: 68  SPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQR 127
           SP+ IAL+ALSHLL+P ++H  LSSLAF LY++I E  WFQWNPKLVA+++AFLDKQG+ 
Sbjct: 79  SPKSIALDALSHLLNPHSSHSHLSSLAFTLYLKIAEARWFQWNPKLVADVVAFLDKQGRY 138

Query: 128 EEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV 187
           +E+ TL+ +++SKL  +ER+L  FYCNL++S  K +S RGFD++ A L QLV +S+SVYV
Sbjct: 139 DESATLVSDSISKLQVKERDLARFYCNLVESQSKQNSIRGFDNSVASLMQLVCNSNSVYV 198

Query: 188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIV 247
           KRQ  KSM++GLCEMG+P EAE LIEEM  +G+ PS FE+KC++Y YG LG  E+M + +
Sbjct: 199 KRQGYKSMVNGLCEMGRPREAETLIEEMGKEGVRPSMFEFKCVVYAYGSLGSFEEMNKCL 258

Query: 248 NQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI 307
           +QME  G RVDTVCSNM+L+SYG HN L  MVLWLQKMKD GIPFS+RT NS LNSC TI
Sbjct: 259 HQMERAGFRVDTVCSNMILASYGAHNALPEMVLWLQKMKDLGIPFSLRTCNSALNSCPTI 318

Query: 308 MSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHL 367
           MSM+Q  NSNDFP+SI +L ++L+E+E  +VKE+  SSVLDEAMKWD  E KLDLHG HL
Sbjct: 319 MSMMQ--NSNDFPISIHDLMKILSEDEALLVKEIVTSSVLDEAMKWDVAEAKLDLHGTHL 376

Query: 368 GSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
            SAY IIL W++EMR RF +  +V P EITVVCGSG HS VRGES VK MVK  MVR 
Sbjct: 377 CSAYLIILLWIEEMRKRFKSVNYVNPTEITVVCGSGNHSIVRGESPVKCMVKDFMVRA 434

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103135|ref|XP_002312938.1| predicted protein [Populus trichocarpa] gi|222849346|gb|EEE86893.1| predicted protein [Populus trichocarpa]

 Score =  495 bits (1274), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 248/399 (62%), Positives = 319/399 (79%), Gaps = 4/399 (1%)

Query: 29  QCLTARLTKQGQRFLSS-LALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH 87
           +CL A ++KQ QRF S+ L    T D+ A +RLI KFVASSP+ IAL+ALS+LLSPD+TH
Sbjct: 51  KCLAA-ISKQAQRFFSAVLPTVATSDTSATNRLIKKFVASSPKSIALDALSNLLSPDSTH 109

Query: 88  -PRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRER 146
            P L  L  PLY++I+E SWF WNPKLVA+++  LDKQG  +E + L+ ET+S+L  +ER
Sbjct: 110 HPLLYLLTLPLYLKISEASWFSWNPKLVAQVVVLLDKQGLDKELKALMSETVSRLQFKER 169

Query: 147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH 206
           ELVLFYCNLI    KH+  RGFDD+Y+RLNQ V+ S+SVYVK+Q  K+MISGLCEMG+  
Sbjct: 170 ELVLFYCNLIGFNSKHNWVRGFDDSYSRLNQFVSDSNSVYVKKQGYKAMISGLCEMGRAR 229

Query: 207 EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL 266
           EAE+LI EMR +GL+P  FE++C++YGYGRLGL +DMERI+++MES    VDTVC+NMVL
Sbjct: 230 EAEDLIGEMRERGLKPKLFEFRCVLYGYGRLGLFKDMERILDKMESGEIEVDTVCANMVL 289

Query: 267 SSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILEL 326
           +SYG HN L  M LWL+KMK  GIP S+RT NSVLNSC TIM+++++L+++ +P+SI EL
Sbjct: 290 ASYGAHNALPEMGLWLRKMKTLGIPLSIRTCNSVLNSCPTIMALMRNLDAS-YPVSIQEL 348

Query: 327 TEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFN 386
            ++L+EEE  +VKEL +SSVL EA KWD+ E KLDLHGMHLGSAY I+LQWM+E RNR +
Sbjct: 349 LKILSEEEAMLVKELIESSVLKEATKWDTSEGKLDLHGMHLGSAYVIMLQWMEETRNRLS 408

Query: 387 NEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           + +HVIPAEITVVCGSG HSTVRGES VK+M+ ++M +T
Sbjct: 409 DGEHVIPAEITVVCGSGNHSTVRGESPVKSMITQIMAQT 447

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18398289|ref|NP_565402.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|13877877|gb|AAK44016.1|AF370201_1 unknown protein [Arabidopsis thaliana] gi|21280879|gb|AAM44931.1| unknown protein [Arabidopsis thaliana] gi|330251481|gb|AEC06575.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  478 bits (1230), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 236/392 (60%), Positives = 298/392 (76%), Gaps = 3/392 (0%)

Query: 35  LTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL 93
           L K G RFLSSL+  A+  D  A +R I KFVA+SP+ +ALN LSHLLS  T+HP LS  
Sbjct: 88  LMKHGDRFLSSLSSPALAGDPSAINRHIKKFVAASPKSVALNVLSHLLSDQTSHPHLSFF 147

Query: 94  AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
           A  LY  ITE SWF WNPKL+AE+IA L+KQ + +E+ETL+   +S+L S ER+  LF C
Sbjct: 148 ALSLYSEITEASWFDWNPKLIAELIALLNKQERFDESETLLSTAVSRLKSNERDFTLFLC 207

Query: 154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
           NL++S  K  S +GF +   RL +++  SSSVYVK QA KSM+SGLC M QPH+AE +IE
Sbjct: 208 NLVESNSKQGSIQGFSEASFRLREIIQRSSSVYVKTQAYKSMVSGLCNMDQPHDAERVIE 267

Query: 214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN 273
           EMR++ ++P  FEYK ++YGYGRLGL +DM R+V++M ++G ++DTVCSNMVLSSYG H+
Sbjct: 268 EMRMEKIKPGLFEYKSVLYGYGRLGLFDDMNRVVHRMGTEGHKIDTVCSNMVLSSYGAHD 327

Query: 274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEE 333
            L +M  WLQK+K   +PFS+RTYNSVLNSC TI+SML+DL+S   P+S+ EL   LNE+
Sbjct: 328 ALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIISMLKDLDS--CPVSLSELRTFLNED 385

Query: 334 EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIP 393
           E  +V EL  SSVLDEA++W++ E KLDLHGMHL S+Y I+LQWMDE R RF+ EK VIP
Sbjct: 386 EALLVHELTQSSVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQWMDETRLRFSEEKCVIP 445

Query: 394 AEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           AEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct: 446 AEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 477

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110738240|dbj|BAF01049.1| hypothetical protein [Arabidopsis thaliana]

 Score =  478 bits (1230), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 236/392 (60%), Positives = 298/392 (76%), Gaps = 3/392 (0%)

Query: 35  LTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL 93
           L K G RFLSSL+  A+  D  A +R I KFVA+SP+ +ALN LSHLLS  T+HP LS  
Sbjct: 85  LMKHGDRFLSSLSSPALAGDPSAINRHIKKFVAASPKSVALNVLSHLLSDQTSHPHLSFF 144

Query: 94  AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
           A  LY  ITE SWF WNPKL+AE+IA L+KQ + +E+ETL+   +S+L S ER+  LF C
Sbjct: 145 ALSLYSEITEASWFDWNPKLIAELIALLNKQERFDESETLLSTAVSRLKSNERDFTLFLC 204

Query: 154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
           NL++S  K  S +GF +   RL +++  SSSVYVK QA KSM+SGLC M QPH+AE +IE
Sbjct: 205 NLVESNSKQGSIQGFSEASFRLREIIQRSSSVYVKTQAYKSMVSGLCNMDQPHDAERVIE 264

Query: 214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN 273
           EMR++ ++P  FEYK ++YGYGRLGL +DM R+V++M ++G ++DTVCSNMVLSSYG H+
Sbjct: 265 EMRMEKIKPGLFEYKSVLYGYGRLGLFDDMNRVVHRMGTEGHKIDTVCSNMVLSSYGAHD 324

Query: 274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEE 333
            L +M  WLQK+K   +PFS+RTYNSVLNSC TI+SML+DL+S   P+S+ EL   LNE+
Sbjct: 325 ALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIISMLKDLDS--CPVSLSELRTFLNED 382

Query: 334 EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIP 393
           E  +V EL  SSVLDEA++W++ E KLDLHGMHL S+Y I+LQWMDE R RF+ EK VIP
Sbjct: 383 EALLVHELTQSSVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQWMDETRLRFSEEKCVIP 442

Query: 394 AEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           AEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct: 443 AEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 474

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30679852|ref|NP_849962.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75244359|sp|Q8GWA9.1|PP157_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At2g17033 gi|26452937|dbj|BAC43545.1| unknown protein [Arabidopsis thaliana] gi|330251482|gb|AEC06576.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  478 bits (1229), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 236/392 (60%), Positives = 298/392 (76%), Gaps = 3/392 (0%)

Query: 35  LTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL 93
           L K G RFLSSL+  A+  D  A +R I KFVA+SP+ +ALN LSHLLS  T+HP LS  
Sbjct: 89  LMKHGDRFLSSLSSPALAGDPSAINRHIKKFVAASPKSVALNVLSHLLSDQTSHPHLSFF 148

Query: 94  AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
           A  LY  ITE SWF WNPKL+AE+IA L+KQ + +E+ETL+   +S+L S ER+  LF C
Sbjct: 149 ALSLYSEITEASWFDWNPKLIAELIALLNKQERFDESETLLSTAVSRLKSNERDFTLFLC 208

Query: 154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
           NL++S  K  S +GF +   RL +++  SSSVYVK QA KSM+SGLC M QPH+AE +IE
Sbjct: 209 NLVESNSKQGSIQGFSEASFRLREIIQRSSSVYVKTQAYKSMVSGLCNMDQPHDAERVIE 268

Query: 214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN 273
           EMR++ ++P  FEYK ++YGYGRLGL +DM R+V++M ++G ++DTVCSNMVLSSYG H+
Sbjct: 269 EMRMEKIKPGLFEYKSVLYGYGRLGLFDDMNRVVHRMGTEGHKIDTVCSNMVLSSYGAHD 328

Query: 274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEE 333
            L +M  WLQK+K   +PFS+RTYNSVLNSC TI+SML+DL+S   P+S+ EL   LNE+
Sbjct: 329 ALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIISMLKDLDS--CPVSLSELRTFLNED 386

Query: 334 EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIP 393
           E  +V EL  SSVLDEA++W++ E KLDLHGMHL S+Y I+LQWMDE R RF+ EK VIP
Sbjct: 387 EALLVHELTQSSVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQWMDETRLRFSEEKCVIP 446

Query: 394 AEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           AEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct: 447 AEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 478

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297832300|ref|XP_002884032.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297329872|gb|EFH60291.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  475 bits (1222), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 234/409 (57%), Positives = 303/409 (74%), Gaps = 3/409 (0%)

Query: 18  CRLRQQRLTLVQCLTARLTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNA 76
           C  R + +   +     L KQG RFLSSL+  A+  D  A  R I KFVA+SP+ + LN 
Sbjct: 71  CTYRTKLVVRCKAGVVPLMKQGDRFLSSLSSPALAGDPSATHRHIKKFVAASPKSVTLNV 130

Query: 77  LSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILE 136
           LSHLLS  T++P LS  A  LY  ITE SWF WNPKL+AE++A L+ Q + +E+ETL+  
Sbjct: 131 LSHLLSDQTSYPHLSFFALSLYSEITEASWFDWNPKLIAELVAVLNNQERFDESETLLST 190

Query: 137 TLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI 196
            +S+L S ER+  LF CNL++S  K  S +GF++   RL + +  SSSVYVK QA KSM+
Sbjct: 191 AVSRLKSNERDFALFLCNLVESNSKQGSIQGFNEACFRLRERIQRSSSVYVKTQAYKSMV 250

Query: 197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR 256
           +GLC M QPH+AE +IEEMRV+ ++P  FE+K ++YGYGRLGL +DM R+V++ME++G +
Sbjct: 251 AGLCNMDQPHDAERVIEEMRVEKIKPGSFEHKSVLYGYGRLGLFDDMNRVVHRMETEGHK 310

Query: 257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNS 316
           +DTVCSNMVLSSYG H+ L +M  WLQK+K   +PFS+RTYNSVLNSC TIMS+L+DLNS
Sbjct: 311 IDTVCSNMVLSSYGAHDALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIMSLLKDLNS 370

Query: 317 NDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQ 376
              P+S+ EL   LNE+E  +V EL  S+VLDEA++W++ E KLDLHGMHL S+Y I+LQ
Sbjct: 371 --CPVSLSELRTFLNEDEALLVLELTQSTVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQ 428

Query: 377 WMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           WMDE+R RF ++K VIPAEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct: 429 WMDEIRLRFRDQKCVIPAEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 477

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51477396|gb|AAU04769.1| pentatricopeptide (PPR) repeat protein-like [Cucumis melo]

 Score =  456 bits (1173), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 232/402 (57%), Positives = 299/402 (74%), Gaps = 6/402 (1%)

Query: 28  VQCLTARLTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT 86
           V+C T  LTKQ  RFLS+L+    T D  A +RLI KFVASSP+ I L+ LS+++S  T 
Sbjct: 40  VKCTT--LTKQTHRFLSTLSTTGATGDQSATNRLIRKFVASSPKSITLSVLSNIVSTHTP 97

Query: 87  HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRER 146
            P L S A  LY RITE SWF WN KLVA+++AFL + G   E+E LI E +SKLGS+ER
Sbjct: 98  QPELCSAALTLYSRITEASWFTWNSKLVADLVAFLGQNGLYSESEALISEAISKLGSQER 157

Query: 147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH 206
           +LV FY  L++S  KH  +RGF D+Y+RL +L+ +S SVYVKR+A +SM++GLC M +PH
Sbjct: 158 KLVNFYSQLVESQSKHGFERGFGDSYSRLFELLYNSPSVYVKRRAYESMVTGLCSMKRPH 217

Query: 207 EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL 266
           EAE+L++EMR KG+ P+ +EY+ IIY YG LGL E+M+R + QME+D   +DTVCSNMVL
Sbjct: 218 EAESLVKEMRSKGITPTAYEYRSIIYAYGTLGLFEEMKRSLKQMENDNIELDTVCSNMVL 277

Query: 267 SSYGDHNELSRMVLWLQKMKDSG-IPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILE 325
           SSYG HN+L  M+LWLQ+MK S     SVRTYNSVLNSC  I SMLQD  S D P+ I +
Sbjct: 278 SSYGAHNKLGDMLLWLQRMKTSSHCKSSVRTYNSVLNSCPKITSMLQDHKSGDLPVLIED 337

Query: 326 LTEVLN-EEEVSVVKE-LEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN 383
           L  +L+ +EE  +VKE L  SSVL+E M WD+ E KLDLHG H+G+AY I+LQW+ EMR 
Sbjct: 338 LIAILDGDEEALLVKELLVGSSVLNEIMVWDAMELKLDLHGAHVGAAYVIMLQWIKEMRL 397

Query: 384 RFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
            F +E +VIPA++T++CGSGKHS VRGES VKA++K++MVRT
Sbjct: 398 NFEDESNVIPAQVTLICGSGKHSIVRGESPVKALIKEIMVRT 439

Source: Cucumis melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449482319|ref|XP_004156246.1| PREDICTED: uncharacterized protein LOC101223617 [Cucumis sativus]

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 231/404 (57%), Positives = 299/404 (74%), Gaps = 10/404 (2%)

Query: 28  VQCLTARLTKQGQRFLSSLA-LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT 86
           V+C +  LTKQ  RFLS+L+  A T D  A +RLI KFVASSP+ I L+ LS+++S  T 
Sbjct: 40  VKCTS--LTKQTHRFLSTLSTTAATGDQSATNRLIRKFVASSPKSITLSVLSNIVSTHTP 97

Query: 87  HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRER 146
            P L S A  LY RITE SWF WN KLVA+++AFLD+ G   E+E LI E +SKLGS+ER
Sbjct: 98  QPELCSAALTLYSRITEASWFTWNSKLVADLVAFLDQNGLYSESEVLISEAISKLGSQER 157

Query: 147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH 206
           +LV FY  L++S  KH  +RGF D+Y+RL +L+ +S SVYVKR+A +SM++GLC M +PH
Sbjct: 158 KLVNFYSQLVESQSKHGFERGFVDSYSRLLELLYNSPSVYVKRRAYESMVTGLCSMKRPH 217

Query: 207 EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL 266
           EAENL++EMR KG+ P+ +EY+ IIY YG LGL E+M+R + QME+D   +DTVCSNMVL
Sbjct: 218 EAENLVKEMRSKGITPTAYEYRSIIYAYGTLGLFEEMKRSLKQMENDNIELDTVCSNMVL 277

Query: 267 SSYGDHNELSRMVLWLQKMKDSGIPF---SVRTYNSVLNSCSTIMSMLQDLNSNDFPLSI 323
           SSYG HN+L  MVLWLQ+MK S  P    SVRTYNSVLNSC  I +MLQD  S + P+ I
Sbjct: 278 SSYGAHNKLGDMVLWLQRMKTS--PHCNSSVRTYNSVLNSCPKITAMLQDHKSTNLPVLI 335

Query: 324 LELTEVLNEE--EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEM 381
            +L  VL+ +   + V + L  SSVL+E M WD+ E KLDLHG H+G+AY I+LQW+ EM
Sbjct: 336 EDLIAVLDGDEEALLVEELLAGSSVLNEIMVWDAMELKLDLHGAHVGAAYVIMLQWIKEM 395

Query: 382 RNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
           R  F +E +VIPA++T++CGSGKHS VRGES VKA++K++MVRT
Sbjct: 396 RLNFEDESYVIPAQVTLICGSGKHSIVRGESPVKALIKEIMVRT 439

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447735|ref|XP_004141623.1| PREDICTED: uncharacterized protein LOC101204365 [Cucumis sativus]

 Score =  445 bits (1145), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 230/402 (57%), Positives = 298/402 (74%), Gaps = 6/402 (1%)

Query: 28  VQCLTARLTKQGQRFLSSLAL-AVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT 86
           V+C +  LTKQ  RFLS+L+  A T D  A +RLI KFVASSP+ I L+ LS+++S  T 
Sbjct: 40  VKCTS--LTKQTHRFLSTLSTTAATGDQSATNRLIRKFVASSPKSITLSVLSNIVSTHTP 97

Query: 87  HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRER 146
            P L S A  LY RITE SWF WN KLVA+++AFLD+ G   E+E LI E +SKLGS+ER
Sbjct: 98  QPELCSAALTLYSRITEASWFTWNSKLVADLVAFLDQNGLYSESEVLISEAISKLGSQER 157

Query: 147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH 206
           +LV FY  L++S  KH  +RGF D+Y+RL +L+ +S SVYVKR+A +SM++GLC M +PH
Sbjct: 158 KLVNFYSQLVESQSKHGFERGFVDSYSRLLELLYNSPSVYVKRRAYESMVTGLCSMKRPH 217

Query: 207 EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL 266
           EAENL++EMR KG+ P+ +EY+ IIY YG LGL E+M+R + QME+D   +DTVCSNMVL
Sbjct: 218 EAENLVKEMRSKGITPTAYEYRSIIYAYGTLGLFEEMKRSLKQMENDNIELDTVCSNMVL 277

Query: 267 SSYGDHNELSRMVLWLQKMKDSG-IPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILE 325
           SSYG HN+L  MVLWLQ+MK S     SVRTYNSVLNSC  I +MLQD  S + P+ I +
Sbjct: 278 SSYGAHNKLGDMVLWLQRMKTSPHCNSSVRTYNSVLNSCPKITAMLQDHKSTNLPVLIED 337

Query: 326 LTEVLNEE--EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN 383
           L  VL+ +   + V + L  SSVL+E M WD+ E KLDLHG H+G+AY I+LQW+ EMR 
Sbjct: 338 LIAVLDGDEEALLVEELLAGSSVLNEIMVWDAMELKLDLHGAHVGAAYVIMLQWIKEMRL 397

Query: 384 RFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
            F +E +VIPA++T++CGSGKHS VRGES VKA++K++MVRT
Sbjct: 398 NFEDESYVIPAQVTLICGSGKHSIVRGESPVKALIKEIMVRT 439

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	425
TAIR|locus:505006249	505	AT2G17033 [Arabidopsis thalian	0.915	0.770	0.568	1e-114
TAIR|locus:2020808	660	AT1G03560 [Arabidopsis thalian	0.463	0.298	0.251	1.1e-11
TAIR|locus:2177028	816	AT5G12100 [Arabidopsis thalian	0.454	0.236	0.258	5.3e-11
TAIR|locus:2146549	727	AT5G28370 [Arabidopsis thalian	0.36	0.210	0.267	9.7e-11
TAIR|locus:2146554	766	AT5G28460 [Arabidopsis thalian	0.36	0.199	0.267	1e-10
TAIR|locus:2082832	766	AT3G61520 "AT3G61520" [Arabido	0.36	0.199	0.260	1.4e-10
TAIR|locus:2061310	918	GUN1 "AT2G31400" [Arabidopsis	0.425	0.197	0.243	1.6e-10
TAIR|locus:2081041	486	PPR2 "pentatricopeptide repeat	0.515	0.450	0.226	1.8e-09
TAIR|locus:2139732	566	AT4G11690 [Arabidopsis thalian	0.463	0.348	0.254	2.4e-09
TAIR|locus:2060226	624	AT2G32630 "AT2G32630" [Arabido	0.402	0.274	0.281	2.8e-08

TAIR|locus:505006249 AT2G17033 [Arabidopsis thaliana (taxid:3702)]

 Score = 1131 (403.2 bits), Expect = 1.0e-114, P = 1.0e-114
 Identities = 223/392 (56%), Positives = 283/392 (72%)

Query:    35 LTKQGQRFLSSLAL-AVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL 93
             L K G RFLSSL+  A+  D  A +R I KFVA+SP+ +ALN LSHLLS  T+HP LS  
Sbjct:    89 LMKHGDRFLSSLSSPALAGDPSAINRHIKKFVAASPKSVALNVLSHLLSDQTSHPHLSFF 148

Query:    94 AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYC 153
             A  LY  ITE SWF WNPKL+AE+IA L+KQ + +E+ETL+   +S+L S ER+  LF C
Sbjct:   149 ALSLYSEITEASWFDWNPKLIAELIALLNKQERFDESETLLSTAVSRLKSNERDFTLFLC 208

Query:   154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE 213
             NL++S  K  S +GF +   RL +++  SSSVYVK QA KSM+SGLC M QPH+AE +IE
Sbjct:   209 NLVESNSKQGSIQGFSEASFRLREIIQRSSSVYVKTQAYKSMVSGLCNMDQPHDAERVIE 268

Query:   214 EMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN 273
             EMR++ ++P  FEYK ++YGYGRLGL +DM R+V++M ++G ++DTVCSNMVLSSYG H+
Sbjct:   269 EMRMEKIKPGLFEYKSVLYGYGRLGLFDDMNRVVHRMGTEGHKIDTVCSNMVLSSYGAHD 328

Query:   274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSIXXXXXXXXXX 333
              L +M  WLQK+K   +PFS+RTYNSVLNSC TI+SML+DL+S   P+S+          
Sbjct:   329 ALPQMGSWLQKLKGFNVPFSIRTYNSVLNSCPTIISMLKDLDS--CPVSLSELRTFLNED 386

Query:   334 XXXXXXXXXXXXXXDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIP 393
                           DEA++W++ E KLDLHGMHL S+Y I+LQWMDE R RF+ EK VIP
Sbjct:   387 EALLVHELTQSSVLDEAIEWNAVEGKLDLHGMHLSSSYLILLQWMDETRLRFSEEKCVIP 446

Query:   394 AEITVVCGSGKHSTVRGESSVKAMVKKMMVRT 425
             AEI VV GSGKHS VRGES VKA+VKK+MVRT
Sbjct:   447 AEIVVVSGSGKHSNVRGESPVKALVKKIMVRT 478

GO:0005739 "mitochondrion" evidence=ISM

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

TAIR|locus:2020808 AT1G03560 [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 52/207 (25%), Positives = 100/207 (48%)

Query:    97 LYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLI 156
             LY  + E+   Q  P   + +I  L K+G+  E  T + E + + GS+    V  Y  LI
Sbjct:   314 LYQEMDEKG-IQVPPHAFSLVIGGLCKEGKLNEGYT-VFENMIRKGSKPN--VAIYTVLI 369

Query:   157 DSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMR 216
             D + K  S    +D    L+++++      V   ++  +++GLC+ G+  EA +     R
Sbjct:   370 DGYAKSGS---VEDAIRLLHRMIDEGFKPDVVTYSV--VVNGLCKNGRVEEALDYFHTCR 424

Query:   217 VKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELS 276
               GL  +   Y  +I G G+ G +++ ER+  +M   G   D+ C N ++ ++  H ++ 
Sbjct:   425 FDGLAINSMFYSSLIDGLGKAGRVDEAERLFEEMSEKGCTRDSYCYNALIDAFTKHRKVD 484

Query:   277 RMVLWLQKMKDS-GIPFSVRTYNSVLN 302
               +   ++M++  G   +V TY  +L+
Sbjct:   485 EAIALFKRMEEEEGCDQTVYTYTILLS 511

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2177028 AT5G12100 [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 5.3e-11, P = 5.3e-11
 Identities = 52/201 (25%), Positives = 98/201 (48%)

Query:   104 ESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHD 163
             +S  + N    + ++  L K+G+ E+AE ++   ++K G    E++  Y  +ID +C+  
Sbjct:   347 DSGVKMNAYTCSILLNALCKEGKIEKAEEILGREMAK-GLVPNEVI--YNTMIDGYCR-- 401

Query:   164 SKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS 223
               +G D   AR+         +     A   +I   CE+G+   AE  + +M++KG+ PS
Sbjct:   402 --KG-DLVGARMKIEAMEKQGMKPDHLAYNCLIRRFCELGEMENAEKEVNKMKLKGVSPS 458

Query:   224 GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQ 283
                Y  +I GYGR    +    I+ +ME +GT  + V    +++     ++L    +  +
Sbjct:   459 VETYNILIGGYGRKYEFDKCFDILKEMEDNGTMPNVVSYGTLINCLCKGSKLLEAQIVKR 518

Query:   284 KMKDSGIPFSVRTYNSVLNSC 304
              M+D G+   VR YN +++ C
Sbjct:   519 DMEDRGVSPKVRIYNMLIDGC 539

GO:0005739 "mitochondrion" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IDA

TAIR|locus:2146549 AT5G28370 [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 9.7e-11, P = 9.7e-11
 Identities = 43/161 (26%), Positives = 88/161 (54%)

Query:   155 LIDSFCKHDSKRGFDDTYARLNQL--VNSSSSVYVKRQAL--KSMISGLCEMGQPHEAEN 210
             LI++ CK  S+R  D+      Q+    +     +K  ++   ++I GLC++G+  EAE 
Sbjct:   335 LINTLCK--SRR-VDEALEVFEQMRGKRTDDGNVIKADSIHFNTLIDGLCKVGRLKEAEE 391

Query:   211 LIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY 269
             L+  M+++    P+   Y C+I GY R G LE  + +V++M+ D  + + V  N ++   
Sbjct:   392 LLVRMKLEERCVPNAVTYNCLIDGYCRAGKLETAKEVVSRMKEDEIKPNVVTVNTIVGGM 451

Query:   270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSM 310
               H+ L+  V++   M+  G+  +V TY +++++C ++ ++
Sbjct:   452 CRHHGLNMAVVFFMDMEKEGVKGNVVTYMTLIHACCSVSNV 492

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2146554 AT5G28460 [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 1.0e-10, P = 1.0e-10
 Identities = 43/161 (26%), Positives = 88/161 (54%)

Query:   155 LIDSFCKHDSKRGFDDTYARLNQL--VNSSSSVYVKRQAL--KSMISGLCEMGQPHEAEN 210
             LI++ CK  S+R  D+      Q+    +     +K  ++   ++I GLC++G+  EAE 
Sbjct:   335 LINTLCK--SRR-VDEALEVFEQMRGKRTDDGNVIKADSIHFNTLIDGLCKVGRLKEAEE 391

Query:   211 LIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY 269
             L+  M+++    P+   Y C+I GY R G LE  + +V++M+ D  + + V  N ++   
Sbjct:   392 LLVRMKLEERCVPNAVTYNCLIDGYCRAGKLETAKEVVSRMKEDEIKPNVVTVNTIVGGM 451

Query:   270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSM 310
               H+ L+  V++   M+  G+  +V TY +++++C ++ ++
Sbjct:   452 CRHHGLNMAVVFFMDMEKEGVKGNVVTYMTLIHACCSVSNV 492

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2082832 AT3G61520 "AT3G61520" [Arabidopsis thaliana (taxid:3702)]

 Score = 180 (68.4 bits), Expect = 1.4e-10, P = 1.4e-10
 Identities = 42/161 (26%), Positives = 90/161 (55%)

Query:   155 LIDSFCKHDSKRGFD--DTYARLNQLVNSSSSVYVKRQAL--KSMISGLCEMGQPHEAEN 210
             LI++ CK  S+R  +  + + ++        +V +K  ++   ++I GLC++G+  EAE 
Sbjct:   335 LINTLCK--SRRVDEALEVFEKMRGKRTDDGNV-IKADSIHFNTLIDGLCKVGRLKEAEE 391

Query:   211 LIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY 269
             L+  M+++    P+   Y C+I GY R G LE  + +V++M+ D  + + V  N ++   
Sbjct:   392 LLVRMKLEERCAPNAVTYNCLIDGYCRAGKLETAKEVVSRMKEDEIKPNVVTVNTIVGGM 451

Query:   270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSM 310
               H+ L+  V++   M+  G+  +V TY +++++C ++ ++
Sbjct:   452 CRHHGLNMAVVFFMDMEKEGVKGNVVTYMTLIHACCSVSNV 492

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 133 (51.9 bits), Expect = 1.6e-10, Sum P(2) = 1.6e-10
 Identities = 46/189 (24%), Positives = 83/189 (43%)

Query:   117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN 176
             ++A   + G  E A  L  E  ++   R  + V  Y  L+D+ CK       D  +  L 
Sbjct:   345 LLAVCSRGGLWEAARNLFDEMTNR---RIEQDVFSYNTLLDAICKGGQ---MDLAFEILA 398

Query:   177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR 236
             Q+      +     +  ++I G  + G+  EA NL  EMR  G+      Y  ++  Y +
Sbjct:   399 QM--PVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYLGIALDRVSYNTLLSIYTK 456

Query:   237 LGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT 296
             +G  E+   I+ +M S G + D V  N +L  YG   +   +     +MK   +  ++ T
Sbjct:   457 VGRSEEALDILREMASVGIKKDVVTYNALLGGYGKQGKYDEVKKVFTEMKREHVLPNLLT 516

Query:   297 YNSVLNSCS 305
             Y+++++  S
Sbjct:   517 YSTLIDGYS 525

GO:0003677 "DNA binding" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

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

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

TAIR|locus:2081041 PPR2 "pentatricopeptide repeat 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 53/234 (22%), Positives = 111/234 (47%)

Query:    74 LNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETL 133
             +N ++  LS D    +    A  ++  + E++++Q       +++  L K GQ   A+ L
Sbjct:    88 VNTVTETLS-DLIAKKQWLQALEVFDMLREQTFYQPKEGTYMKLLVLLGKSGQPNRAQKL 146

Query:   134 ILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVN---SSSSVYVKRQ 190
               E L + G      V  Y  L+ ++ + +     DD ++ L+++ +       V+    
Sbjct:   147 FDEMLEE-GLEPT--VELYTALLAAYTRSNL---IDDAFSILDKMKSFPQCQPDVFTYST 200

Query:   191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQM 250
              LK+ +    +  Q    ++L +EM  + + P+      ++ GYGR+G  + ME++++ M
Sbjct:   201 LLKACV----DASQFDLVDSLYKEMDERLITPNTVTQNIVLSGYGRVGRFDQMEKVLSDM 256

Query:   251 -ESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS 303
               S   + D    N++LS +G+  ++  M  W +K ++ GI    RT+N ++ S
Sbjct:   257 LVSTACKPDVWTMNIILSVFGNMGKIDMMESWYEKFRNFGIEPETRTFNILIGS 310

GO:0005739 "mitochondrion" evidence=ISM

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

GO:0048868 "pollen tube development" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

GO:0009553 "embryo sac development" evidence=IMP

GO:0009555 "pollen development" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0019843 "rRNA binding" evidence=IDA

TAIR|locus:2139732 AT4G11690 [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 2.4e-09, P = 2.4e-09
 Identities = 54/212 (25%), Positives = 106/212 (50%)

Query:    94 AFPLYMRITEESWFQWNPKLV--AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLF 151
             +F L + +TE   F ++P +V    +I    K+G+ E+A+ L  E + KLG    E    
Sbjct:   182 SFDLLIELTE---FGFSPNVVIYTTLIDGCCKKGEIEKAKDLFFE-MGKLGLVANERT-- 235

Query:   152 YCNLIDSFCKHD-SKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAEN 210
             Y  LI+   K+   K+GF+  Y ++ +       V+        +++ LC+ G+  +A  
Sbjct:   236 YTVLINGLFKNGVKKQGFE-MYEKMQE-----DGVFPNLYTYNCVMNQLCKDGRTKDAFQ 289

Query:   211 LIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG 270
             + +EMR +G+  +   Y  +I G  R   L +  ++V+QM+SDG   + +  N ++  + 
Sbjct:   290 VFDEMRERGVSCNIVTYNTLIGGLCREMKLNEANKVVDQMKSDGINPNLITYNTLIDGFC 349

Query:   271 DHNELSRMVLWLQKMKDSGIPFSVRTYNSVLN 302
                +L + +   + +K  G+  S+ TYN +++
Sbjct:   350 GVGKLGKALSLCRDLKSRGLSPSLVTYNILVS 381

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 158 (60.7 bits), Expect = 2.8e-08, P = 2.8e-08
 Identities = 51/181 (28%), Positives = 88/181 (48%)

Query:   123 KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFC-KHDSKRGFDDTYARLNQLVNS 181
             K G+  +AE L  E + + G  E + V  Y +LI   C K + KR F   +  L +   S
Sbjct:   306 KNGKMSDAEKLFDE-MRERGI-ESD-VHVYTSLISWNCRKGNMKRAFL-LFDELTEKGLS 361

Query:   182 SSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLE 241
              SS Y       ++I G+C++G+   AE L+ EM+ KG+  +   +  +I GY R G+++
Sbjct:   362 PSS-YT----YGALIDGVCKVGEMGAAEILMNEMQSKGVNITQVVFNTLIDGYCRKGMVD 416

Query:   242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVL 301
             +   I + ME  G + D    N + S +           WL +M + G+  S  +Y +++
Sbjct:   417 EASMIYDVMEQKGFQADVFTCNTIASCFNRLKRYDEAKQWLFRMMEGGVKLSTVSYTNLI 476

Query:   302 N 302
             +
Sbjct:   477 D 477

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8GWA9	PP157_ARATH	No assigned EC number	0.6020	0.9152	0.7702	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.IX.1053.1 hypothetical protein (418 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	425
smart00463	80	smart00463, SMR, Small MutS-related domain	1e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	4e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.003

>gnl|CDD|214676 smart00463, SMR, Small MutS-related domain

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 360 LDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVK 419
           LDLHG+ +  A   + ++++  R +   +K      + ++ G GKHS + G+S VK  +K
Sbjct: 4   LDLHGLTVEEALTALDKFLNNARLKGLEQK------LVIITGKGKHS-LGGKSGVKPALK 56

Query: 420 KMM 422
           + +
Sbjct: 57  EHL 59

Length = 80

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

 Score = 43.9 bits (105), Expect = 2e-06
 Identities = 14/43 (32%), Positives = 26/43 (60%)

Query: 194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR 236
           ++I G C+ G+  EA  L  EM+ +G++P+ + Y  +I G  +
Sbjct: 8   TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 13/30 (43%), Positives = 21/30 (70%)

Query: 194 SMISGLCEMGQPHEAENLIEEMRVKGLEPS 223
           ++I GLC+ G+  EA  L +EM+ +G+EP 
Sbjct: 5   TLIDGLCKAGRVEEALELFKEMKERGIEPD 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|144943 pfam01535, PPR, PPR repeat

 Score = 37.4 bits (88), Expect = 4e-04
 Identities = 13/27 (48%), Positives = 19/27 (70%)

Query: 194 SMISGLCEMGQPHEAENLIEEMRVKGL 220
           S+ISG C+ G+  EA  L +EM+ KG+
Sbjct: 5   SLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 36.2 bits (85), Expect = 0.001
 Identities = 11/47 (23%), Positives = 22/47 (46%)

Query: 258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC 304
           D V  N ++  Y    ++   +    +MK  GI  +V TY+ +++  
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 34.7 bits (81), Expect = 0.003
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 227 YKCIIYGYGRLGLLEDMERIVNQMESDGTRVDT 259
           Y  +I G  + G +E+   +  +M+  G   D 
Sbjct: 3   YNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	425
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; 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
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.8
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.76
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.74
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.72
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.58
PF13041	50	PPR_2: PPR repeat family	99.55
PF13041	50	PPR_2: PPR repeat family	99.53
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.44
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.4
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.37
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.33
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.3
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.29
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.25
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.21
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.2
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.12
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.11
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.1
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.06
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.04
PF12854	34	PPR_1: PPR repeat	99.03
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.99
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.97
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.96
PF12854	34	PPR_1: PPR repeat	98.95
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.93
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.93
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.92
KOG1126	638	consensus DNA-binding cell division cycle control	98.88
PRK14574	822	hmsH outer membrane protein; Provisional	98.87
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.87
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.85
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.85
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.84
PRK12370	553	invasion protein regulator; Provisional	98.82
PRK14574	822	hmsH outer membrane protein; Provisional	98.8
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.78
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.77
PRK12370	553	invasion protein regulator; Provisional	98.75
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.73
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.72
KOG1126	638	consensus DNA-binding cell division cycle control	98.7
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.68
KOG2076	895	consensus RNA polymerase III transcription factor	98.6
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.56
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.49
KOG1129	478	consensus TPR repeat-containing protein [General f	98.48
KOG2003	840	consensus TPR repeat-containing protein [General f	98.46
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.45
KOG2003	840	consensus TPR repeat-containing protein [General f	98.45
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.45
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.45
PRK11189	296	lipoprotein NlpI; Provisional	98.44
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.39
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.39
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.34
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.32
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.25
PRK11189	296	lipoprotein NlpI; Provisional	98.25
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.25
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.24
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.22
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.2
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.19
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.16
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.08
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.08
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.02
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.99
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.99
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.95
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.92
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.9
KOG2076	895	consensus RNA polymerase III transcription factor	97.89
KOG1129	478	consensus TPR repeat-containing protein [General f	97.88
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.88
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.88
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.87
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.86
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.84
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.83
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.8
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.78
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.78
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.68
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.66
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.61
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.6
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.59
PRK15359	144	type III secretion system chaperone protein SscB;	97.59
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.56
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.55
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.53
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.51
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.5
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.48
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.46
PLN02789	320	farnesyltranstransferase	97.45
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.44
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.39
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.35
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.35
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.35
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.33
PRK04841	903	transcriptional regulator MalT; Provisional	97.29
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.25
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.24
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.24
PRK15359	144	type III secretion system chaperone protein SscB;	97.21
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.2
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.2
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.19
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.18
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.14
PRK04841	903	transcriptional regulator MalT; Provisional	97.14
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.13
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.11
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.11
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.08
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.04
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.03
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.92
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.91
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.89
PRK14720	906	transcript cleavage factor/unknown domain fusion p	96.85
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.84
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.82
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.81
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.79
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.74
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.7
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.69
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.67
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.66
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.63
KOG2047	835	consensus mRNA splicing factor [RNA processing and	96.53
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.49
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.48
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.44
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.42
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.4
KOG3941	406	consensus Intermediate in Toll signal transduction	96.37
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.29
KOG1125	579	consensus TPR repeat-containing protein [General f	96.29
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	96.25
PLN02789	320	farnesyltranstransferase	96.23
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.21
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.18
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.17
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.12
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.06
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.03
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.97
PF12688	120	TPR_5: Tetratrico peptide repeat	95.96
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.89
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.89
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.87
KOG3941	406	consensus Intermediate in Toll signal transduction	95.84
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.84
KOG1125	579	consensus TPR repeat-containing protein [General f	95.68
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	95.65
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	95.64
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.57
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.54
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	95.5
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.49
PRK10803	263	tol-pal system protein YbgF; Provisional	95.32
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.28
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	95.26
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.21
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	95.18
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.12
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	95.04
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	94.95
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	94.78
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.77
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.73
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	94.69
KOG0553	304	consensus TPR repeat-containing protein [General f	94.64
KOG2376	652	consensus Signal recognition particle, subunit Srp	94.42
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.37
PF13371	73	TPR_9: Tetratricopeptide repeat	94.35
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	94.35
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	94.33
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.12
KOG2376	652	consensus Signal recognition particle, subunit Srp	94.1
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.04
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	93.89
KOG2041	1189	consensus WD40 repeat protein [General function pr	93.71
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	93.66
KOG0553	304	consensus TPR repeat-containing protein [General f	93.66
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	93.52
KOG3060	289	consensus Uncharacterized conserved protein [Funct	93.19
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	93.08
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	92.92
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	92.7
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.64
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	92.62
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	92.62
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.48
PRK10803	263	tol-pal system protein YbgF; Provisional	92.46
PF13371	73	TPR_9: Tetratricopeptide repeat	92.32
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.09
PF13512	142	TPR_18: Tetratricopeptide repeat	91.84
PF12688	120	TPR_5: Tetratrico peptide repeat	91.8
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	91.7
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	91.46
KOG2796	366	consensus Uncharacterized conserved protein [Funct	91.4
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	91.19
smart00299	140	CLH Clathrin heavy chain repeat homology.	91.17
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	91.01
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	91.0
PF13762	145	MNE1: Mitochondrial splicing apparatus component	89.91
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	89.88
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.66
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	89.55
PF13512	142	TPR_18: Tetratricopeptide repeat	89.42
KOG2796	366	consensus Uncharacterized conserved protein [Funct	89.29
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.85
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	88.55
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	87.96
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	87.89
COG4105	254	ComL DNA uptake lipoprotein [General function pred	87.59
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	87.21
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	86.96
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	86.62
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	86.45
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	86.35
PF13762	145	MNE1: Mitochondrial splicing apparatus component	86.2
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	86.15
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	85.39
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	85.08
PRK15331	165	chaperone protein SicA; Provisional	84.75
PF13428	44	TPR_14: Tetratricopeptide repeat	84.68
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	84.54
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	84.44
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	84.3
KOG2610	491	consensus Uncharacterized conserved protein [Funct	84.18
KOG1585	308	consensus Protein required for fusion of vesicles	83.93
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	83.57
PF13929	292	mRNA_stabil: mRNA stabilisation	83.25
KOG4570	418	consensus Uncharacterized conserved protein [Funct	83.05
PF13428	44	TPR_14: Tetratricopeptide repeat	82.99
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	82.96
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	82.87
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	82.61
COG3118	304	Thioredoxin domain-containing protein [Posttransla	82.53
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	81.78
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	81.38
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	81.3
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	81.28
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	81.16
PRK15331	165	chaperone protein SicA; Provisional	80.95
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	80.69
KOG1941	518	consensus Acetylcholine receptor-associated protei	80.41
COG4700	251	Uncharacterized protein conserved in bacteria cont	80.29

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.3e-52  Score=436.32  Aligned_cols=374  Identities=11%  Similarity=0.120  Sum_probs=328.0

Q ss_pred             HHHhhHHHHHHHHHHhHHh--cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC----------CCchhhhHHHHH
Q 042756           31 LTARLTKQGQRFLSSLALA--VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT----------HPRLSSLAFPLY   98 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~--~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~----------~~~~~~~a~~lf   98 (425)
                      +..|++++|.++|+.|...  ..++..+++.++.+|++.|....|+.++..|..++..          ..+.++.|.++|
T Consensus       381 ~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a~~k~g~~e~A~~lf  460 (1060)
T PLN03218        381 LRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVL  460 (1060)
T ss_pred             HHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHhCcCHHHHHHHH
Confidence            4557999999999999988  6788899999999999999999999888887542211          124678999999


Q ss_pred             HHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756           99 MRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus        99 ~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      ++|.+.+ +.||..+|+.||.+|++.|++++|.++|++|.+.+..+.   ..+|+++|.+|++.|+   .+++++.+.+|
T Consensus       461 ~~M~~~G-l~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~Pd---vvTynaLI~gy~k~G~---~eeAl~lf~~M  533 (1060)
T PLN03218        461 RLVQEAG-LKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAN---VHTFGALIDGCARAGQ---VAKAFGAYGIM  533 (1060)
T ss_pred             HHHHHcC-CCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHHCcC---HHHHHHHHHHH
Confidence            9999887 789999999999999999999999999999998766544   4589999999999999   66777777777


Q ss_pred             hhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          179 VNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRV--KGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       179 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ...+  +.||..+||+||.+|++.|++++|.++|++|..  .|+.||..||+++|.+|++.|++++|.++|+.|.+.|+.
T Consensus       534 ~~~G--v~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~  611 (1060)
T PLN03218        534 RSKN--VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIK  611 (1060)
T ss_pred             HHcC--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence            7666  789999999999999999999999999999986  678999999999999999999999999999999999999


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc-------------cCCchhhH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN-------------SNDFPLSI  323 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~-------------~~~~~~~~  323 (425)
                      |+..+||++|.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|+++.++.             ...|+.++
T Consensus       612 p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI  691 (1060)
T PLN03218        612 GTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM  691 (1060)
T ss_pred             CChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999888877742             34567778


Q ss_pred             HHHHhhcchhhHHHHHH-HHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeecc
Q 042756          324 LELTEVLNEEEVSVVKE-LEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGS  402 (425)
Q Consensus       324 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~  402 (425)
                      ..|++.+..+++..+++ +.+.+..||..+||+||.+|++.|++++|     +++|++|.+     .|+.||..||++++
T Consensus       692 ~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeA-----lelf~eM~~-----~Gi~Pd~~Ty~sLL  761 (1060)
T PLN03218        692 GACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKA-----LEVLSEMKR-----LGLCPNTITYSILL  761 (1060)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH-----cCCCCCHHHHHHHH
Confidence            88888888777765554 44688999999999999999999999999     999999998     89999999999999


Q ss_pred             ccccccccchHHHHHHHHHhh
Q 042756          403 GKHSTVRGESSVKAMVKKMMV  423 (425)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~~  423 (425)
                      .+|++.+..+...++.++|..
T Consensus       762 ~a~~k~G~le~A~~l~~~M~k  782 (1060)
T PLN03218        762 VASERKDDADVGLDLLSQAKE  782 (1060)
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            999998888888888888764

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.4e-51  Score=428.78  Aligned_cols=376  Identities=11%  Similarity=0.126  Sum_probs=322.1

Q ss_pred             HHHhhHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC--------------CchhhhHH
Q 042756           31 LTARLTKQGQRFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH--------------PRLSSLAF   95 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~--------------~~~~~~a~   95 (425)
                      ...|+++.|.++|+.|.+. +.||..+||.||++|++.|..+.|..+|.+|...+..+              .+.+++|.
T Consensus       448 ~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl  527 (1060)
T PLN03218        448 ASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAF  527 (1060)
T ss_pred             HhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHH
Confidence            3445888899999999999 99999999999999999999999999999998765432              23578999


Q ss_pred             HHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756           96 PLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus        96 ~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                      ++|++|.+.+ +.||..+|+.||.+|++.|++++|.++|++|.+.+....|+ ..+|+++|.+|++.|+   ++++.+++
T Consensus       528 ~lf~~M~~~G-v~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD-~vTynaLI~ay~k~G~---ldeA~elf  602 (1060)
T PLN03218        528 GAYGIMRSKN-VKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPD-HITVGALMKACANAGQ---VDRAKEVY  602 (1060)
T ss_pred             HHHHHHHHcC-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCc-HHHHHHHHHHHHHCCC---HHHHHHHH
Confidence            9999999887 88999999999999999999999999999998743322333 4589999999999999   66777777


Q ss_pred             HHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          176 NQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       176 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .+|...+  +.|+..+||++|.+|++.|++++|.++|++|.+.|+.||..||+++|++|++.|++++|.++|++|.+.|+
T Consensus       603 ~~M~e~g--i~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~  680 (1060)
T PLN03218        603 QMIHEYN--IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI  680 (1060)
T ss_pred             HHHHHcC--CCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            7776665  77899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc-------------cCCchhh
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN-------------SNDFPLS  322 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~-------------~~~~~~~  322 (425)
                      .||..+||+||.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|++++++.             ..+|..+
T Consensus       681 ~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sL  760 (1060)
T PLN03218        681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL  760 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999888887743             2345566


Q ss_pred             HHHHHhhcchhhHH-HHHHHHhCCCCcccceeeccccchhc----c-------------------cCcchhHHHHHHHHH
Q 042756          323 ILELTEVLNEEEVS-VVKELEDSSVLDEAMKWDSGETKLDL----H-------------------GMHLGSAYFIILQWM  378 (425)
Q Consensus       323 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~li~~~~~----~-------------------~~~~~a~~~~~~~~~  378 (425)
                      +.++.+.+..+.+. .+.++.+.|+.||..+|+++|..|.+    .                   +..++|     +.+|
T Consensus       761 L~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~A-----l~lf  835 (1060)
T PLN03218        761 LVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWA-----LMVY  835 (1060)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHH-----HHHH
Confidence            66777777766665 44555688999999999999865432    1                   122456     8999


Q ss_pred             HHHHhhccCCCCCCCCeeeeeeccccccccccchHHHHHHHHHhh
Q 042756          379 DEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMMV  423 (425)
Q Consensus       379 ~~m~~~~~~~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~  423 (425)
                      ++|++     .|+.||..||++++.++++.++...+..|.++|.+
T Consensus       836 ~eM~~-----~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m~~  875 (1060)
T PLN03218        836 RETIS-----AGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGI  875 (1060)
T ss_pred             HHHHH-----CCCCCCHHHHHHHHHHhcccccHHHHHHHHHHhcc
Confidence            99999     99999999999999777778888899999988764

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.3e-48  Score=409.35  Aligned_cols=362  Identities=14%  Similarity=0.117  Sum_probs=292.8

Q ss_pred             hhHHHHHHHHHHhHHh-cCCCHHH-----------------------------------HHHHHHHHHhcCChHHHHHHH
Q 042756           34 RLTKQGQRFLSSLALA-VTRDSKA-----------------------------------ASRLISKFVASSPQFIALNAL   77 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~-~~~d~~~-----------------------------------~~~ll~~~~~~~~~~~a~~~~   77 (425)
                      |.+++|.++|++|... +.||..|                                   ||.||++|++.|+.+.|..+|
T Consensus       166 g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf  245 (857)
T PLN03077        166 GYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF  245 (857)
T ss_pred             CCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHH
Confidence            3566777777777665 5565554                                   466677777778888888888


Q ss_pred             HhhhCCCCC----------CCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchh
Q 042756           78 SHLLSPDTT----------HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERE  147 (425)
Q Consensus        78 ~~~l~~~~~----------~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~  147 (425)
                      .+|..++..          ..+..++|+++|++|.+.+ +.||..||+.+|.+|++.|+++.|.+++..|.+.+..++  
T Consensus       246 ~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g-~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d--  322 (857)
T PLN03077        246 DRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELS-VDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVD--  322 (857)
T ss_pred             hcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcC-CCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccc--
Confidence            887654332          2346788999999998877 789999999999999999999999999999988776554  


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH
Q 042756          148 LVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEY  227 (425)
Q Consensus       148 ~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty  227 (425)
                       ..+|++||.+|++.|+   ++++.+++.+|.      .||..+||+||.+|++.|++++|+++|++|.+.|+.||..||
T Consensus       323 -~~~~n~Li~~y~k~g~---~~~A~~vf~~m~------~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~  392 (857)
T PLN03077        323 -VSVCNSLIQMYLSLGS---WGEAEKVFSRME------TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITI  392 (857)
T ss_pred             -hHHHHHHHHHHHhcCC---HHHHHHHHhhCC------CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeH
Confidence             4489999999999999   566666666663      467779999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC-------------------
Q 042756          228 KCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS-------------------  288 (425)
Q Consensus       228 ~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~-------------------  288 (425)
                      +++|.+|++.|+++.|.++++.|.+.|+.|+..+||+||++|++.|++++|.++|++|.+.                   
T Consensus       393 ~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~  472 (857)
T PLN03077        393 ASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCF  472 (857)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHH
Confidence            9999999999999999999998888888888777777777777777777766666665432                   


Q ss_pred             -----------CCCCCHHHHHHHHHHHHHHHHHHHhhc-------------cCCchhhHHHHHhhcchhhHHHHHHHHhC
Q 042756          289 -----------GIPFSVRTYNSVLNSCSTIMSMLQDLN-------------SNDFPLSILELTEVLNEEEVSVVKELEDS  344 (425)
Q Consensus       289 -----------g~~pd~~t~~~ll~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (425)
                                 ++.||..||+++|.+|++.|.++.+.+             ...++.++..|.++|..+++..+++   .
T Consensus       473 eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~---~  549 (857)
T PLN03077        473 EALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFN---S  549 (857)
T ss_pred             HHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHH---h
Confidence                       578999999999999999998887743             4456788889999998877765443   3


Q ss_pred             CCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccccccchHHHHHHHHHh
Q 042756          345 SVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKMM  422 (425)
Q Consensus       345 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~  422 (425)
                      . .||..+||+||.+|+++|+.++|     +++|++|.+     .|+.||.+||++++.+|++.+..+....+.++|.
T Consensus       550 ~-~~d~~s~n~lI~~~~~~G~~~~A-----~~lf~~M~~-----~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~  616 (857)
T PLN03077        550 H-EKDVVSWNILLTGYVAHGKGSMA-----VELFNRMVE-----SGVNPDEVTFISLLCACSRSGMVTQGLEYFHSME  616 (857)
T ss_pred             c-CCChhhHHHHHHHHHHcCCHHHH-----HHHHHHHHH-----cCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHH
Confidence            3 79999999999999999999999     999999998     9999999999999999998766666555555554

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

Probab=100.00  E-value=9.3e-48  Score=395.84  Aligned_cols=368  Identities=13%  Similarity=0.114  Sum_probs=273.1

Q ss_pred             HHHHHhhHHHHHHHHHHhHHh--cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC--------------Cchhh
Q 042756           29 QCLTARLTKQGQRFLSSLALA--VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH--------------PRLSS   92 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~--~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~--------------~~~~~   92 (425)
                      .....|++++|.++|+.|...  ..||..+|+.++.+|++.+..+.+..++..|...+..+              .+.++
T Consensus        96 ~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~  175 (697)
T PLN03081         96 KLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLI  175 (697)
T ss_pred             HHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHH
Confidence            334567899999999999876  68999999999999999998888888887776554322              13567


Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      .|.++|++|.+     ||..+||++|.+|++.|++++|.++|++|.+.+..++   ..+|+.++.+|++.|..   ..+.
T Consensus       176 ~A~~lf~~m~~-----~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~---~~t~~~ll~a~~~~~~~---~~~~  244 (697)
T PLN03081        176 DARRLFDEMPE-----RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAE---PRTFVVMLRASAGLGSA---RAGQ  244 (697)
T ss_pred             HHHHHHhcCCC-----CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCC---hhhHHHHHHHHhcCCcH---HHHH
Confidence            78888887754     4666777788888888888888888888876655443   33677788888877773   3444


Q ss_pred             HHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          173 ARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ++...+...+  +.||..+||+||++|++.|++++|.++|++|.    .+|..+||+||.+|++.|++++|.++|++|.+
T Consensus       245 ~l~~~~~~~g--~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~  318 (697)
T PLN03081        245 QLHCCVLKTG--VVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALCLYYEMRD  318 (697)
T ss_pred             HHHHHHHHhC--CCccceeHHHHHHHHHHCCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4444444333  56777788888888888888888888888774    35777888888888888888888888888887


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cCCchhhH
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SNDFPLSI  323 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~~~~~~~  323 (425)
                      .|+.||..||+++|.+|++.|++++|.+++.+|.+.|+.||..+|++|+++|++.|+++.+..         ..+|+.++
T Consensus       319 ~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI  398 (697)
T PLN03081        319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALI  398 (697)
T ss_pred             cCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHH
Confidence            788888888888888888888888888888888888888888888888888888777766632         45667777


Q ss_pred             HHHHhhcchhhHH-HHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeecc
Q 042756          324 LELTEVLNEEEVS-VVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGS  402 (425)
Q Consensus       324 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~  402 (425)
                      .+|.+.+..+++. .+.++.+.|+.||..||+++|.+|++.|+.++|     .++|++|.+    ..|+.||..+|++++
T Consensus       399 ~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a-----~~~f~~m~~----~~g~~p~~~~y~~li  469 (697)
T PLN03081        399 AGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQG-----WEIFQSMSE----NHRIKPRAMHYACMI  469 (697)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHH-----HHHHHHHHH----hcCCCCCccchHhHH
Confidence            7777777655554 444455677777777788888878777777777     777777765    257777777787777


Q ss_pred             ccccccccchHHHHHHHHHh
Q 042756          403 GKHSTVRGESSVKAMVKKMM  422 (425)
Q Consensus       403 ~~~~~~~~~~~~~~~~~~~~  422 (425)
                      .++++.+..+.+.+++++|.
T Consensus       470 ~~l~r~G~~~eA~~~~~~~~  489 (697)
T PLN03081        470 ELLGREGLLDEAYAMIRRAP  489 (697)
T ss_pred             HHHHhcCCHHHHHHHHHHCC
Confidence            77777777777777776654

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

Probab=100.00  E-value=1.3e-46  Score=387.39  Aligned_cols=366  Identities=14%  Similarity=0.136  Sum_probs=289.5

Q ss_pred             HHHHHHHh-----hHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC----------CCch
Q 042756           27 LVQCLTAR-----LTKQGQRFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT----------HPRL   90 (425)
Q Consensus        27 ~~~~l~~~-----~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~----------~~~~   90 (425)
                      +|..++.+     ..+.|.+++..|.+. +.||..+||.||+.|++.|..+.|..+|.+|..++..          ..+.
T Consensus       125 t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~  204 (697)
T PLN03081        125 TYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGN  204 (697)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcC
Confidence            45554444     667799999999999 9999999999999999999999999999999765432          2246


Q ss_pred             hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHH
Q 042756           91 SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDD  170 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~  170 (425)
                      .++|+++|++|.+.+ +.|+..+|+.++.+|++.|+.+.+.+++..+.+.+..+.   ..+|++||++|++.|+   +++
T Consensus       205 ~~~A~~lf~~M~~~g-~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d---~~~~n~Li~~y~k~g~---~~~  277 (697)
T PLN03081        205 YREAFALFREMWEDG-SDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGD---TFVSCALIDMYSKCGD---IED  277 (697)
T ss_pred             HHHHHHHHHHHHHhC-CCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCcc---ceeHHHHHHHHHHCCC---HHH
Confidence            899999999999877 778888888888888888888888888888777665543   3367888888888888   556


Q ss_pred             HHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          171 TYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       171 ~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                      +.+.+.+|.      .+|..+||+||.+|++.|+.++|+++|++|.+.|+.||..||++++.+|++.|++++|.++++.|
T Consensus       278 A~~vf~~m~------~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m  351 (697)
T PLN03081        278 ARCVFDGMP------EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGL  351 (697)
T ss_pred             HHHHHHhCC------CCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHH
Confidence            666666652      35666888888888888888888888888888888888888888888888888888888888888


Q ss_pred             HHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc-------------cC
Q 042756          251 ESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN-------------SN  317 (425)
Q Consensus       251 ~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~-------------~~  317 (425)
                      .+.|+.||..+||+||++|++.|++++|.++|++|.    .||..|||+||.+|++.|+.++++.             ..
T Consensus       352 ~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~  427 (697)
T PLN03081        352 IRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHV  427 (697)
T ss_pred             HHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHH
Confidence            888888888888888888888888888888888775    3677788888888887777666632             22


Q ss_pred             CchhhHHHHHhhcchhhHHHHHHHH-h-CCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCe
Q 042756          318 DFPLSILELTEVLNEEEVSVVKELE-D-SSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAE  395 (425)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~  395 (425)
                      +|..++.++.+.+..+++..+++.+ + .++.|+..+|++||.+|++.|++++|     .+++++|        +++||.
T Consensus       428 T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA-----~~~~~~~--------~~~p~~  494 (697)
T PLN03081        428 TFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEA-----YAMIRRA--------PFKPTV  494 (697)
T ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHH-----HHHHHHC--------CCCCCH
Confidence            3444455555666666666666655 3 68999999999999999999999999     8887764        568999


Q ss_pred             eeeeeccccccccccchHHHHHHHHHh
Q 042756          396 ITVVCGSGKHSTVRGESSVKAMVKKMM  422 (425)
Q Consensus       396 ~t~~~l~~~~~~~~~~~~~~~~~~~~~  422 (425)
                      .+|++++.+|+..+..+..+.+.+++.
T Consensus       495 ~~~~~Ll~a~~~~g~~~~a~~~~~~l~  521 (697)
T PLN03081        495 NMWAALLTACRIHKNLELGRLAAEKLY  521 (697)
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHh
Confidence            999999999999888888888777654

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=3.6e-46  Score=392.70  Aligned_cols=363  Identities=15%  Similarity=0.154  Sum_probs=249.7

Q ss_pred             HHHHHhhHHHHHHHHHHhHHh-cCCCHHHH-----------------------------------HHHHHHHHhcCChHH
Q 042756           29 QCLTARLTKQGQRFLSSLALA-VTRDSKAA-----------------------------------SRLISKFVASSPQFI   72 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~-~~~d~~~~-----------------------------------~~ll~~~~~~~~~~~   72 (425)
                      .....|.+++|.++|+.|... ..||..+|                                   |.||+.|++.|+.+.
T Consensus        60 ~l~~~g~~~~A~~l~~~m~~~g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~n~li~~~~~~g~~~~  139 (857)
T PLN03077         60 ALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVH  139 (857)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCCCChhHHHHHHHHHhhCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHhCCChHH
Confidence            344556777777777777765 55555444                                   556666666666667


Q ss_pred             HHHHHHhhhCCCCC----------CCchhhhHHHHHHHhhhcCCCccCHHHHHHHH------------------------
Q 042756           73 ALNALSHLLSPDTT----------HPRLSSLAFPLYMRITEESWFQWNPKLVAEII------------------------  118 (425)
Q Consensus        73 a~~~~~~~l~~~~~----------~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll------------------------  118 (425)
                      |+.+|.+|..++..          ..+.+++|+++|++|...+ +.||..||+.+|                        
T Consensus       140 A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g-~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~  218 (857)
T PLN03077        140 AWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAG-VRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGF  218 (857)
T ss_pred             HHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcC-CCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCC
Confidence            77777666443321          1234677777777776655 556655554444                        


Q ss_pred             -----------HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          119 -----------AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       119 -----------~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                                 .+|++.|++++|.++|++|..      ++ ..+||++|.+|++.|+   .+++++.+.+|...+  +.|
T Consensus       219 ~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~------~d-~~s~n~li~~~~~~g~---~~eAl~lf~~M~~~g--~~P  286 (857)
T PLN03077        219 ELDVDVVNALITMYVKCGDVVSARLVFDRMPR------RD-CISWNAMISGYFENGE---CLEGLELFFTMRELS--VDP  286 (857)
T ss_pred             CcccchHhHHHHHHhcCCCHHHHHHHHhcCCC------CC-cchhHHHHHHHHhCCC---HHHHHHHHHHHHHcC--CCC
Confidence                       444444455555555554431      11 2245555555555555   444444555554443  455


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      |..||+++|.+|++.|+.+.|.+++..|.+.|+.||..+||++|.+|++.|++++|.++|++|.+    ||.++||+||.
T Consensus       287 d~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s~n~li~  362 (857)
T PLN03077        287 DLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMIS  362 (857)
T ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeeeHHHHHH
Confidence            55566666666666566666666666666666666666666666666666666666666666653    57777888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc-------------cCCchhhHHHHHhhcchhh
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN-------------SNDFPLSILELTEVLNEEE  334 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~  334 (425)
                      +|++.|++++|+++|++|.+.|+.||..||++++.+|++.|+++.+.+             ...++.++..|.+.+..++
T Consensus       363 ~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~  442 (857)
T PLN03077        363 GYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDK  442 (857)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHH
Confidence            888888888999999999999999999999999999999999888743             2345667778888887766


Q ss_pred             HHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccccccchHH
Q 042756          335 VSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSV  414 (425)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~~~~~~~~  414 (425)
                      +.   ++++.+..+|.++||+||.+|++.|+.++|     +++|++|..      +++||..||++++.+|++.+..+..
T Consensus       443 A~---~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA-----~~lf~~m~~------~~~pd~~t~~~lL~a~~~~g~l~~~  508 (857)
T PLN03077        443 AL---EVFHNIPEKDVISWTSIIAGLRLNNRCFEA-----LIFFRQMLL------TLKPNSVTLIAALSACARIGALMCG  508 (857)
T ss_pred             HH---HHHHhCCCCCeeeHHHHHHHHHHCCCHHHH-----HHHHHHHHh------CCCCCHhHHHHHHHHHhhhchHHHh
Confidence            66   555566679999999999999999999999     999999975      6999999999999999998777777


Q ss_pred             HHHHHHHh
Q 042756          415 KAMVKKMM  422 (425)
Q Consensus       415 ~~~~~~~~  422 (425)
                      +++...+.
T Consensus       509 ~~i~~~~~  516 (857)
T PLN03077        509 KEIHAHVL  516 (857)
T ss_pred             HHHHHHHH
Confidence            76665543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.80  E-value=8.1e-17  Score=155.44  Aligned_cols=305  Identities=9%  Similarity=-0.028  Sum_probs=229.1

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCcc
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQW  109 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~  109 (425)
                      .+..|.+++|.+.|..+....+.+..++..+...+...|+++.|...+..++....                  .. ...
T Consensus        45 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~------------------~~-~~~  105 (389)
T PRK11788         45 FLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPD------------------LT-REQ  105 (389)
T ss_pred             HHhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCC------------------CC-HHH
Confidence            35567899999999999887445677899999999999988888877777654310                  00 001


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc--c
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY--V  187 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~--p  187 (425)
                      +...+..+...|.+.|++++|.++|+++.+.    .+....++..+...+.+.|+++++.+.++   ++....+...  .
T Consensus       106 ~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~----~~~~~~~~~~la~~~~~~g~~~~A~~~~~---~~~~~~~~~~~~~  178 (389)
T PRK11788        106 RLLALQELGQDYLKAGLLDRAEELFLQLVDE----GDFAEGALQQLLEIYQQEKDWQKAIDVAE---RLEKLGGDSLRVE  178 (389)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHcC----CcchHHHHHHHHHHHHHhchHHHHHHHHH---HHHHhcCCcchHH
Confidence            2356788899999999999999999999864    22224478899999999999655544444   4433321110  0


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      ....|..+...+.+.|++++|..+|+++.+.. +.+...+..+...+.+.|++++|.++|+++.+.+-.....+++.++.
T Consensus       179 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~  257 (389)
T PRK11788        179 IAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLME  257 (389)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHH
Confidence            12246678888899999999999999998753 22456888888999999999999999999987643333567899999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCC
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVL  347 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  347 (425)
                      +|...|++++|..+++++.+.  .|+...+..+...+.+.|+.+++                     ...+.+.++.  .
T Consensus       258 ~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A---------------------~~~l~~~l~~--~  312 (389)
T PRK11788        258 CYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAA---------------------QALLREQLRR--H  312 (389)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHH---------------------HHHHHHHHHh--C
Confidence            999999999999999999876  57777778888888887776553                     2233344443  4


Q ss_pred             cccceeeccccchhc---ccCcchhHHHHHHHHHHHHHhhccCCCCCCCCee
Q 042756          348 DEAMKWDSGETKLDL---HGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEI  396 (425)
Q Consensus       348 ~~~~~~~~li~~~~~---~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~  396 (425)
                      |+..+++.++..+..   +|+.+++     +.+|++|.+     .+++|+..
T Consensus       313 P~~~~~~~l~~~~~~~~~~g~~~~a-----~~~~~~~~~-----~~~~~~p~  354 (389)
T PRK11788        313 PSLRGFHRLLDYHLAEAEEGRAKES-----LLLLRDLVG-----EQLKRKPR  354 (389)
T ss_pred             cCHHHHHHHHHHhhhccCCccchhH-----HHHHHHHHH-----HHHhCCCC
Confidence            888888888877664   5688899     999999998     78877776

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

Probab=99.76  E-value=5.8e-16  Score=164.86  Aligned_cols=362  Identities=8%  Similarity=-0.010  Sum_probs=228.4

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC-------------CchhhhHHHHHH
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH-------------PRLSSLAFPLYM   99 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~-------------~~~~~~a~~lf~   99 (425)
                      .|++++|.+.|+.+....+.+..++..+...+.+.|+.+.+...+.+++......             .+..++|..+++
T Consensus       512 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  591 (899)
T TIGR02917       512 EGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILN  591 (899)
T ss_pred             CCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHH
Confidence            3456666666666655544456666666666666667667766666664432211             124566777777


Q ss_pred             HhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 042756          100 RITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLV  179 (425)
Q Consensus       100 ~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~  179 (425)
                      .+....  +.+..+|..+...+.+.|++++|.+.|+++.+...    .....+..+...+.+.|++   +++...+.+..
T Consensus       592 ~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~---~~A~~~~~~~~  662 (899)
T TIGR02917       592 EAADAA--PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP----DSALALLLLADAYAVMKNY---AKAITSLKRAL  662 (899)
T ss_pred             HHHHcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC----CChHHHHHHHHHHHHcCCH---HHHHHHHHHHH
Confidence            765432  23566677777777777777777777777765421    1122456677777777774   34444444443


Q ss_pred             hcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCH
Q 042756          180 NSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDT  259 (425)
Q Consensus       180 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~  259 (425)
                      ...   ..+..+|..+...+...|++++|.++++.+.+.+ .++...+..+...+.+.|++++|.+.|+.+.+.+  |+.
T Consensus       663 ~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~  736 (899)
T TIGR02917       663 ELK---PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSS  736 (899)
T ss_pred             hcC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCc
Confidence            221   1124577777777777777777777777777654 3456677777777778888888888888777653  444


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc--------cCCchhhH----HHHH
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN--------SNDFPLSI----LELT  327 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~--------~~~~~~~~----~~~~  327 (425)
                      .++..+..++.+.|+.++|.+.+.++.+.. ..+...+..+...|...|+.+++..        .+......    ..+.
T Consensus       737 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~  815 (899)
T TIGR02917       737 QNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYL  815 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            667777778888888888888888777642 3456677777777777777666632        11111111    1233


Q ss_pred             hhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccc
Q 042756          328 EVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHST  407 (425)
Q Consensus       328 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~  407 (425)
                      ..+..+....+.+.++.. .-+..++..+...|...|++++|     .++|+++.+     .+.. |..++..+...+..
T Consensus       816 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A-----~~~~~~a~~-----~~~~-~~~~~~~l~~~~~~  883 (899)
T TIGR02917       816 ELKDPRALEYAEKALKLA-PNIPAILDTLGWLLVEKGEADRA-----LPLLRKAVN-----IAPE-AAAIRYHLALALLA  883 (899)
T ss_pred             hcCcHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHH-----HHHHHHHHh-----hCCC-ChHHHHHHHHHHHH
Confidence            334422222333333321 22345677778888899999999     999999987     4432 67777777777777


Q ss_pred             cccchHHHHHHHHHh
Q 042756          408 VRGESSVKAMVKKMM  422 (425)
Q Consensus       408 ~~~~~~~~~~~~~~~  422 (425)
                      .+..+....+++++.
T Consensus       884 ~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       884 TGRKAEARKELDKLL  898 (899)
T ss_pred             cCCHHHHHHHHHHHh
Confidence            777777777777764

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=99.74  E-value=3.8e-15  Score=158.63  Aligned_cols=334  Identities=8%  Similarity=-0.016  Sum_probs=216.5

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC-------------CchhhhHH
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH-------------PRLSSLAF   95 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~-------------~~~~~~a~   95 (425)
                      ..+..|..++|.++++.+....+.+..+++.+...+...|+.+.|...+.+++......             .+..++|.
T Consensus       440 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~  519 (899)
T TIGR02917       440 SYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAI  519 (899)
T ss_pred             HHHhcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHCCCHHHHH
Confidence            34456678888888888877666678888999999999999999999998887544321             23567788


Q ss_pred             HHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756           96 PLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus        96 ~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                      +.|+.+...+  +.+..++..+...+.+.|+.++|..+|+++.+...    .....+..+...|.+.|+   .+++...+
T Consensus       520 ~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~---~~~A~~~~  590 (899)
T TIGR02917       520 QRFEKVLTID--PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNP----QEIEPALALAQYYLGKGQ---LKKALAIL  590 (899)
T ss_pred             HHHHHHHHhC--cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc----cchhHHHHHHHHHHHCCC---HHHHHHHH
Confidence            8888877654  23666777788888888888888888888765421    112345667777888877   44444444


Q ss_pred             HHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          176 NQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       176 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .++....   ..+...|..+..+|.+.|++++|...|+++.+.. +.+...+..+..++.+.|++++|..+|+.+.+.. 
T Consensus       591 ~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-  665 (899)
T TIGR02917       591 NEAADAA---PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-  665 (899)
T ss_pred             HHHHHcC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-
Confidence            4443322   1234577788888888888888888888777642 2345667777777777788888888877776643 


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cC--CchhhHH
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SN--DFPLSIL  324 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~--~~~~~~~  324 (425)
                      +.+..+|..+...+...|++++|.++++.+.+.+ .++...+..+...+...|+++.++.         +.  .+..+..
T Consensus       666 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~  744 (899)
T TIGR02917       666 PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHR  744 (899)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHH
Confidence            2346777777777777777777777777776654 3455566666666666666655532         00  0111122


Q ss_pred             HHHhhcchhhHHH-HHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          325 ELTEVLNEEEVSV-VKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       325 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .+...+..+++.. +.+.++ ....+..+++.+...|...|+.++|     .++|+++.+
T Consensus       745 ~~~~~g~~~~A~~~~~~~l~-~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~~~~  798 (899)
T TIGR02917       745 ALLASGNTAEAVKTLEAWLK-THPNDAVLRTALAELYLAQKDYDKA-----IKHYRTVVK  798 (899)
T ss_pred             HHHHCCCHHHHHHHHHHHHH-hCCCCHHHHHHHHHHHHHCcCHHHH-----HHHHHHHHH
Confidence            3344444444332 222222 2233455666666666667777777     777777665

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

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.72  E-value=1.7e-15  Score=146.15  Aligned_cols=289  Identities=11%  Similarity=0.053  Sum_probs=211.0

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+++|+..|.++.+.+  +.+..++..+...+.+.|++++|.++++.+..............+..+...|.+.|++   +
T Consensus        50 ~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~---~  124 (389)
T PRK11788         50 QPDKAIDLFIEMLKVD--PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLL---D  124 (389)
T ss_pred             ChHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCH---H
Confidence            4455666666655543  1356688889999999999999999999988753322222234678899999999994   5


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHcCCCHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS----GFEYKCIIYGYGRLGLLEDMER  245 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~ty~~ll~~~~~~g~~~~a~~  245 (425)
                      ++...+.++....   .++..+++.++..+.+.|++++|.+.|+.+...+-.++    ...|..+...+.+.|++++|.+
T Consensus       125 ~A~~~~~~~l~~~---~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  201 (389)
T PRK11788        125 RAEELFLQLVDEG---DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARA  201 (389)
T ss_pred             HHHHHHHHHHcCC---cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence            5555555554321   23456999999999999999999999999988653332    2245677788899999999999


Q ss_pred             HHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHH
Q 042756          246 IVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILE  325 (425)
Q Consensus       246 ~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~  325 (425)
                      +|+++.+.. +.+...+..+...|.+.|++++|.++|+++.+.+-.....+++.+..+|.+.|+.+++.           
T Consensus       202 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~-----------  269 (389)
T PRK11788        202 LLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGL-----------  269 (389)
T ss_pred             HHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHH-----------
Confidence            999998753 23467888899999999999999999999987532222456788888888877765542           


Q ss_pred             HHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccc
Q 042756          326 LTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKH  405 (425)
Q Consensus       326 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~  405 (425)
                                ..+.++.+.  .|+...++.+...+.+.|++++|     .++|+++.+       ..|+..++..++..+
T Consensus       270 ----------~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A-----~~~l~~~l~-------~~P~~~~~~~l~~~~  325 (389)
T PRK11788        270 ----------EFLRRALEE--YPGADLLLALAQLLEEQEGPEAA-----QALLREQLR-------RHPSLRGFHRLLDYH  325 (389)
T ss_pred             ----------HHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHH-----HHHHHHHHH-------hCcCHHHHHHHHHHh
Confidence                      222333332  36666678889999999999999     999999887       369999888777644


Q ss_pred             cc-------cccchHHHHHHHHHh
Q 042756          406 ST-------VRGESSVKAMVKKMM  422 (425)
Q Consensus       406 ~~-------~~~~~~~~~~~~~~~  422 (425)
                      ..       .+....+++++++..
T Consensus       326 ~~~~~~g~~~~a~~~~~~~~~~~~  349 (389)
T PRK11788        326 LAEAEEGRAKESLLLLRDLVGEQL  349 (389)
T ss_pred             hhccCCccchhHHHHHHHHHHHHH
Confidence            32       234445666665443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.58  E-value=4.6e-13  Score=121.68  Aligned_cols=323  Identities=13%  Similarity=0.194  Sum_probs=212.5

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcC
Q 042756           27 LVQCLTARLTKQGQRFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEES  105 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~  105 (425)
                      ....+..|-++++.-+++.|.+. ...+...--.|+..-+-.++...-+.                  -++-|-.|.+.+
T Consensus       122 L~kmIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~------------------E~~~Fv~~~~~~  183 (625)
T KOG4422|consen  122 LLKMISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFA------------------EWEEFVGMRNFG  183 (625)
T ss_pred             HHHHHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcch------------------hHHHHhhccccc
Confidence            56667778888888888888888 55555555555444333221111010                  122333443332


Q ss_pred             CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCC
Q 042756          106 WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSV  185 (425)
Q Consensus       106 ~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  185 (425)
                      .-  +..+        -+.|++.+   ++-+..    +..+   .+|.+||.++|+-..   .+.+.+++.+.....  .
T Consensus       184 E~--S~~s--------WK~G~vAd---L~~E~~----PKT~---et~s~mI~Gl~K~~~---~ERA~~L~kE~~~~k--~  238 (625)
T KOG4422|consen  184 ED--STSS--------WKSGAVAD---LLFETL----PKTD---ETVSIMIAGLCKFSS---LERARELYKEHRAAK--G  238 (625)
T ss_pred             cc--cccc--------cccccHHH---HHHhhc----CCCc---hhHHHHHHHHHHHHh---HHHHHHHHHHHHHhh--h
Confidence            11  1111        12355443   333332    1122   378889999988876   666666666665554  4


Q ss_pred             ccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHH----HHHHHHHHHHCCCCcCHHh
Q 042756          186 YVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLED----MERIVNQMESDGTRVDTVC  261 (425)
Q Consensus       186 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~----a~~~~~~m~~~g~~~~~~~  261 (425)
                      ..+..+||.+|.+-.-...    .++..+|.+..+.||..|||+++++.++.|+++.    |.+++.+|++-|+.|...+
T Consensus       239 kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsS  314 (625)
T KOG4422|consen  239 KVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSS  314 (625)
T ss_pred             eeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhh
Confidence            5677799999887664433    7889999999999999999999999999998765    6778889999999999999


Q ss_pred             HHHHHHHHHhcCCHHH-HHHHHHHHH----hCCCCC----CHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcch
Q 042756          262 SNMVLSSYGDHNELSR-MVLWLQKMK----DSGIPF----SVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNE  332 (425)
Q Consensus       262 yn~li~~~~~~g~~~~-A~~l~~~M~----~~g~~p----d~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  332 (425)
                      |..+|..+++.++..+ |..+..+..    ...++|    |..-|...|+.|.+..+.+.+.+       ++++.+.+..
T Consensus       315 yh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~-------v~~ll~tg~N  387 (625)
T KOG4422|consen  315 YHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQ-------VHGLLKTGDN  387 (625)
T ss_pred             HHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHH-------HHHHHHcCCc
Confidence            9999999999888755 444444432    233343    55678888888888777655433       3333333321


Q ss_pred             hhHHHHHHHHhCCCCccc---ceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccccc
Q 042756          333 EEVSVVKELEDSSVLDEA---MKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVR  409 (425)
Q Consensus       333 ~~~~~~~~~~~~~~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~~~  409 (425)
                      ..          .+.|+.   .-|.-+....|.....+.-     +.+|+.|.-     .-+-|+..|-..+++|....+
T Consensus       388 ~~----------~ig~~~~~~fYyr~~~~licq~es~~~~-----~~~Y~~lVP-----~~y~p~~~~m~~~lrA~~v~~  447 (625)
T KOG4422|consen  388 WK----------FIGPDQHRNFYYRKFFDLICQMESIDVT-----LKWYEDLVP-----SAYFPHSQTMIHLLRALDVAN  447 (625)
T ss_pred             hh----------hcChHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHhcc-----ceecCCchhHHHHHHHHhhcC
Confidence            11          011221   2344455566666666776     888999887     778899999999999888888


Q ss_pred             cchHHHHHHHHHhh
Q 042756          410 GESSVKAMVKKMMV  423 (425)
Q Consensus       410 ~~~~~~~~~~~~~~  423 (425)
                      ..+.+.+++.++..
T Consensus       448 ~~e~ipRiw~D~~~  461 (625)
T KOG4422|consen  448 RLEVIPRIWKDSKE  461 (625)
T ss_pred             cchhHHHHHHHHHH
Confidence            88999988888753

>PF13041 PPR_2: PPR repeat family

Probab=99.55  E-value=1.1e-14  Score=95.85  Aligned_cols=50  Identities=26%  Similarity=0.391  Sum_probs=37.6

Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      ||+++||++|++|++.|++++|.++|++|.+.|+.||..||++||++||+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            67777777777777777777777777777777777777777777777763

>PF13041 PPR_2: PPR repeat family

Probab=99.53  E-value=2.1e-14  Score=94.47  Aligned_cols=50  Identities=30%  Similarity=0.644  Sum_probs=33.1

Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR  236 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~  236 (425)
                      ||+.+||++|++|++.|++++|+++|++|++.|++||..||+++|++|+|
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            56666666666666666666666666666666666666666666666654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.44  E-value=1.5e-10  Score=118.44  Aligned_cols=315  Identities=13%  Similarity=0.063  Sum_probs=212.8

Q ss_pred             hHHHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chh
Q 042756           25 LTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLS   91 (425)
Q Consensus        25 ~~~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~   91 (425)
                      ..+..++.+|...+|+.+++......+-+......+.-+....|+.+.|...+.+++......+             +..
T Consensus        47 ~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~  126 (656)
T PRK15174         47 LFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQY  126 (656)
T ss_pred             HHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCH
Confidence            3467778889999999999999888444455555566677778999999999999876544322             356


Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDT  171 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~  171 (425)
                      ++|...|++.....  +-+...+..+...+...|+.++|.+.++.+...... .+.   .+..+ ..+.+.|++   .++
T Consensus       127 ~~Ai~~l~~Al~l~--P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~-~~~---a~~~~-~~l~~~g~~---~eA  196 (656)
T PRK15174        127 ATVADLAEQAWLAF--SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPP-RGD---MIATC-LSFLNKSRL---PED  196 (656)
T ss_pred             HHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC-CHH---HHHHH-HHHHHcCCH---HHH
Confidence            77888888876643  135667777888888889999999888877654221 221   22233 336777884   444


Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHH----HHHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLED----MERIV  247 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~----a~~~~  247 (425)
                      ...+.+.....  ..++...+..+..++.+.|++++|...|++..... +.+...+..+-.++...|++++    |...|
T Consensus       197 ~~~~~~~l~~~--~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~  273 (656)
T PRK15174        197 HDLARALLPFF--ALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHW  273 (656)
T ss_pred             HHHHHHHHhcC--CCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHH
Confidence            44454443332  11233455566778888899999999999888753 2346677788888888898875    78888


Q ss_pred             HHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHHHHHHHHhhccCCchhhHHHH
Q 042756          248 NQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVLNSCSTIMSMLQDLNSNDFPLSILEL  326 (425)
Q Consensus       248 ~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~  326 (425)
                      +...+.. +.+...+..+...+...|++++|...+++..+.  .|+. ..+..+..++.+.|+++.+.            
T Consensus       274 ~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l--~P~~~~a~~~La~~l~~~G~~~eA~------------  338 (656)
T PRK15174        274 RHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLAT--HPDLPYVRAMYARALRQVGQYTAAS------------  338 (656)
T ss_pred             HHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHH------------
Confidence            8877653 225678888888888999999999998887764  4543 44555556666666654442            


Q ss_pred             HhhcchhhHHHHHHHHhCCCCcccce-eeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          327 TEVLNEEEVSVVKELEDSSVLDEAMK-WDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                               ..+.++++.  .|+... +..+..++...|+.++|     .+.|++..+
T Consensus       339 ---------~~l~~al~~--~P~~~~~~~~~a~al~~~G~~deA-----~~~l~~al~  380 (656)
T PRK15174        339 ---------DEFVQLARE--KGVTSKWNRYAAAALLQAGKTSEA-----ESVFEHYIQ  380 (656)
T ss_pred             ---------HHHHHHHHh--CccchHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH
Confidence                     222333332  244322 33345667888999998     888888776

>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=99.40  E-value=1.2e-09  Score=111.62  Aligned_cols=337  Identities=10%  Similarity=-0.073  Sum_probs=220.3

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHH
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAF   95 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~   95 (425)
                      .....|.++.|.+.|+.... ..|+...|..+-.+|.+.|+++.|...+.+.+..+....             +.+++|+
T Consensus       136 ~~~~~~~~~~Ai~~y~~al~-~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~~lg~~~eA~  214 (615)
T TIGR00990       136 KAYRNKDFNKAIKLYSKAIE-CKPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGLGKYADAL  214 (615)
T ss_pred             HHHHcCCHHHHHHHHHHHHh-cCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            34556789999999988765 467888899999999999999999999988876543321             2355555


Q ss_pred             HHHHHhhhcCCC-------------------------------ccCHHHHHHH---------------------------
Q 042756           96 PLYMRITEESWF-------------------------------QWNPKLVAEI---------------------------  117 (425)
Q Consensus        96 ~lf~~m~~~~~~-------------------------------~~~~~~~~~l---------------------------  117 (425)
                      .-|......+.+                               .|........                           
T Consensus       215 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  294 (615)
T TIGR00990       215 LDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGNGQ  294 (615)
T ss_pred             HHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccccccccch
Confidence            444322111100                               0110000000                           


Q ss_pred             HHHH------HhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          118 IAFL------DKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       118 l~~~------~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      +...      ...+++++|.+.|++..+.+.. .+.....|..+-..+...|++   +++...+.+.....+.   ....
T Consensus       295 ~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~-~~~~a~a~~~lg~~~~~~g~~---~eA~~~~~kal~l~P~---~~~~  367 (615)
T TIGR00990       295 LQLGLKSPESKADESYEEAARAFEKALDLGKL-GEKEAIALNLRGTFKCLKGKH---LEALADLSKSIELDPR---VTQS  367 (615)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHcCCH---HHHHHHHHHHHHcCCC---cHHH
Confidence            0000      1225788999999988765422 233344677777888888984   4555555555443321   2347


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      |..+...+...|++++|...|++..+.. +-+..+|..+...+...|++++|...|+...+.. +.+...|..+...+.+
T Consensus       368 ~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~  445 (615)
T TIGR00990       368 YIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYK  445 (615)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHH
Confidence            8888888899999999999999887752 2246788888888999999999999999887753 2256777888888889


Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHhhc--------cCCc-------hhhHH----HHHhhcc
Q 042756          272 HNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQDLN--------SNDF-------PLSIL----ELTEVLN  331 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~~~--------~~~~-------~~~~~----~~~~~~~  331 (425)
                      .|++++|+..|++..+.  .| +...|+.+-..+...|+++++..        .+..       .+++.    .+...+.
T Consensus       446 ~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~  523 (615)
T TIGR00990       446 EGSIASSMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQD  523 (615)
T ss_pred             CCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhh
Confidence            99999999999988764  34 45677778888888887777642        1110       01111    1111233


Q ss_pred             hhhHHHH-HHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          332 EEEVSVV-KELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       332 ~~~~~~~-~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .+++... .+.++.. ..+...|..+...+...|++++|     +++|++..+
T Consensus       524 ~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eA-----i~~~e~A~~  570 (615)
T TIGR00990       524 FIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEA-----LKLFERAAE  570 (615)
T ss_pred             HHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHH-----HHHHHHHHH
Confidence            3333332 2223321 22335688899999999999999     999999876

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

Probab=99.37  E-value=8.3e-11  Score=111.79  Aligned_cols=337  Identities=12%  Similarity=0.018  Sum_probs=225.8

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC-------------CCchhhhHHHHH
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT-------------HPRLSSLAFPLY   98 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~-------------~~~~~~~a~~lf   98 (425)
                      .+|.+.+|+.+++.+.+.-+-.+..|..+-.++...|+.+.|...+.+.+.-...             ..|++++|...|
T Consensus       128 erg~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLlka~Grl~ea~~cY  207 (966)
T KOG4626|consen  128 ERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNLLKAEGRLEEAKACY  207 (966)
T ss_pred             HhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHHHHhhcccchhHHHH
Confidence            3568999999999998864447899999999999999999999999888654321             224577788877


Q ss_pred             HHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756           99 MRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus        99 ~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      .+..+...  .=++.|+.|-..|-.+|++..|.+-|++..+-    +|...-.|-.|-+.|...+.++.+..++.....+
T Consensus       208 lkAi~~qp--~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl----dP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~l  281 (966)
T KOG4626|consen  208 LKAIETQP--CFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL----DPNFLDAYINLGNVYKEARIFDRAVSCYLRALNL  281 (966)
T ss_pred             HHHHhhCC--ceeeeehhcchHHhhcchHHHHHHHHHHhhcC----CCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhc
Confidence            77554431  13446777888888899999999999987753    3333346778888888888876666666555554


Q ss_pred             hhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          179 VNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       179 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      .+..      ..++..|-..|-..|.+|-|++.|++..+  +.|+ ...|+.|-+++-..|++.+|...++....... -
T Consensus       282 rpn~------A~a~gNla~iYyeqG~ldlAI~~Ykral~--~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p-~  352 (966)
T KOG4626|consen  282 RPNH------AVAHGNLACIYYEQGLLDLAIDTYKRALE--LQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCP-N  352 (966)
T ss_pred             CCcc------hhhccceEEEEeccccHHHHHHHHHHHHh--cCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCC-c
Confidence            3222      23666666777777888888888877776  4555 45777887787777888888877777665432 1


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHHHHHHHHhhc----cCCchhhHH-HHHhhcc
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVLNSCSTIMSMLQDLN----SNDFPLSIL-ELTEVLN  331 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~~~~~~~~~~~~~~----~~~~~~~~~-~~~~~~~  331 (425)
                      .....|.|-..|...|.+++|..+|....+  +.|.- ..++.|-..|-..|++.+++.    .-...|... .|.++|.
T Consensus       353 hadam~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGn  430 (966)
T KOG4626|consen  353 HADAMNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGN  430 (966)
T ss_pred             cHHHHHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcch
Confidence            355667777777777777777777777654  34443 466777777777777776643    111112211 3333332


Q ss_pred             h----hhHHHHHHHHhCCCC--cc-cceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeee
Q 042756          332 E----EEVSVVKELEDSSVL--DE-AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEIT  397 (425)
Q Consensus       332 ~----~~~~~~~~~~~~~~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t  397 (425)
                      .    ++...+.+...+.+.  |. +...+-|-+.|...|+..+|     ++-+++...       ++||..-
T Consensus       431 t~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~A-----I~sY~~aLk-------lkPDfpd  491 (966)
T KOG4626|consen  431 TYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEA-----IQSYRTALK-------LKPDFPD  491 (966)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHH-----HHHHHHHHc-------cCCCCch
Confidence            1    111112222222222  22 34678888999999999999     999998765       7888643

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.33  E-value=2.8e-09  Score=109.11  Aligned_cols=269  Identities=8%  Similarity=-0.060  Sum_probs=180.2

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC-------------CchhhhH
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH-------------PRLSSLA   94 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~-------------~~~~~~a   94 (425)
                      ...+..|+.++|.+.|+.+...-+.+...+..+...+...|+.+.|...+.+.+......             .+..++|
T Consensus        84 ~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA  163 (656)
T PRK15174         84 ISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQA  163 (656)
T ss_pred             hhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHH
Confidence            555678889999999999887655567788888888899999999999998887643322             1346778


Q ss_pred             HHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 042756           95 FPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYAR  174 (425)
Q Consensus        95 ~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~  174 (425)
                      ...++.+.....  .+...+..+ ..+.+.|++++|..+++.+.+......   ...+..+..++.+.|++++   +...
T Consensus       164 ~~~~~~~~~~~P--~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~---~~~~~~l~~~l~~~g~~~e---A~~~  234 (656)
T PRK15174        164 ISLARTQAQEVP--PRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALER---QESAGLAVDTLCAVGKYQE---AIQT  234 (656)
T ss_pred             HHHHHHHHHhCC--CCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcc---hhHHHHHHHHHHHCCCHHH---HHHH
Confidence            888887755431  123333333 347778888888888888765422111   1233455667778888444   4444


Q ss_pred             HHHHhhcCCCCccChhHHHHHHHHHHhcCChhH----HHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          175 LNQLVNSSSSVYVKRQALKSMISGLCEMGQPHE----AENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       175 ~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~----a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      +.+.....+   -+...+..+-..+.+.|++++    |...|++..+.  .| +...+..+...+.+.|++++|...++.
T Consensus       235 ~~~al~~~p---~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~  309 (656)
T PRK15174        235 GESALARGL---DGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQ  309 (656)
T ss_pred             HHHHHhcCC---CCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            444433221   124477778888888888875    78888887764  34 456778888888888888888888888


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH-HHHHHHHHHHHHHHHHh
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT-YNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t-~~~ll~~~~~~~~~~~~  313 (425)
                      ..+..- -+...+..+...|.+.|++++|...|+++.+.  .|+... +..+..++...|+.+.+
T Consensus       310 al~l~P-~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~--~P~~~~~~~~~a~al~~~G~~deA  371 (656)
T PRK15174        310 SLATHP-DLPYVRAMYARALRQVGQYTAASDEFVQLARE--KGVTSKWNRYAAAALLQAGKTSEA  371 (656)
T ss_pred             HHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHCCCHHHH
Confidence            776532 24556777778888888888888888887764  455433 22334456666665555

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.30  E-value=1.1e-08  Score=93.59  Aligned_cols=321  Identities=11%  Similarity=0.047  Sum_probs=208.9

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc----------hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHH
Q 042756           52 RDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR----------LSSLAFPLYMRITEESWFQWNPKLVAEIIAFL  121 (425)
Q Consensus        52 ~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~----------~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~  121 (425)
                      -+..+|..||.++|+....+.|++++.+.-...+....          -+....++..+|.... .+||..|+|+++++.
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqk-m~Pnl~TfNalL~c~  283 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQK-MTPNLFTFNALLSCA  283 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhh-cCCchHhHHHHHHHH
Confidence            45566777777777766666677666665333222111          1333467788888776 889999999999999


Q ss_pred             HhcCChhH----HHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc--CCCCcc----ChhH
Q 042756          122 DKQGQREE----AETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS--SSSVYV----KRQA  191 (425)
Q Consensus       122 ~~~g~~~~----A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~--~~~~~p----~~~~  191 (425)
                      ++.|+++.    |.+++.+|++-|..|.-   .+|..+|.-+++.++..+  -+...+.+...+  |...+|    |..-
T Consensus       284 akfg~F~~ar~aalqil~EmKeiGVePsL---sSyh~iik~f~re~dp~k--~as~~i~dI~N~ltGK~fkp~~p~d~~F  358 (625)
T KOG4422|consen  284 AKFGKFEDARKAALQILGEMKEIGVEPSL---SSYHLIIKNFKRESDPQK--VASSWINDIQNSLTGKTFKPITPTDNKF  358 (625)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHhCCCcch---hhHHHHHHHhcccCCchh--hhHHHHHHHHHhhccCcccCCCCchhHH
Confidence            99998876    45677888888776663   489999999999998643  233333333222  212333    3456


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCH---HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKG----LEPSG---FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNM  264 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~---~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~  264 (425)
                      |-.-+..|.+..+.+-|.++-...+...    +.|+.   +=|..+..+.|....++...+.++.|.-+-+-|+..+..-
T Consensus       359 F~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~  438 (625)
T KOG4422|consen  359 FQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIH  438 (625)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHH
Confidence            7778888889999999999988776532    44442   3467788888999999999999999998888899999999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH-------------------HH--HH------HHhhccC
Q 042756          265 VLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST-------------------IM--SM------LQDLNSN  317 (425)
Q Consensus       265 li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~-------------------~~--~~------~~~~~~~  317 (425)
                      ++.+.-..|.++-.-+++.+|+..|..-....-.-++.-+|+                   +.  .+      ...+...
T Consensus       439 ~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~~  518 (625)
T KOG4422|consen  439 LLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRAQ  518 (625)
T ss_pred             HHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHhc
Confidence            999999999988888888888776633222222222222222                   10  00      0012233


Q ss_pred             Cch-----hhHHHHHhhcchhhHHHHHHHH-hCCCC-cccceeeccc---cchhcccCcchhHHHHHHHHHHHHHh
Q 042756          318 DFP-----LSILELTEVLNEEEVSVVKELE-DSSVL-DEAMKWDSGE---TKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       318 ~~~-----~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~li---~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      +++     ...-.+.+.|...++..+..++ +++.+ |-....|.|+   .+-.+.+.+..|     +.++.-|..
T Consensus       519 ~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA-----~~~lQ~a~~  589 (625)
T KOG4422|consen  519 DWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQA-----IEVLQLASA  589 (625)
T ss_pred             cCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHH-----HHHHHHHHH
Confidence            333     2223456666667777666666 44433 4444556444   444456677777     666666643

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.29  E-value=6.6e-09  Score=113.46  Aligned_cols=336  Identities=10%  Similarity=-0.023  Sum_probs=212.1

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC----------------------
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH----------------------   87 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~----------------------   87 (425)
                      .+..|++++|.+.|+...+.-+-|..++..+-..+.+.|+.++|...|.+.+......                      
T Consensus       279 ~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g  358 (1157)
T PRK11447        279 AVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG  358 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence            3456789999999999887655588999999999999999999999999988644322                      


Q ss_pred             -----CchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc
Q 042756           88 -----PRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH  162 (425)
Q Consensus        88 -----~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~  162 (425)
                           .+.+++|.+.|++....+.  .+...+..+-..+...|++++|++.|++..+...    +....+..+...|. .
T Consensus       359 ~~~~~~g~~~eA~~~~~~Al~~~P--~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p----~~~~a~~~L~~l~~-~  431 (1157)
T PRK11447        359 DAALKANNLAQAERLYQQARQVDN--TDSYAVLGLGDVAMARKDYAAAERYYQQALRMDP----GNTNAVRGLANLYR-Q  431 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC----CCHHHHHHHHHHHH-h
Confidence                 1246778888988877642  3566777788999999999999999999886522    11224455666664 3


Q ss_pred             CCcccHHHHHHHHHHHhhcCCC-C-----ccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHH
Q 042756          163 DSKRGFDDTYARLNQLVNSSSS-V-----YVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYG  235 (425)
Q Consensus       163 g~~~~~~~~~~~~~~~~~~~~~-~-----~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~  235 (425)
                      ++   .+++...+.+....... .     ......+..+...+...|++++|.+.|++..+.  .| +...+..+...|.
T Consensus       432 ~~---~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~--~P~~~~~~~~LA~~~~  506 (1157)
T PRK11447        432 QS---PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLAL--DPGSVWLTYRLAQDLR  506 (1157)
T ss_pred             cC---HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            44   34444444433221100 0     001124566778888899999999999999874  45 4567788888999


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH---------HHHHHHHHH
Q 042756          236 RLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTY---------NSVLNSCST  306 (425)
Q Consensus       236 ~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~---------~~ll~~~~~  306 (425)
                      +.|++++|...++...+..- -+...+..+...+...|+.++|...++++......++...+         ..+.+.+..
T Consensus       507 ~~G~~~~A~~~l~~al~~~P-~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~  585 (1157)
T PRK11447        507 QAGQRSQADALMRRLAQQKP-NDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRD  585 (1157)
T ss_pred             HcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHH
Confidence            99999999999999876431 24444444555566788888888888776543333322211         122233444


Q ss_pred             HHHHHHhhc-----cCCch---hhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHH
Q 042756          307 IMSMLQDLN-----SNDFP---LSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWM  378 (425)
Q Consensus       307 ~~~~~~~~~-----~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  378 (425)
                      .|+.+++..     +....   .+...+...+..+++....+..-.....+...+..+...|...|+.++|     .+.+
T Consensus       586 ~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA-----~~~l  660 (1157)
T PRK11447        586 SGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAA-----RAQL  660 (1157)
T ss_pred             CCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHH-----HHHH
Confidence            444444321     11111   1111334444444444333222222223445566666777777777777     6666


Q ss_pred             HHHHh
Q 042756          379 DEMRN  383 (425)
Q Consensus       379 ~~m~~  383 (425)
                      +...+
T Consensus       661 ~~ll~  665 (1157)
T PRK11447        661 AKLPA  665 (1157)
T ss_pred             HHHhc
Confidence            65543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.25  E-value=5.7e-09  Score=113.96  Aligned_cols=333  Identities=11%  Similarity=0.015  Sum_probs=205.6

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc------------hhhhHHHH
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR------------LSSLAFPL   97 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~------------~~~~a~~l   97 (425)
                      .+..|++++|.+.|++.....+.+...+..+-..+...|+++.|...+.+.+........            ..++|+..
T Consensus       361 ~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A~~~  440 (1157)
T PRK11447        361 ALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKALAF  440 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHHHHH
Confidence            345678999999999998875567788888999999999999999999999865433221            23455555


Q ss_pred             HHHhhhcCCC-------ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHH
Q 042756           98 YMRITEESWF-------QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDD  170 (425)
Q Consensus        98 f~~m~~~~~~-------~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~  170 (425)
                      ++.+.....-       ......+..+...+...|++++|.+.|++..+..    |+....+..+...|.+.|+++++.+
T Consensus       441 l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~----P~~~~~~~~LA~~~~~~G~~~~A~~  516 (1157)
T PRK11447        441 IASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD----PGSVWLTYRLAQDLRQAGQRSQADA  516 (1157)
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            5554322100       0012234556677888999999999999987652    2223356678888999999555444


Q ss_pred             HHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH---------HHHHHHHHHHcCCCHH
Q 042756          171 TYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF---------EYKCIIYGYGRLGLLE  241 (425)
Q Consensus       171 ~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~---------ty~~ll~~~~~~g~~~  241 (425)
                      .++.+.+..+.      +...+..+.-.+.+.++.++|+..++.+......++..         .+......+...|+.+
T Consensus       517 ~l~~al~~~P~------~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~  590 (1157)
T PRK11447        517 LMRRLAQQKPN------DPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEA  590 (1157)
T ss_pred             HHHHHHHcCCC------CHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHH
Confidence            44444332211      12244444445667788888888887764332222221         1223455677778888


Q ss_pred             HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc------
Q 042756          242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN------  315 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~------  315 (425)
                      +|.++++.     .+.+...+..+-..|.+.|+.++|+..|++..+.. .-+...+..+...+...|+..++..      
T Consensus       591 eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll  664 (1157)
T PRK11447        591 EAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLP  664 (1157)
T ss_pred             HHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            88777762     13345566677777777888888888888776642 2245667777777777666666532      


Q ss_pred             -c--CCchh---hHHHHHhhcchhhHHHHHHH-HhCCCC-c----ccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          316 -S--NDFPL---SILELTEVLNEEEVSVVKEL-EDSSVL-D----EAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       316 -~--~~~~~---~~~~~~~~~~~~~~~~~~~~-~~~~~~-~----~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                       .  .....   +...+...+..+++..+.+. +..... |    +...+..+-..+...|++++|     ++.|++...
T Consensus       665 ~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A-----~~~y~~Al~  739 (1157)
T PRK11447        665 ATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQA-----LETYKDAMV  739 (1157)
T ss_pred             ccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHh
Confidence             1  11111   11133444555555444333 332211 1    123455556778889999999     999988764

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.21  E-value=3.8e-08  Score=102.93  Aligned_cols=132  Identities=7%  Similarity=0.033  Sum_probs=91.7

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhh
Q 042756           27 LVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSL   93 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~   93 (425)
                      +--....|+.++|++++......-+.+...+..+...+...|++..|...+.+.+......+             +..++
T Consensus        22 ~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~e  101 (765)
T PRK10049         22 LQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDE  101 (765)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH
Confidence            34445677888888888887754445566788888888888999999999988776543322             35778


Q ss_pred             HHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCc
Q 042756           94 AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSK  165 (425)
Q Consensus        94 a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~  165 (425)
                      |+..+++.....  +-+.. +..+-..+...|+.++|...+++..+.... .   ...+..+..++...+..
T Consensus       102 A~~~l~~~l~~~--P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~---~~~~~~la~~l~~~~~~  166 (765)
T PRK10049        102 ALVKAKQLVSGA--PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ-T---QQYPTEYVQALRNNRLS  166 (765)
T ss_pred             HHHHHHHHHHhC--CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-C---HHHHHHHHHHHHHCCCh
Confidence            888888877654  23455 777788888889999999999988775221 1   22334455566555553

>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=99.20  E-value=6.6e-08  Score=98.99  Aligned_cols=292  Identities=10%  Similarity=-0.079  Sum_probs=155.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhhhCCCCCC------------CchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhc
Q 042756           57 ASRLISKFVASSPQFIALNALSHLLSPDTTH------------PRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQ  124 (425)
Q Consensus        57 ~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~------------~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~  124 (425)
                      +...-..+.+.|+++.|...+.+.+......            -+.+++|++.++...+.+  +-+...+..+-.+|...
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~--p~~~~a~~~~a~a~~~l  207 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIECKPDPVYYSNRAACHNALGDWEKVVEDTTAALELD--PDYSKALNRRANAYDGL  207 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHc
Confidence            4455667777888888888888876543210            124677787777766544  12556777788888888


Q ss_pred             CChhHHHHHHHHHHHhcCCCchhHHHHHHHH-------------------------HHHHHh------------------
Q 042756          125 GQREEAETLILETLSKLGSRERELVLFYCNL-------------------------IDSFCK------------------  161 (425)
Q Consensus       125 g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~l-------------------------i~~~~~------------------  161 (425)
                      |++++|..-|.................+..+                         +..|..                  
T Consensus       208 g~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  287 (615)
T TIGR00990       208 GKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELD  287 (615)
T ss_pred             CCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccc
Confidence            8888887766544322111110000000000                         000000                  


Q ss_pred             ----------------cCCcccHHHHHHHHHHHhhcCCCCcc-ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-
Q 042756          162 ----------------HDSKRGFDDTYARLNQLVNSSSSVYV-KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-  223 (425)
Q Consensus       162 ----------------~g~~~~~~~~~~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-  223 (425)
                                      ....+..+++...+.+....+. ..| +...|+.+-..+...|++++|+..|++..+.  .|+ 
T Consensus       288 ~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~-~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~  364 (615)
T TIGR00990       288 EETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGK-LGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--DPRV  364 (615)
T ss_pred             cccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCC-CChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCc
Confidence                            0000112233333333332221 112 2235555555666666666666666665543  343 


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHH
Q 042756          224 GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVLN  302 (425)
Q Consensus       224 ~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll~  302 (425)
                      ..+|..+...+...|++++|...|+...+.. +-+..+|..+...|...|++++|...|++..+.  .|+ ...+..+-.
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~  441 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGV  441 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHH
Confidence            3355555566666666666666666555432 123555666666666666666666666665543  232 233333333


Q ss_pred             HHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHH
Q 042756          303 SCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMR  382 (425)
Q Consensus       303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~  382 (425)
                      .+.+.|+                      .+++....+-.......+...|+.+-..+...|++++|     ++.|++..
T Consensus       442 ~~~~~g~----------------------~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A-----~~~~~~Al  494 (615)
T TIGR00990       442 TQYKEGS----------------------IASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEA-----IEKFDTAI  494 (615)
T ss_pred             HHHHCCC----------------------HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHH-----HHHHHHHH
Confidence            3333333                      33333333322222233456788888999999999999     99999987


Q ss_pred             h
Q 042756          383 N  383 (425)
Q Consensus       383 ~  383 (425)
                      +
T Consensus       495 ~  495 (615)
T TIGR00990       495 E  495 (615)
T ss_pred             h
Confidence            6

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

Probab=99.12  E-value=1.3e-09  Score=107.71  Aligned_cols=207  Identities=14%  Similarity=0.092  Sum_probs=148.7

Q ss_pred             HHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc---------------------CCCchhHHHHHHHH
Q 042756           97 LYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL---------------------GSRERELVLFYCNL  155 (425)
Q Consensus        97 lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~---------------------~~~~~~~~~~y~~l  155 (425)
                      ++-.+...| +.||-.||..+|..||..|+++.|- +|..|..+.                     ..+..+...+|..|
T Consensus        12 fla~~e~~g-i~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~L   89 (1088)
T KOG4318|consen   12 FLALHEISG-ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNL   89 (1088)
T ss_pred             HHHHHHHhc-CCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHH
Confidence            344566666 7899999999999999999999998 888876321                     11222234589999


Q ss_pred             HHHHHhcCCcccHHHHHHHHHHHhhc----CC---------------CCccCh----------hHHHHHHHHHHhcC---
Q 042756          156 IDSFCKHDSKRGFDDTYARLNQLVNS----SS---------------SVYVKR----------QALKSMISGLCEMG---  203 (425)
Q Consensus       156 i~~~~~~g~~~~~~~~~~~~~~~~~~----~~---------------~~~p~~----------~~~~~li~~~~~~g---  203 (425)
                      .++|...||...++.+-+.+.+...+    +.               ..-||.          ..|..+++-..+.-   
T Consensus        90 l~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa  169 (1088)
T KOG4318|consen   90 LKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSA  169 (1088)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCccc
Confidence            99999999977655554434443322    10               111332          24555555543321   


Q ss_pred             --------------ChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          204 --------------QPHEAENLIEEMRVKGL-EPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       204 --------------~~~~a~~~~~~m~~~g~-~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                                    ..+-..++.+.. ..+. .||..+|..++++-..+|+++.|..++.+|++.|+..+.+-|..|+-+
T Consensus       170 ~~~p~~vfLrqnv~~ntpvekLl~~c-ksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g  248 (1088)
T KOG4318|consen  170 WNAPFQVFLRQNVVDNTPVEKLLNMC-KSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG  248 (1088)
T ss_pred             ccchHHHHHHHhccCCchHHHHHHHH-HHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc
Confidence                          111122222222 2222 599999999999999999999999999999999999999988888877


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~  309 (425)
                         .+...-++.+++-|.+.|+.|+..|+..-+-.+.+.|.
T Consensus       249 ---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  249 ---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             ---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence               78888999999999999999999999988877777444

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.11  E-value=2.1e-07  Score=89.86  Aligned_cols=271  Identities=9%  Similarity=-0.017  Sum_probs=194.3

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC--------------Cchhhh
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH--------------PRLSSL   93 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~--------------~~~~~~   93 (425)
                      ...+..|++++|++.+..-.....-....|-....+..+.|+.+.+...+.++.......              .+..+.
T Consensus        92 l~a~~eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~  171 (398)
T PRK10747         92 LLKLAEGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHA  171 (398)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHH
Confidence            334556899999988877554311123334333445477899999999999987654332              235788


Q ss_pred             HHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHH----HHHHHHHHHHHhcCCcccHH
Q 042756           94 AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELV----LFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        94 a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~----~~y~~li~~~~~~g~~~~~~  169 (425)
                      |...++...+.+  +-++.....+...|.+.|++++|.+++..+.+....++....    ..|..++....+..+   .+
T Consensus       172 Al~~l~~~~~~~--P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~---~~  246 (398)
T PRK10747        172 ARHGVDKLLEVA--PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQG---SE  246 (398)
T ss_pred             HHHHHHHHHhcC--CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcC---HH
Confidence            999999987765  236778889999999999999999999999987655333222    133333444333333   34


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      .....+.+....   ...+......+..++...|+.++|.+++++..+.  .||..  -.++.+....++.+++.+..+.
T Consensus       247 ~l~~~w~~lp~~---~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~al~~~e~  319 (398)
T PRK10747        247 GLKRWWKNQSRK---TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTNNPEQLEKVLRQ  319 (398)
T ss_pred             HHHHHHHhCCHH---HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCCChHHHHHHHHH
Confidence            444444443322   1124458889999999999999999999999874  45542  2244555677999999999999


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      ..+.. +-|...+.++-..+.+.|++++|.+.|+...+.  .|+..+|..+-..+.+.|+.+.+
T Consensus       320 ~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A  380 (398)
T PRK10747        320 QIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEA  380 (398)
T ss_pred             HHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHH
Confidence            88763 235667888999999999999999999999875  79999999999998888877665

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

Probab=99.10  E-value=8.6e-10  Score=101.40  Aligned_cols=247  Identities=12%  Similarity=0.110  Sum_probs=108.7

Q ss_pred             HHHhhHHHHHHHHHHhHHhc-CCCHHHHHHHHHHHHh-cCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           31 LTARLTKQGQRFLSSLALAV-TRDSKAASRLISKFVA-SSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~-~~d~~~~~~ll~~~~~-~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      +..|+++.|.++++...... +|+-..|-.++..++. .++                     .+.|.+.++.+...+.. 
T Consensus        19 ~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~---------------------~~~A~~ay~~l~~~~~~-   76 (280)
T PF13429_consen   19 YQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGD---------------------YDEAIEAYEKLLASDKA-   76 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccc---------------------ccccccccccccccccc-
Confidence            34667788888886544442 4444444433333333 343                     44555555555444423 


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                       ++..+..++.. ...++.++|.+++.+.-++..  .+   ..+...+..+.+.++++.+.++++.+.+..    ...++
T Consensus        77 -~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~--~~---~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~----~~~~~  145 (280)
T PF13429_consen   77 -NPQDYERLIQL-LQDGDPEEALKLAEKAYERDG--DP---RYLLSALQLYYRLGDYDEAEELLEKLEELP----AAPDS  145 (280)
T ss_dssp             ------------------------------------------------H-HHHTT-HHHHHHHHHHHHH-T-------T-
T ss_pred             -ccccccccccc-ccccccccccccccccccccc--cc---chhhHHHHHHHHHhHHHHHHHHHHHHHhcc----CCCCC
Confidence             45556667766 688999999999887655432  22   246778888899999666666665554321    13356


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      ...|..+...+.+.|+.++|++.|++..+.  .|+ ....+.++..+...|+.+++.++++...+.. ..|...|..+..
T Consensus       146 ~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~  222 (280)
T PF13429_consen  146 ARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAA  222 (280)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHH
Confidence            678999999999999999999999999884  564 6788899999999999999999999887754 456778899999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      +|...|+.++|+.+|++..+.. +.|..+...+..++...|+.+.+.
T Consensus       223 ~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~  268 (280)
T PF13429_consen  223 AYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEAL  268 (280)
T ss_dssp             HHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT---------
T ss_pred             Hhcccccccccccccccccccc-cccccccccccccccccccccccc
Confidence            9999999999999999987642 347788888888888888887664

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.06  E-value=2.8e-07  Score=97.37  Aligned_cols=273  Identities=8%  Similarity=-0.059  Sum_probs=166.7

Q ss_pred             cccchhHHHHHHHHhhHHHHHHHHHHhHHh---cCCCHHHHHHHHHHHHhcCC---hHHHHHHHHhhhCCCCC-CCchhh
Q 042756           20 LRQQRLTLVQCLTARLTKQGQRFLSSLALA---VTRDSKAASRLISKFVASSP---QFIALNALSHLLSPDTT-HPRLSS   92 (425)
Q Consensus        20 ~~~~~~~~~~~l~~~~~~~a~~~~~~m~~~---~~~d~~~~~~ll~~~~~~~~---~~~a~~~~~~~l~~~~~-~~~~~~   92 (425)
                      +..+-+.+|..+..|+.++|.++|+.....   ..++....+.++..|.+...   ...+..+...+-..+.. .-+...
T Consensus       376 ~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  455 (987)
T PRK09782        376 LTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLP  455 (987)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhhh
Confidence            333445689999999999999999998874   44466677799999999866   44444443222111100 001111


Q ss_pred             h---HHHHHHHhhhcCCCcc--CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCccc
Q 042756           93 L---AFPLYMRITEESWFQW--NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRG  167 (425)
Q Consensus        93 ~---a~~lf~~m~~~~~~~~--~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~  167 (425)
                      +   +...+.......  +.  +...|..+-.++.. ++.++|...|.+.....    |+.. ....+...+...|++  
T Consensus       456 ~~~~~~~~~~~al~~~--p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~----Pd~~-~~L~lA~al~~~Gr~--  525 (987)
T PRK09782        456 GIADNCPAIVRLLGDM--SPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ----PDAW-QHRAVAYQAYQVEDY--  525 (987)
T ss_pred             hhhhhHHHHHHhcccC--CCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC----CchH-HHHHHHHHHHHCCCH--
Confidence            1   222233322211  12  55666666666665 77888888777766542    1211 122233444577884  


Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERI  246 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~  246 (425)
                       +++...+.+....    .|+...+..+..++.+.|++++|...|++..+..  |+ ...+..+.....+.|++++|...
T Consensus       526 -eeAi~~~rka~~~----~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~eAl~~  598 (987)
T PRK09782        526 -ATALAAWQKISLH----DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGDNALYWWLHAQRYIPGQPELALND  598 (987)
T ss_pred             -HHHHHHHHHHhcc----CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHhCCCHHHHHHH
Confidence             4444444444322    1233356666777888888888888888887753  43 33333444445566888888888


Q ss_pred             HHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHHHHHHHHh
Q 042756          247 VNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       247 ~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~~~~~~~~~~~~  313 (425)
                      ++...+.  .|+...|..+...+.+.|+.++|+..|++..+.  .|+. ..++.+-..+...|+.+++
T Consensus       599 ~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeA  662 (987)
T PRK09782        599 LTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQS  662 (987)
T ss_pred             HHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHH
Confidence            8887765  366778888888888888888888888887765  4544 4555555566666665544

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

Probab=99.04  E-value=8e-07  Score=85.30  Aligned_cols=251  Identities=13%  Similarity=0.062  Sum_probs=185.0

Q ss_pred             HhhHHHHHHHHHHhHHhcCCC-HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC-------------CCchhhhHHHHH
Q 042756           33 ARLTKQGQRFLSSLALAVTRD-SKAASRLISKFVASSPQFIALNALSHLLSPDTT-------------HPRLSSLAFPLY   98 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d-~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~-------------~~~~~~~a~~lf   98 (425)
                      +|.+-.|++.|++.... .|+ ..+|-.|-..|...+.++.|...+.+.+.....             ..|.+|.|+.-|
T Consensus       231 ~Gei~~aiq~y~eAvkl-dP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Y  309 (966)
T KOG4626|consen  231 QGEIWLAIQHYEEAVKL-DPNFLDAYINLGNVYKEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTY  309 (966)
T ss_pred             cchHHHHHHHHHHhhcC-CCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHH
Confidence            45667777777776543 443 578888888999999999999988888654332             335788899999


Q ss_pred             HHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756           99 MRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus        99 ~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      ++-.+...-  =+..|+.|-.++-..|++.+|+..|.+...- .+...+   .-+.|-+.|...|.++   ++..++...
T Consensus       310 kral~~~P~--F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l-~p~had---am~NLgni~~E~~~~e---~A~~ly~~a  380 (966)
T KOG4626|consen  310 KRALELQPN--FPDAYNNLANALKDKGSVTEAVDCYNKALRL-CPNHAD---AMNNLGNIYREQGKIE---EATRLYLKA  380 (966)
T ss_pred             HHHHhcCCC--chHHHhHHHHHHHhccchHHHHHHHHHHHHh-CCccHH---HHHHHHHHHHHhccch---HHHHHHHHH
Confidence            887654421  2457999999999999999999999886643 222322   4578888898888854   444444444


Q ss_pred             hhcCCCCccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          179 VNSSSSVYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG-FEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       179 ~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ..    +.|. ...+|.|-..|-..|++++|+..|++..+  +.|+. ..|+.+-+.|-..|+++.|.+.+...+..+  
T Consensus       381 l~----v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~n--  452 (966)
T KOG4626|consen  381 LE----VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQIN--  452 (966)
T ss_pred             Hh----hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcC--
Confidence            32    3343 24788899999999999999999998877  78874 489999999999999999999988877653  


Q ss_pred             cC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHH
Q 042756          257 VD-TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR-TYNSVLNS  303 (425)
Q Consensus       257 ~~-~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~-t~~~ll~~  303 (425)
                      |. ....+.|-..|-..|++.+|++-|++..+  ++||.. .|-.++.+
T Consensus       453 Pt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~cNllh~  499 (966)
T KOG4626|consen  453 PTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPDAYCNLLHC  499 (966)
T ss_pred             cHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCchhhhHHHHH
Confidence            43 67888899999999999999999998765  467653 34444443

>PF12854 PPR_1: PPR repeat

Probab=99.03  E-value=3.1e-10  Score=67.33  Aligned_cols=33  Identities=18%  Similarity=0.326  Sum_probs=22.4

Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM  285 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M  285 (425)
                      +|+.||..|||+||.+||+.|++++|.++|++|
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            366666666666666666666666666666666

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.99  E-value=2.7e-06  Score=89.16  Aligned_cols=105  Identities=10%  Similarity=-0.034  Sum_probs=70.7

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC------------chhhhHHHH
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP------------RLSSLAFPL   97 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~------------~~~~~a~~l   97 (425)
                      ....|.+.+|.++|+.....-+.+...+..+...+...|+.+.|...+.+.+......+            +..++|+..
T Consensus        59 ~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P~~~~~~~la~~l~~~g~~~~Al~~  138 (765)
T PRK10049         59 YRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAKQLVSGAPDKANLLALAYVYKRAGRHWDELRA  138 (765)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHCCCHHHHHHH
Confidence            34556788888888887766455566777788888888888888888888876543322            235667778


Q ss_pred             HHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 042756           98 YMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILE  136 (425)
Q Consensus        98 f~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~  136 (425)
                      +++..+...  -+...+..+...+.+.|..+.|.+.++.
T Consensus       139 l~~al~~~P--~~~~~~~~la~~l~~~~~~e~Al~~l~~  175 (765)
T PRK10049        139 MTQALPRAP--QTQQYPTEYVQALRNNRLSAPALGAIDD  175 (765)
T ss_pred             HHHHHHhCC--CCHHHHHHHHHHHHHCCChHHHHHHHHh
Confidence            877766541  2444555566666666777766666653

>TIGR00540 hemY_coli hemY protein

Probab=98.97  E-value=1.3e-06  Score=84.82  Aligned_cols=273  Identities=7%  Similarity=-0.046  Sum_probs=185.7

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCC-HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC--------------Cchhh
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRD-SKAASRLISKFVASSPQFIALNALSHLLSPDTTH--------------PRLSS   92 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d-~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~--------------~~~~~   92 (425)
                      .-.+..|+++.|++.+....+. .|+ ...|-..-.+....|+.+.+...+.+........              .+..+
T Consensus        92 lla~~~g~~~~A~~~l~~~~~~-~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~  170 (409)
T TIGR00540        92 LLKLAEGDYAKAEKLIAKNADH-AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELH  170 (409)
T ss_pred             HHHHhCCCHHHHHHHHHHHhhc-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHH
Confidence            3346677999999999776554 454 3444555677777899999999999975543221              24578


Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH---HhcCCcccHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSF---CKHDSKRGFD  169 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~---~~~g~~~~~~  169 (425)
                      .|...++.+.+...  -++.+...+...+.+.|++++|.+++..+.+.+...+....   ..-..++   ...+..+   
T Consensus       171 ~Al~~l~~l~~~~P--~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~---~l~~~a~~~~l~~~~~~---  242 (409)
T TIGR00540       171 AARHGVDKLLEMAP--RHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFA---DLEQKAEIGLLDEAMAD---  242 (409)
T ss_pred             HHHHHHHHHHHhCC--CCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHH---HHHHHHHHHHHHHHHHh---
Confidence            89999999988752  26678889999999999999999999999987554333211   1111111   2222211   


Q ss_pred             HHHHHHHHHhhcCCC-CccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHH---HHHHHHHHHcCCCHHHHHH
Q 042756          170 DTYARLNQLVNSSSS-VYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFE---YKCIIYGYGRLGLLEDMER  245 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t---y~~ll~~~~~~g~~~~a~~  245 (425)
                      +..+.+.+.....+. ...+...+-.+...+...|+.++|.+++++..+.  .||...   .....-.....++.+.+.+
T Consensus       243 ~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~~~~~  320 (409)
T TIGR00540       243 EGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNEKLEK  320 (409)
T ss_pred             cCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChHHHHH
Confidence            111222222221110 1124568899999999999999999999999985  454432   1222222344578888999


Q ss_pred             HHHHHHHCCCCcCH---HhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          246 IVNQMESDGTRVDT---VCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       246 ~~~~m~~~g~~~~~---~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .++...+.  .|+.   ....++-..+.+.|++++|.+.|+........||...+..+...+.+.|+.+.+
T Consensus       321 ~~e~~lk~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A  389 (409)
T TIGR00540       321 LIEKQAKN--VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEA  389 (409)
T ss_pred             HHHHHHHh--CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHH
Confidence            99877664  3443   556688889999999999999999655545589999999998888887776554

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.96  E-value=3.9e-07  Score=80.56  Aligned_cols=193  Identities=12%  Similarity=0.066  Sum_probs=143.8

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .....+..+...+...|++++|.+.+++..+..    +.....+..+...+...|+++.+.+.++...+..+      .+
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~----p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~------~~   98 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHD----PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNP------NN   98 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC------CC
Confidence            456678888999999999999999999987642    22234677788889999995554444444433321      23


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      ...+..+...+...|++++|.+.|++.......| ....+..+...+.+.|++++|.+.++...+.. +.+...+..+..
T Consensus        99 ~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~  177 (234)
T TIGR02521        99 GDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAE  177 (234)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHH
Confidence            3478888999999999999999999998753323 34567778888999999999999999988753 225678889999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .+...|++++|...+++..+. ...+...+..+...+...|+...+
T Consensus       178 ~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a  222 (234)
T TIGR02521       178 LYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAA  222 (234)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHH
Confidence            999999999999999998876 234455665566666555655443

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.

>PF12854 PPR_1: PPR repeat

Probab=98.95  E-value=9.2e-10  Score=65.27  Aligned_cols=34  Identities=26%  Similarity=0.607  Sum_probs=24.3

Q ss_pred             cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          218 KGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       218 ~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      +|+.||.+|||+||++||+.|++++|.++|++|+
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            3667777777777777777777777777777663

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

Probab=98.93  E-value=3.5e-06  Score=74.98  Aligned_cols=264  Identities=12%  Similarity=0.115  Sum_probs=156.0

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC-----------------Cch
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH-----------------PRL   90 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~-----------------~~~   90 (425)
                      .+.+++...+.|.++|-.|.+.-+-+..+--+|=+.|-+.|..+.|..+-...+.+-...                 .|.
T Consensus        43 lNfLLs~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl  122 (389)
T COG2956          43 LNFLLSNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGL  122 (389)
T ss_pred             HHHHhhcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhh
Confidence            677888899999999999987533445555567777777888888888777766543321                 234


Q ss_pred             hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHHHHhcCCcccHH
Q 042756           91 SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRE-RELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~-~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      +|.|+.+|..+...+.+  -....-.|+..|-...+|++|.++-+++.+.++.+. ......|.-|-..+.-..+   .+
T Consensus       123 ~DRAE~~f~~L~de~ef--a~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~---~d  197 (389)
T COG2956         123 LDRAEDIFNQLVDEGEF--AEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSD---VD  197 (389)
T ss_pred             hhHHHHHHHHHhcchhh--hHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhh---HH
Confidence            67777777776664434  333455677777777777777777776665433322 1222334444444433444   44


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      .+...+.+.......+.   ..=-.+-+.+...|++++|.+.++...+.+..--..+...+..+|...|+.++....+..
T Consensus       198 ~A~~~l~kAlqa~~~cv---RAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~  274 (389)
T COG2956         198 RARELLKKALQADKKCV---RASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRR  274 (389)
T ss_pred             HHHHHHHHHHhhCccce---ehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            45555555544443321   111122344566677777777777777765444455667777777777777777777777


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS  303 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~  303 (425)
                      +.+..  ++...-++|-+--....-.+.|...+.+-...  +|+..-+.-+|..
T Consensus       275 ~~~~~--~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~  324 (389)
T COG2956         275 AMETN--TGADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDY  324 (389)
T ss_pred             HHHcc--CCccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHh
Confidence            66642  22223333333333333345555555554433  5777766666654

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.93  E-value=1e-06  Score=85.63  Aligned_cols=258  Identities=13%  Similarity=0.052  Sum_probs=179.2

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHh-------cCCCHHHHHH-HHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHH
Q 042756           28 VQCLTARLTKQGQRFLSSLALA-------VTRDSKAASR-LISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYM   99 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~-------~~~d~~~~~~-ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~   99 (425)
                      ..+..+|+++.|++++++....       ..|++.+... +-..|...+++.+|..++.+              |+.+++
T Consensus       207 ~~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  207 EMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEE--------------ALTIRE  272 (508)
T ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHH--------------HHHHHH
Confidence            4556788999999999887765       2344433322 44556666777777766666              445555


Q ss_pred             HhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHH----hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756          100 RITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLS----KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus       100 ~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~----~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                      .....+ -+--+.+++.|-..|.+.|++++|...+++..+    ..+...+.....++.+...++..++++.+...+...
T Consensus       273 ~~~G~~-h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~a  351 (508)
T KOG1840|consen  273 EVFGED-HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKA  351 (508)
T ss_pred             HhcCCC-CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence            554443 223445788888899999999999998887654    233345555556677888888889877666655555


Q ss_pred             HHHhhcCCCCccC----hhHHHHHHHHHHhcCChhHHHHHHHHHHHcC------CCC-CHHHHHHHHHHHHcCCCHHHHH
Q 042756          176 NQLVNSSSSVYVK----RQALKSMISGLCEMGQPHEAENLIEEMRVKG------LEP-SGFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       176 ~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g------~~p-~~~ty~~ll~~~~~~g~~~~a~  244 (425)
                      .+.....  +.++    ..+++.|-..|...|++++|.++|++.....      ..+ ....++.|-.+|.+.+...+|.
T Consensus       352 l~i~~~~--~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~  429 (508)
T KOG1840|consen  352 LKIYLDA--PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAE  429 (508)
T ss_pred             HHHHHhh--ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHH
Confidence            5544422  2222    2599999999999999999999999987541      223 3557888999999999999999


Q ss_pred             HHHHHHHH----CCC--CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH---h---CCCCCCHHHHHHHHH
Q 042756          245 RIVNQMES----DGT--RVDTVCSNMVLSSYGDHNELSRMVLWLQKMK---D---SGIPFSVRTYNSVLN  302 (425)
Q Consensus       245 ~~~~~m~~----~g~--~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~---~---~g~~pd~~t~~~ll~  302 (425)
                      ++|.+-..    .|.  +-...+|-.|...|.+.|++++|+++.+...   +   .+..|+.........
T Consensus       430 ~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  499 (508)
T KOG1840|consen  430 QLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLNAREQRLGTASPTVEDEKLRLA  499 (508)
T ss_pred             HHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcCCCCCcchhHHHHhhh
Confidence            99987543    332  1236889999999999999999999988764   2   233455555444443

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.92  E-value=8.1e-07  Score=78.48  Aligned_cols=202  Identities=10%  Similarity=0.059  Sum_probs=146.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      ....+..+...+...|+++.|...+.+.+                     ..+  +.+...+..+...+...|++++|.+
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l---------------------~~~--p~~~~~~~~la~~~~~~~~~~~A~~   86 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKAL---------------------EHD--PDDYLAYLALALYYQQLGELEKAED   86 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------HhC--cccHHHHHHHHHHHHHcCCHHHHHH
Confidence            34566667777777776666666555543                     222  1245677788889999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      .|++..+.... .   ...+..+...+...|++   +++...+.+...... .......+..+..++...|++++|...|
T Consensus        87 ~~~~al~~~~~-~---~~~~~~~~~~~~~~g~~---~~A~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~  158 (234)
T TIGR02521        87 SFRRALTLNPN-N---GDVLNNYGTFLCQQGKY---EQAMQQFEQAIEDPL-YPQPARSLENAGLCALKAGDFDKAEKYL  158 (234)
T ss_pred             HHHHHHhhCCC-C---HHHHHHHHHHHHHcccH---HHHHHHHHHHHhccc-cccchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99988765322 2   22566778888889984   445555555443211 1112346777888899999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ++..... +.+...+..+...+...|++++|.+.+++..+. ...+...+..+...+...|+.++|..+.+.+..
T Consensus       159 ~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       159 TRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            9988753 224668888899999999999999999998876 344667778888899999999999998887764

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.

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

Probab=98.88  E-value=1.5e-07  Score=90.90  Aligned_cols=268  Identities=10%  Similarity=-0.036  Sum_probs=191.5

Q ss_pred             hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHH
Q 042756           91 SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDD  170 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~  170 (425)
                      ..+|..+|..+...  +.-+..+...+-.+|...+++++|+.+|+...+.......+ ...|.+.+=-+-+.=.   +..
T Consensus       335 ~~~A~~~~~klp~h--~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~-meiyST~LWHLq~~v~---Ls~  408 (638)
T KOG1126|consen  335 CREALNLFEKLPSH--HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKG-MEIYSTTLWHLQDEVA---LSY  408 (638)
T ss_pred             HHHHHHHHHhhHHh--cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccc-hhHHHHHHHHHHhhHH---HHH
Confidence            57788888885543  33355677778899999999999999999998753332222 3356666544433211   233


Q ss_pred             HHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          171 TYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       171 ~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      ..+.+-+..+..    |.  +|.++-++|.-.++.+.|++.|++..+  +.| ..++|+-+-.-+....++|.|...|+.
T Consensus       409 Laq~Li~~~~~s----Pe--sWca~GNcfSLQkdh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~  480 (638)
T KOG1126|consen  409 LAQDLIDTDPNS----PE--SWCALGNCFSLQKDHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRK  480 (638)
T ss_pred             HHHHHHhhCCCC----cH--HHHHhcchhhhhhHHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHh
Confidence            333333333322    33  999999999999999999999999987  456 678999888888999999999999987


Q ss_pred             HHHCCCCcCHHhHHHHH---HHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHhhc---------c
Q 042756          250 MESDGTRVDTVCSNMVL---SSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQDLN---------S  316 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li---~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~~~---------~  316 (425)
                      ...    .|...||++-   -.|.+.++.+.|+-.|++..+-  .| +.+....+...+-+.|.-+++++         .
T Consensus       481 Al~----~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~I--NP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~  554 (638)
T KOG1126|consen  481 ALG----VDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEI--NPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDP  554 (638)
T ss_pred             hhc----CCchhhHHHHhhhhheeccchhhHHHHHHHhhhcC--CccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCC
Confidence            665    5788888865   5688999999999999998764  45 44555666666677777777643         3


Q ss_pred             CCchhhHH---HHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          317 NDFPLSIL---ELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       317 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ....+..+   .+...+..+++.+..|.++....-+..+|-.+-..|.+.|+.+.|     +.-|--|.+
T Consensus       555 kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~A-----l~~f~~A~~  619 (638)
T KOG1126|consen  555 KNPLCKYHRASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLA-----LLHFSWALD  619 (638)
T ss_pred             CCchhHHHHHHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHH-----HHhhHHHhc
Confidence            33334444   345555566666666666665555667788888999999999999     777766655

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.87  E-value=2.8e-06  Score=88.12  Aligned_cols=367  Identities=11%  Similarity=0.045  Sum_probs=231.7

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCH--HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC-------------CCchhh
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDS--KAASRLISKFVASSPQFIALNALSHLLSPDTT-------------HPRLSS   92 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~--~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~-------------~~~~~~   92 (425)
                      .....+|+...|++.|++..+. .|+.  ..+ .++..+...|+.+.|...+.+.+.+...             ..+.++
T Consensus        42 ii~~r~Gd~~~Al~~L~qaL~~-~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd  119 (822)
T PRK14574         42 IIRARAGDTAPVLDYLQEESKA-GPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWD  119 (822)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhh-CccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHH
Confidence            4446677899999999998876 3432  333 8888888999999999999998844322             113578


Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      +|+++|+++.+.+.-  |+..+..++..+...++.++|++.++++...    .+. ...|  +..++...+ ..+..+++
T Consensus       120 ~Aiely~kaL~~dP~--n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~----dp~-~~~~--l~layL~~~-~~~~~~AL  189 (822)
T PRK14574        120 QALALWQSSLKKDPT--NPDLISGMIMTQADAGRGGVVLKQATELAER----DPT-VQNY--MTLSYLNRA-TDRNYDAL  189 (822)
T ss_pred             HHHHHHHHHHhhCCC--CHHHHHHHHHHHhhcCCHHHHHHHHHHhccc----Ccc-hHHH--HHHHHHHHh-cchHHHHH
Confidence            999999999887633  4566677889999999999999999998764    222 2234  334544433 22244467


Q ss_pred             HHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHH---------------------------------------
Q 042756          173 ARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE---------------------------------------  213 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~---------------------------------------  213 (425)
                      ..++++....+.   +...+.-++.+..+.|-...|.++..                                       
T Consensus       190 ~~~ekll~~~P~---n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~  266 (822)
T PRK14574        190 QASSEAVRLAPT---SEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDI  266 (822)
T ss_pred             HHHHHHHHhCCC---CHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHH
Confidence            777776654321   22345555555555554444433333                                       


Q ss_pred             ---------HHHHc-CCCCCHH-----HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHH
Q 042756          214 ---------EMRVK-GLEPSGF-----EYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRM  278 (425)
Q Consensus       214 ---------~m~~~-g~~p~~~-----ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A  278 (425)
                               .+... +-.|...     ..--.+-++.+.|+..++.+-++.+...|.+....+--.+.++|...+++++|
T Consensus       267 ~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA  346 (822)
T PRK14574        267 ADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKA  346 (822)
T ss_pred             HHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHH
Confidence                     22221 1223211     22234567888999999999999999888776677888999999999999999


Q ss_pred             HHHHHHHHhCC-----CCCCHHHHHHHHHHHHHHHHHHHhhc------c-CCc----------------h----hhHHHH
Q 042756          279 VLWLQKMKDSG-----IPFSVRTYNSVLNSCSTIMSMLQDLN------S-NDF----------------P----LSILEL  326 (425)
Q Consensus       279 ~~l~~~M~~~g-----~~pd~~t~~~ll~~~~~~~~~~~~~~------~-~~~----------------~----~~~~~~  326 (425)
                      +.+|+......     ..++......|.-++...++++++..      . ..+                .    ..+..+
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            99999986532     22344446778888888888777732      1 111                0    012234


Q ss_pred             HhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeecc-ccc
Q 042756          327 TEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGS-GKH  405 (425)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~-~~~  405 (425)
                      ...+..+.++...+-+...-.-|...+..+-..+...|++.+|     .+.++....       +.|+........ .+.
T Consensus       427 ~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A-----~~~~k~a~~-------l~P~~~~~~~~~~~~a  494 (822)
T PRK14574        427 VALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKA-----EQELKAVES-------LAPRSLILERAQAETA  494 (822)
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHH-----HHHHHHHhh-------hCCccHHHHHHHHHHH
Confidence            4555555554333333222224556777777888888999888     888855543       466654433222 233


Q ss_pred             cccccchHHHHHHHHH
Q 042756          406 STVRGESSVKAMVKKM  421 (425)
Q Consensus       406 ~~~~~~~~~~~~~~~~  421 (425)
                      ...+.....+.++++.
T Consensus       495 l~l~e~~~A~~~~~~l  510 (822)
T PRK14574        495 MALQEWHQMELLTDDV  510 (822)
T ss_pred             HhhhhHHHHHHHHHHH
Confidence            3334444444444443

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

Probab=98.87  E-value=9.5e-08  Score=94.85  Aligned_cols=227  Identities=11%  Similarity=0.102  Sum_probs=149.1

Q ss_pred             HHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHH----HHHhhhcCCCccCHHHHH
Q 042756           41 RFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPL----YMRITEESWFQWNPKLVA  115 (425)
Q Consensus        41 ~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~l----f~~m~~~~~~~~~~~~~~  115 (425)
                      .++..+... +.|+.+||.++|..||..|+.+.|- +|.-|-.+.....+.+-.++..    -.++..+.  .|.+.+|.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk--ep~aDtyt   87 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK--EPLADTYT   87 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC--CCchhHHH
Confidence            456666667 9999999999999999999988877 7766655544333221111111    01233333  47889999


Q ss_pred             HHHHHHHhcCChh---HHHHHHHHHHHh---cCCCchhH---------------H----------HHHHHHHHHHHhcCC
Q 042756          116 EIIAFLDKQGQRE---EAETLILETLSK---LGSREREL---------------V----------LFYCNLIDSFCKHDS  164 (425)
Q Consensus       116 ~ll~~~~~~g~~~---~A~~l~~~m~~~---~~~~~~~~---------------~----------~~y~~li~~~~~~g~  164 (425)
                      .|+.+|.+.||+.   .+++.+..+...   .+..++..               .          ..|.-++..+.+...
T Consensus        88 ~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pv  167 (1088)
T KOG4318|consen   88 NLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPV  167 (1088)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCc
Confidence            9999999999854   444433332221   01111110               0          011112222211100


Q ss_pred             c--ccHHH-----------HHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042756          165 K--RGFDD-----------TYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII  231 (425)
Q Consensus       165 ~--~~~~~-----------~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll  231 (425)
                      .  ..-..           -++.+..+...... .|+..+|.+++.+-..+|+.+.|..+..+|+++|+..+.+-|-.++
T Consensus       168 sa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e-~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl  246 (1088)
T KOG4318|consen  168 SAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVE-APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLL  246 (1088)
T ss_pred             ccccchHHHHHHHhccCCchHHHHHHHHHHhhc-CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhh
Confidence            0  00000           01122222222222 4788899999999999999999999999999999999999888887


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          232 YGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      .+   .++...++.+...|.+.|+.|+..||...+-.+..+|.
T Consensus       247 ~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  247 LG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             hc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            76   88999999999999999999999999999998888666

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.85  E-value=4e-06  Score=80.97  Aligned_cols=238  Identities=8%  Similarity=0.013  Sum_probs=174.4

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHH--HHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHH
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAAS--RLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAF   95 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~--~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~   95 (425)
                      ...|+.+.|.+.|..+.+. .||...+-  .....+...|+++.|...+.+........+             +.+++|.
T Consensus       129 ~~~g~~~~A~~~l~~A~~~-~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~  207 (398)
T PRK10747        129 QQRGDEARANQHLERAAEL-ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLL  207 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhc-CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHH
Confidence            5667888999999998764 45543332  446678888999999999999987766554             3578899


Q ss_pred             HHHHHhhhcCCCccCH------HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           96 PLYMRITEESWFQWNP------KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        96 ~lf~~m~~~~~~~~~~------~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      +++..+.+.....+..      ..|..++..-.+..+.+...++++.+.+.. +..+   .....+..++...|+   .+
T Consensus       208 ~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~-~~~~---~~~~~~A~~l~~~g~---~~  280 (398)
T PRK10747        208 DILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKT-RHQV---ALQVAMAEHLIECDD---HD  280 (398)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHH-hCCH---HHHHHHHHHHHHCCC---HH
Confidence            9999998887553332      123334444444455666666666654432 1222   245778899999999   56


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVN  248 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~  248 (425)
                      ++...+.+.....    ||  .--.++.+....++.+++++..+...+.  .|+ ...+..+-..|.+.|++++|.+.|+
T Consensus       281 ~A~~~L~~~l~~~----~~--~~l~~l~~~l~~~~~~~al~~~e~~lk~--~P~~~~l~l~lgrl~~~~~~~~~A~~~le  352 (398)
T PRK10747        281 TAQQIILDGLKRQ----YD--ERLVLLIPRLKTNNPEQLEKVLRQQIKQ--HGDTPLLWSTLGQLLMKHGEWQEASLAFR  352 (398)
T ss_pred             HHHHHHHHHHhcC----CC--HHHHHHHhhccCCChHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            6666666665432    22  2233456666779999999999999875  454 5568888999999999999999999


Q ss_pred             HHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          249 QMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       249 ~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                      ...+.  .|+..+|-.|...+.+.|+.++|.++|++-.
T Consensus       353 ~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        353 AALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99876  5999999999999999999999999999764

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

Probab=98.85  E-value=5.5e-08  Score=89.43  Aligned_cols=220  Identities=12%  Similarity=0.100  Sum_probs=98.5

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCH
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNP  111 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~  111 (425)
                      ..++.+.|.+.++.+....+-+...+..++.. ...+++..|..++.....+                     .   +++
T Consensus        56 ~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~---------------------~---~~~  110 (280)
T PF13429_consen   56 SLGDYDEAIEAYEKLLASDKANPQDYERLIQL-LQDGDPEEALKLAEKAYER---------------------D---GDP  110 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccc-ccccccccccccccccccc---------------------c---ccc
Confidence            34577788888888876633356667777776 5666666666555554321                     1   345


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..+..++..+.+.++++++.+++++.......+  .....|..+...+.+.|+.+.+.+.++...+..+.      |...
T Consensus       111 ~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~--~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~------~~~~  182 (280)
T PF13429_consen  111 RYLLSALQLYYRLGDYDEAEELLEKLEELPAAP--DSARFWLALAEIYEQLGDPDKALRDYRKALELDPD------DPDA  182 (280)
T ss_dssp             -------H-HHHTT-HHHHHHHHHHHHH-T-----T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-------HHH
T ss_pred             chhhHHHHHHHHHhHHHHHHHHHHHHHhccCCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC------CHHH
Confidence            556668888888899999999999877532222  22345777778888889855444444444444222      2347


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      .+.++..+...|+.+++.++++...... ..|...+..+-.+|...|+.++|...|+...+.. +.|......+.+++..
T Consensus       183 ~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~  260 (280)
T PF13429_consen  183 RNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQ  260 (280)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT-
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-cccccccccccccccc
Confidence            8888999999999999888888887764 4455677888888999999999999999877643 2377888888899999


Q ss_pred             cCCHHHHHHHHHHHH
Q 042756          272 HNELSRMVLWLQKMK  286 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~  286 (425)
                      .|+.++|.++..+..
T Consensus       261 ~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  261 AGRKDEALRLRRQAL  275 (280)
T ss_dssp             ---------------
T ss_pred             ccccccccccccccc
Confidence            999999998877653

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.84  E-value=4.9e-06  Score=88.14  Aligned_cols=245  Identities=9%  Similarity=-0.019  Sum_probs=164.8

Q ss_pred             HHHHhhHHHHHHHHHHhHHh---cCC--CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC------------CCchhh
Q 042756           30 CLTARLTKQGQRFLSSLALA---VTR--DSKAASRLISKFVASSPQFIALNALSHLLSPDTT------------HPRLSS   92 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~---~~~--d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~------------~~~~~~   92 (425)
                      |...|....+...++.....   -++  +...|..+-.++.. +....|...+.+.+.....            ..+.++
T Consensus       448 ~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~Pd~~~~L~lA~al~~~Gr~e  526 (987)
T PRK09782        448 RQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQPDAWQHRAVAYQAYQVEDYA  526 (987)
T ss_pred             HHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhCCchHHHHHHHHHHHHCCCHH
Confidence            44455555555555555444   234  66777777777766 5666777766665443221            123477


Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      +|...|+.+....   |+...+..+...+.+.|++++|.+.|++..+..    ++....+..+.....+.|+   .+++.
T Consensus       527 eAi~~~rka~~~~---p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~----P~~~~l~~~La~~l~~~Gr---~~eAl  596 (987)
T PRK09782        527 TALAAWQKISLHD---MSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG----LGDNALYWWLHAQRYIPGQ---PELAL  596 (987)
T ss_pred             HHHHHHHHHhccC---CCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----CccHHHHHHHHHHHHhCCC---HHHHH
Confidence            7888888764432   333445556777888899999999998887642    1111123333334445588   45555


Q ss_pred             HHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          173 ARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      ..+.+...    ..|+...|..+-..+.+.|++++|...|++....  .| +...++.+-.++...|+.++|...++...
T Consensus       597 ~~~~~AL~----l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL  670 (987)
T PRK09782        597 NDLTRSLN----IAPSANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREMLERAH  670 (987)
T ss_pred             HHHHHHHH----hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55555543    2345568888889999999999999999998875  45 45577777788999999999999999887


Q ss_pred             HCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          252 SDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       252 ~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      +..- -+...+..+-.++...|++++|+..|++..+.  .|+.
T Consensus       671 ~l~P-~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l--~P~~  710 (987)
T PRK09782        671 KGLP-DDPALIRQLAYVNQRLDDMAATQHYARLVIDD--IDNQ  710 (987)
T ss_pred             HhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCC
Confidence            7532 35778888999999999999999999988754  3543

>PRK12370 invasion protein regulator; Provisional

Probab=98.82  E-value=3.7e-06  Score=84.77  Aligned_cols=242  Identities=8%  Similarity=-0.026  Sum_probs=153.0

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHH
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLV  114 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~  114 (425)
                      ..++|.++|++..+.-+-+...|..+-.++...+...            .....+..++|...+++..+.+.  -++..+
T Consensus       276 ~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g------------~~~~~~~~~~A~~~~~~Al~ldP--~~~~a~  341 (553)
T PRK12370        276 SLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMG------------IFDKQNAMIKAKEHAIKATELDH--NNPQAL  341 (553)
T ss_pred             HHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcC------------CcccchHHHHHHHHHHHHHhcCC--CCHHHH
Confidence            3456777777766542223445554444333221100            00122356778888888766552  266777


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      ..+-..+...|++++|...|++..+..    |+....+..+-..+...|++   +++...+.+...-.+. .|  ..+..
T Consensus       342 ~~lg~~~~~~g~~~~A~~~~~~Al~l~----P~~~~a~~~lg~~l~~~G~~---~eAi~~~~~Al~l~P~-~~--~~~~~  411 (553)
T PRK12370        342 GLLGLINTIHSEYIVGSLLFKQANLLS----PISADIKYYYGWNLFMAGQL---EEALQTINECLKLDPT-RA--AAGIT  411 (553)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHCCCH---HHHHHHHHHHHhcCCC-Ch--hhHHH
Confidence            778788889999999999999987752    22233567788889999995   4555555555433321 11  13344


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g  273 (425)
                      +...+...|++++|...+++..... .| +...+..+-.++...|+.++|...+..+.... .-+....+.+...|+..|
T Consensus       412 ~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        412 KLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             HHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHHHHHHHhccH
Confidence            4555677899999999999987653 34 34557777888899999999999999876542 124455666667778777


Q ss_pred             CHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHH
Q 042756          274 ELSRMVLWLQKMKD-SGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       274 ~~~~A~~l~~~M~~-~g~~pd~~t~~~ll~~~  304 (425)
                        ++|...++++.+ .+-.|...-+..++.++
T Consensus       490 --~~a~~~l~~ll~~~~~~~~~~~~~~~~~~~  519 (553)
T PRK12370        490 --ERALPTIREFLESEQRIDNNPGLLPLVLVA  519 (553)
T ss_pred             --HHHHHHHHHHHHHhhHhhcCchHHHHHHHH
Confidence              478887887754 22344444444444443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.80  E-value=1.2e-05  Score=83.63  Aligned_cols=341  Identities=10%  Similarity=-0.006  Sum_probs=195.4

Q ss_pred             hhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC------------chhhhHHHHHHHh
Q 042756           34 RLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP------------RLSSLAFPLYMRI  101 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~------------~~~~~a~~lf~~m  101 (425)
                      |+++.|.++|+.+.+..+-+...+..++..+...++.++|+..+.++....+...            ....+|++.++++
T Consensus       116 gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekl  195 (822)
T PRK14574        116 KRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEA  195 (822)
T ss_pred             CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHH
Confidence            5666666666666655333455555556666666666666666666655443211            1122355556665


Q ss_pred             hhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHH----HHHHHHHHH-----HhcCCcccHHHHH
Q 042756          102 TEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVL----FYCNLIDSF-----CKHDSKRGFDDTY  172 (425)
Q Consensus       102 ~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~----~y~~li~~~-----~~~g~~~~~~~~~  172 (425)
                      .+.+  +-+...+..++.++.+.|-...|.++..+-..-..  +.+...    ....+|+.-     ....++..++.++
T Consensus       196 l~~~--P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~--~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~al  271 (822)
T PRK14574        196 VRLA--PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVS--AEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKAL  271 (822)
T ss_pred             HHhC--CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccC--HHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHH
Confidence            5543  12455555566666666666666555444221100  000000    001111110     0122333456666


Q ss_pred             HHHHHHhhcCCCCccC----hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 042756          173 ARLNQLVNSSSSVYVK----RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVN  248 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~  248 (425)
                      ..+..+...-....+.    ....--.+-++...|+++++++-|+.+...|.+.-.++-..+.++|...+..++|+.++.
T Consensus       272 a~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~  351 (822)
T PRK14574        272 ADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILS  351 (822)
T ss_pred             HHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHH
Confidence            6666665432222121    123335667888899999999999999988866456788899999999999999999999


Q ss_pred             HHHHCC-----CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-------------CCCCHHH-HHHHHHHHHHHHH
Q 042756          249 QMESDG-----TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG-------------IPFSVRT-YNSVLNSCSTIMS  309 (425)
Q Consensus       249 ~m~~~g-----~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g-------------~~pd~~t-~~~ll~~~~~~~~  309 (425)
                      ......     ..++......|.-+|...+++++|..+++++.+..             -.||-.. +..+...+.-.|+
T Consensus       352 ~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gd  431 (822)
T PRK14574        352 SLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALND  431 (822)
T ss_pred             HHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCC
Confidence            886532     23345556788999999999999999999998621             1123232 2334455566666


Q ss_pred             HHHhhc-------cCCchhhHH-----HHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHH
Q 042756          310 MLQDLN-------SNDFPLSIL-----ELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQW  377 (425)
Q Consensus       310 ~~~~~~-------~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  377 (425)
                      +.++..       ...-++.+.     .+...+...++....+....-..-+..+.-.....+...|++.+|     ..+
T Consensus       432 l~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A-----~~~  506 (822)
T PRK14574        432 LPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQM-----ELL  506 (822)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHH-----HHH
Confidence            666532       111111111     344555556665444443333223345566677777888999998     777


Q ss_pred             HHHHHh
Q 042756          378 MDEMRN  383 (425)
Q Consensus       378 ~~~m~~  383 (425)
                      .++...
T Consensus       507 ~~~l~~  512 (822)
T PRK14574        507 TDDVIS  512 (822)
T ss_pred             HHHHHh
Confidence            766655

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

Probab=98.78  E-value=2.4e-06  Score=79.48  Aligned_cols=165  Identities=12%  Similarity=0.126  Sum_probs=137.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      .+.|...+-+.|+-.++.++|...|+...+-    .|.....|+.+-+-|........+-++++...++      ...|-
T Consensus       329 R~ETCCiIaNYYSlr~eHEKAv~YFkRALkL----Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi------~p~Dy  398 (559)
T KOG1155|consen  329 RPETCCIIANYYSLRSEHEKAVMYFKRALKL----NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDI------NPRDY  398 (559)
T ss_pred             CccceeeehhHHHHHHhHHHHHHHHHHHHhc----CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhc------CchhH
Confidence            3446777888999999999999999998763    4444567888999999998865566666665554      33456


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ..|-.+-.+|.-.+...-|+-.|++...  ++| |...|.+|-++|.+.++.++|++.|......|= .+...|..|-+.
T Consensus       399 RAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te~~~l~~LakL  475 (559)
T KOG1155|consen  399 RAWYGLGQAYEIMKMHFYALYYFQKALE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TEGSALVRLAKL  475 (559)
T ss_pred             HHHhhhhHHHHHhcchHHHHHHHHHHHh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cchHHHHHHHHH
Confidence            7999999999999999999999999887  566 688999999999999999999999999988763 366899999999


Q ss_pred             HHhcCCHHHHHHHHHHHHh
Q 042756          269 YGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~  287 (425)
                      |-+.++.++|.+.|.+-++
T Consensus       476 ye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  476 YEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHhHHHHHHHHHHHHH
Confidence            9999999999998887654

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.77  E-value=6.1e-06  Score=80.32  Aligned_cols=199  Identities=15%  Similarity=0.096  Sum_probs=148.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH----hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-CccCh-
Q 042756          116 EIIAFLDKQGQREEAETLILETLS----KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYVKR-  189 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~----~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p~~-  189 (425)
                      .+-..|...+++++|.-+|+++.+    ..+...+....+++.|-.+|.+.|+++++...++...+....... ..|.+ 
T Consensus       246 ~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~  325 (508)
T KOG1840|consen  246 ILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVA  325 (508)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHH
Confidence            356678888999999999999865    344556666778888888999999988877666655555444211 12332 


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc---CCCCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----C--C
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVK---GLEPS----GFEYKCIIYGYGRLGLLEDMERIVNQMESD-----G--T  255 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~----~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~-----g--~  255 (425)
                      .-++.+...|...+++++|..++.+..+.   -..++    ..+|+.|-..|-+.|++++|+++|+.....     |  .
T Consensus       326 ~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~  405 (508)
T KOG1840|consen  326 AQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKD  405 (508)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcC
Confidence            36777888888899999999999977653   12222    459999999999999999999999987642     1  1


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH----hCCC-CCCH-HHHHHHHHHHHHHHHHHHhh
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMK----DSGI-PFSV-RTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~----~~g~-~pd~-~t~~~ll~~~~~~~~~~~~~  314 (425)
                      .-....+|.|-..|.+.+..++|.++|.+-.    ..|. .||. .||..|...|...|+++.+.
T Consensus       406 ~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~  470 (508)
T KOG1840|consen  406 YGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAE  470 (508)
T ss_pred             hhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHH
Confidence            2235678889999999999999999999853    3332 3333 67888888888888887764

>PRK12370 invasion protein regulator; Provisional

Probab=98.75  E-value=4.3e-06  Score=84.31  Aligned_cols=204  Identities=11%  Similarity=-0.073  Sum_probs=136.3

Q ss_pred             chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHH---------hcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH
Q 042756           89 RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLD---------KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSF  159 (425)
Q Consensus        89 ~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~---------~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~  159 (425)
                      ...++|..+|++..+.+.-  ++..|..+-.++.         ..+++++|...+++..+.    .|+....+..+-..+
T Consensus       275 ~~~~~A~~~~~~Al~ldP~--~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l----dP~~~~a~~~lg~~~  348 (553)
T PRK12370        275 YSLQQALKLLTQCVNMSPN--SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL----DHNNPQALGLLGLIN  348 (553)
T ss_pred             HHHHHHHHHHHHHHhcCCc--cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc----CCCCHHHHHHHHHHH
Confidence            3567888888887765511  3445554444433         234578999999988764    222234567777778


Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCC
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG-FEYKCIIYGYGRLG  238 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~g  238 (425)
                      ...|+++++.+.++...+..+.      +...|..+-..+...|++++|...+++..+.  .|+. ..+..++..+...|
T Consensus       349 ~~~g~~~~A~~~~~~Al~l~P~------~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~~~~~~~~~~~~g  420 (553)
T PRK12370        349 TIHSEYIVGSLLFKQANLLSPI------SADIKYYYGWNLFMAGQLEEALQTINECLKL--DPTRAAAGITKLWITYYHT  420 (553)
T ss_pred             HHccCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHhcc
Confidence            8889955544444444443211      2347888889999999999999999999885  4542 23334455577789


Q ss_pred             CHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH-HHHHHHHHH
Q 042756          239 LLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNS-VLNSCSTIM  308 (425)
Q Consensus       239 ~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~-ll~~~~~~~  308 (425)
                      ++++|...+++..+..-.-+...+..+-..|...|+.++|...+.++...  .|+..+... +...++..|
T Consensus       421 ~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        421 GIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             CHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccH
Confidence            99999999998876532224556777888889999999999999987654  455444433 333445544

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

Probab=98.73  E-value=7.6e-06  Score=72.90  Aligned_cols=212  Identities=11%  Similarity=0.044  Sum_probs=94.2

Q ss_pred             ChHHHHHHHHhhhCCCCCC-------------CchhhhHHHHHHHhhhcCCCccCHHHH--HHHHHHHHhcCChhHHHHH
Q 042756           69 PQFIALNALSHLLSPDTTH-------------PRLSSLAFPLYMRITEESWFQWNPKLV--AEIIAFLDKQGQREEAETL  133 (425)
Q Consensus        69 ~~~~a~~~~~~~l~~~~~~-------------~~~~~~a~~lf~~m~~~~~~~~~~~~~--~~ll~~~~~~g~~~~A~~l  133 (425)
                      +.++|.+.|.+|+..+...             .|.+|.|+++...+.++...+.+-...  --|-.-|...|-+|.|+++
T Consensus        50 Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~  129 (389)
T COG2956          50 QPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDI  129 (389)
T ss_pred             CcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHH
Confidence            5566666666665433211             123455555555544332232222221  1233344455555555555


Q ss_pred             HHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHH
Q 042756          134 ILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE  213 (425)
Q Consensus       134 ~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  213 (425)
                      |..+.+.+...+.    .-..|+.-|-...+++++.++.+.+..+.+....+. =..-|.-+-..+....+++.|..++.
T Consensus       130 f~~L~de~efa~~----AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~e-IAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         130 FNQLVDEGEFAEG----ALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVE-IAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHhcchhhhHH----HHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhH-HHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            5555543222111    234455555555554444444444433322211100 00122222233333445555555555


Q ss_pred             HHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          214 EMRVKGLEPSGF-EYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       214 ~m~~~g~~p~~~-ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +..+.+  |+.+ .--.+-+.+...|+++.|.+.++...+.+...-..+-..|..+|...|+.++...++.++.+
T Consensus       205 kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~  277 (389)
T COG2956         205 KALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAME  277 (389)
T ss_pred             HHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            555432  2211 22222344555555555555555555554333445555555555555555555555555544

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

Probab=98.72  E-value=3.5e-05  Score=70.72  Aligned_cols=286  Identities=11%  Similarity=0.011  Sum_probs=187.8

Q ss_pred             CCCccccccccchhHH--HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-
Q 042756           12 PWNSRCCRLRQQRLTL--VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-   88 (425)
Q Consensus        12 ~~~~~~~~~~~~~~~~--~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-   88 (425)
                      +|.++.+..+......  --.+..|++.+|+++...-.+...-....|..-.++--..|+.+.+-..+.+.-...+... 
T Consensus        74 ~w~~~rKrrra~~~~~egl~~l~eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l  153 (400)
T COG3071          74 GWFSRRKRRRARKALNEGLLKLFEGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTL  153 (400)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchH
Confidence            3544444333333322  2336678999999999886555444556677777777788899999888888755422211 


Q ss_pred             -------------chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHH----HH
Q 042756           89 -------------RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELV----LF  151 (425)
Q Consensus        89 -------------~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~----~~  151 (425)
                                   +.++.|..-.+...+..  +-++.+......+|.+.|++..+..++.++.+.+...++...    .+
T Consensus       154 ~v~ltrarlll~~~d~~aA~~~v~~ll~~~--pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a  231 (400)
T COG3071         154 AVELTRARLLLNRRDYPAARENVDQLLEMT--PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQA  231 (400)
T ss_pred             HHHHHHHHHHHhCCCchhHHHHHHHHHHhC--cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHH
Confidence                         23455666666665554  236778999999999999999999999999987776554432    25


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042756          152 YCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII  231 (425)
Q Consensus       152 y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll  231 (425)
                      |..+++-....+.   .+.......+...+-   .-+...--+++.-+.++|+.++|.++.++-.+++.-|+..    .+
T Consensus       232 ~~glL~q~~~~~~---~~gL~~~W~~~pr~l---r~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~  301 (400)
T COG3071         232 WEGLLQQARDDNG---SEGLKTWWKNQPRKL---RNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RL  301 (400)
T ss_pred             HHHHHHHHhcccc---chHHHHHHHhccHHh---hcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HH
Confidence            5566665555555   444333444433221   1122266778888999999999999999999887766622    22


Q ss_pred             HHHHcCCCHHHHHHHHHHHH-HCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHH
Q 042756          232 YGYGRLGLLEDMERIVNQME-SDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSM  310 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~-~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~  310 (425)
                      -.+.+-++...-.+..+.-. ..+-.|  -.+.+|-..|.+.+.+.+|.+.|+...+  ..|+..+|+.+-.++.+.|+.
T Consensus       302 ~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~  377 (400)
T COG3071         302 IPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEP  377 (400)
T ss_pred             HhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCCh
Confidence            34455566655555555433 333333  5677777777788888888888885554  367888888888888777766


Q ss_pred             HHh
Q 042756          311 LQD  313 (425)
Q Consensus       311 ~~~  313 (425)
                      ..+
T Consensus       378 ~~A  380 (400)
T COG3071         378 EEA  380 (400)
T ss_pred             HHH
Confidence            655

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

Probab=98.70  E-value=2.6e-06  Score=82.65  Aligned_cols=266  Identities=9%  Similarity=0.026  Sum_probs=184.2

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-c--h---------hhhHH
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-R--L---------SSLAF   95 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-~--~---------~~~a~   95 (425)
                      |..+..-.+++|...|..+.....-+.-....+-.+|..-+.++++..+|...-......- +  .         -+-++
T Consensus       327 ~~~~s~y~~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~L  406 (638)
T KOG1126|consen  327 YRSLSQYNCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVAL  406 (638)
T ss_pred             HHHHHHHHHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHH
Confidence            4555556888899999995554333345556677788888899999999988743322110 0  0         01111


Q ss_pred             HHH-HHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 042756           96 PLY-MRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYAR  174 (425)
Q Consensus        96 ~lf-~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~  174 (425)
                      ..+ +++...+  +-.+.+|..+-++|+-+++.+.|++.|+...+.    ++....+|+.+-+-+.....   .+.+..-
T Consensus       407 s~Laq~Li~~~--~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl----dp~faYayTLlGhE~~~~ee---~d~a~~~  477 (638)
T KOG1126|consen  407 SYLAQDLIDTD--PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL----DPRFAYAYTLLGHESIATEE---FDKAMKS  477 (638)
T ss_pred             HHHHHHHHhhC--CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc----CCccchhhhhcCChhhhhHH---HHhHHHH
Confidence            111 1122222  235678999999999999999999999988763    55445566666666666555   4455555


Q ss_pred             HHHHhhcCCCCccChhHHH---HHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          175 LNQLVNSSSSVYVKRQALK---SMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       175 ~~~~~~~~~~~~p~~~~~~---~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                      ++..      +..|...||   .+--.|.|.++++.|+-.|+...+  +.| +.+....+...+-+.|+.++|.+++++.
T Consensus       478 fr~A------l~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A  549 (638)
T KOG1126|consen  478 FRKA------LGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKA  549 (638)
T ss_pred             HHhh------hcCCchhhHHHHhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHH
Confidence            5554      334444555   567789999999999999998877  556 5667778888899999999999999998


Q ss_pred             HHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHHh
Q 042756          251 ESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR-TYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       251 ~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~-t~~~ll~~~~~~~~~~~~  313 (425)
                      .-..-+ |..+---....+...++.++|+..|++.++.  .|+.. .|-.+-..|.+.|+-..+
T Consensus       550 ~~ld~k-n~l~~~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~A  610 (638)
T KOG1126|consen  550 IHLDPK-NPLCKYHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLA  610 (638)
T ss_pred             HhcCCC-CchhHHHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHH
Confidence            766543 5555555677778889999999999999874  77765 455555667776665554

>TIGR00540 hemY_coli hemY protein

Probab=98.68  E-value=3.5e-06  Score=81.80  Aligned_cols=192  Identities=10%  Similarity=0.014  Sum_probs=123.9

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHH-HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKL-VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~-~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      .++.|.+.+....+..   |++.. |-....+..+.|+.+.|.+.+.+..+...  .+. ....-.....+...|+++.+
T Consensus        99 ~~~~A~~~l~~~~~~~---~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p--~~~-l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        99 DYAKAEKLIAKNADHA---AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAG--NDN-ILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             CHHHHHHHHHHHhhcC---CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--cCc-hHHHHHHHHHHHHCCCHHHH
Confidence            6777777776654432   45433 33345666778999999999999876432  221 11223346677788996655


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH---HcCCCHHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGY---GRLGLLEDMER  245 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~---~~~g~~~~a~~  245 (425)
                      .+.++.+.+..+..      ..++..+...+...|++++|.+++....+.+..+.......-..++   ...+..+.+.+
T Consensus       173 l~~l~~l~~~~P~~------~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~  246 (409)
T TIGR00540       173 RHGVDKLLEMAPRH------KEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGID  246 (409)
T ss_pred             HHHHHHHHHhCCCC------HHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHH
Confidence            55555555543222      2488899999999999999999999999987543332211111222   22233333333


Q ss_pred             HHHHHHHCC---CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          246 IVNQMESDG---TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       246 ~~~~m~~~g---~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      .+..+.+..   .+.+...+-.+...+...|+.++|.+++++..+.  .||..
T Consensus       247 ~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~  297 (409)
T TIGR00540       247 GLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDR  297 (409)
T ss_pred             HHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcc
Confidence            444444331   1137889999999999999999999999999875  45543

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=98.60  E-value=0.00028  Score=71.12  Aligned_cols=276  Identities=13%  Similarity=0.022  Sum_probs=183.6

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhh--hCCCCC-----------CCchhhhHHHH
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHL--LSPDTT-----------HPRLSSLAFPL   97 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~--l~~~~~-----------~~~~~~~a~~l   97 (425)
                      ..+|+.++|.+++.++.+..+.....|-+|-..|-..|+.++++....-+  +.+...           ..+.++.|.-.
T Consensus       150 farg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~~c  229 (895)
T KOG2076|consen  150 FARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQARYC  229 (895)
T ss_pred             HHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHHHH
Confidence            44589999999999999987788899999999999999999888766544  332211           11245666666


Q ss_pred             HHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhH-HHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756           98 YMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSREREL-VLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus        98 f~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~-~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      |.+..+.+.  ++...+---...|-+.|+...|.+-|.++-+...+.+-.- ...--..++.+...++   -+.+++.+.
T Consensus       230 y~rAI~~~p--~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~---~e~a~~~le  304 (895)
T KOG2076|consen  230 YSRAIQANP--SNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNE---RERAAKALE  304 (895)
T ss_pred             HHHHHhcCC--cchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhH---HHHHHHHHH
Confidence            666555442  3444444456778888999999999999887533211110 0111234556666666   355666666


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC---------------------------CHHHHHH
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP---------------------------SGFEYKC  229 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p---------------------------~~~ty~~  229 (425)
                      ....... -..+...+|+++..|.+...++.|......+.....++                           +...+ -
T Consensus       305 ~~~s~~~-~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~-r  382 (895)
T KOG2076|consen  305 GALSKEK-DEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVI-R  382 (895)
T ss_pred             HHHhhcc-ccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhH-h
Confidence            6554221 22344489999999999999999999999888732222                           22221 2


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCC--CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESDG--TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI  307 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~g--~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~  307 (425)
                      ++-++......+...-+..-..+..  +.-+...|--+.++|-+.|++.+|+.+|.........-+...|--+-++|-..
T Consensus       383 l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l  462 (895)
T KOG2076|consen  383 LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMEL  462 (895)
T ss_pred             HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHH
Confidence            2334445555555555555555555  33457889999999999999999999999998765444566676676666666


Q ss_pred             HHHHHh
Q 042756          308 MSMLQD  313 (425)
Q Consensus       308 ~~~~~~  313 (425)
                      +..+.+
T Consensus       463 ~e~e~A  468 (895)
T KOG2076|consen  463 GEYEEA  468 (895)
T ss_pred             hhHHHH
Confidence            665444

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.56  E-value=1e-07  Score=57.07  Aligned_cols=34  Identities=15%  Similarity=0.241  Sum_probs=28.9

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS  293 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd  293 (425)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            3688888888888888888888888888888887

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.49  E-value=1.9e-07  Score=55.88  Aligned_cols=33  Identities=39%  Similarity=0.782  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS  223 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  223 (425)
                      +||++|++|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            677777777777777777777777777777776

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.

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

Probab=98.48  E-value=8.8e-06  Score=72.58  Aligned_cols=228  Identities=11%  Similarity=0.001  Sum_probs=164.1

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCcc
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQW  109 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~  109 (425)
                      -+.-|..++|++.|..-+.. .|-+.||-.|-+.|.+-+++..|+.++.+.+..                       ++.
T Consensus       233 ylrLgm~r~AekqlqssL~q-~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-----------------------fP~  288 (478)
T KOG1129|consen  233 YLRLGMPRRAEKQLQSSLTQ-FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-----------------------FPF  288 (478)
T ss_pred             HHHhcChhhhHHHHHHHhhc-CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-----------------------CCc
Confidence            35556888888888877666 444556666888899888888888888776532                       333


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      |.....-+...+-..++.++|.++|+...+....    ++.....+-..|.-.++++-+...++.+.+|....+.     
T Consensus       289 ~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~~----nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~spe-----  359 (478)
T KOG1129|consen  289 DVTYLLGQARIHEAMEQQEDALQLYKLVLKLHPI----NVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPE-----  359 (478)
T ss_pred             hhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCCc----cceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChH-----
Confidence            4433334555666678899999999988764222    1223344555666677777677777777777544432     


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF--EYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                       .|+.+--+|.-.+++|-++.-|.+....--.|+..  +|-.+-...+.-||+..|.+.|+....+.- -+...+|.|--
T Consensus       360 -Lf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~-~h~ealnNLav  437 (478)
T KOG1129|consen  360 -LFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDA-QHGEALNNLAV  437 (478)
T ss_pred             -HHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCc-chHHHHHhHHH
Confidence             88888888888999999999999988775556543  666666677788999999999998776543 26788999988


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      .-.+.|++++|..++.....  +.|+.
T Consensus       438 L~~r~G~i~~Arsll~~A~s--~~P~m  462 (478)
T KOG1129|consen  438 LAARSGDILGARSLLNAAKS--VMPDM  462 (478)
T ss_pred             HHhhcCchHHHHHHHHHhhh--hCccc
Confidence            88999999999999988664  35553

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

Probab=98.46  E-value=0.00013  Score=67.95  Aligned_cols=265  Identities=10%  Similarity=-0.025  Sum_probs=180.3

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHh-cC-ChHHHHHHHHhhhCCCCC-------------CCchh
Q 042756           28 VQCLTARLTKQGQRFLSSLALA-VTRDSKAASRLISKFVA-SS-PQFIALNALSHLLSPDTT-------------HPRLS   91 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~-~~-~~~~a~~~~~~~l~~~~~-------------~~~~~   91 (425)
                      ...+.+|+++.|.+++.-+.+. -+.-..+.|.|--.+.- .| ++..|-..-...+..+..             ..+.+
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~  506 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDL  506 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcH
Confidence            4457788999999998887766 33333333333322222 22 455565555555544322             23568


Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDT  171 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~  171 (425)
                      ++|.+.|++....+ .+.....||+=+ .+-+.|++++|++.|-++..-...    ...+.--+.+-|-...+   ..++
T Consensus       507 dka~~~ykeal~nd-asc~ealfnigl-t~e~~~~ldeald~f~klh~il~n----n~evl~qianiye~led---~aqa  577 (840)
T KOG2003|consen  507 DKAAEFYKEALNND-ASCTEALFNIGL-TAEALGNLDEALDCFLKLHAILLN----NAEVLVQIANIYELLED---PAQA  577 (840)
T ss_pred             HHHHHHHHHHHcCc-hHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHHHHh----hHHHHHHHHHHHHHhhC---HHHH
Confidence            99999999988777 555666777444 456679999999999887653221    12233345555555555   4455


Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      .+++.+..   ..+.-|.....-|-..|-+.|+-..|++.+-+--.- .+-|..|..-+-.-|....-++.+..+|+...
T Consensus       578 ie~~~q~~---slip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaa  653 (840)
T KOG2003|consen  578 IELLMQAN---SLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAA  653 (840)
T ss_pred             HHHHHHhc---ccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            55554442   223335568889999999999999999877654332 34467777777777888888899999999754


Q ss_pred             HCCCCcCHHhHHHHHHHHH-hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 042756          252 SDGTRVDTVCSNMVLSSYG-DHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIM  308 (425)
Q Consensus       252 ~~g~~~~~~~yn~li~~~~-~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~  308 (425)
                      -  +.|+..-|..||..|. +.|++.+|.++|+..... +.-|......|++.|..+|
T Consensus       654 l--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlg  708 (840)
T KOG2003|consen  654 L--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLG  708 (840)
T ss_pred             h--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhcccc
Confidence            3  5799999999998775 789999999999998654 5667778888888776644

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.45  E-value=2.9e-07  Score=54.71  Aligned_cols=33  Identities=15%  Similarity=0.248  Sum_probs=22.5

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF  292 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p  292 (425)
                      .+||++|.+|++.|+++.|.++|++|++.|++|
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            466666667766666666666666666666665

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

Probab=98.45  E-value=4e-05  Score=71.26  Aligned_cols=334  Identities=13%  Similarity=0.043  Sum_probs=192.2

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhH
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLA   94 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a   94 (425)
                      +..+..|..+.|..-|+...+. .|+..+--.|+-.+..-|+-++..+.|.+++.--+.+.             ..+.++
T Consensus       284 vtfiq~gqy~dainsfdh~m~~-~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~ea  362 (840)
T KOG2003|consen  284 VTFIQAGQYDDAINSFDHCMEE-APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEA  362 (840)
T ss_pred             eeEEecccchhhHhhHHHHHHh-CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHH
Confidence            4556778899999999887664 67766555555555556688888888888854322111             112222


Q ss_pred             H--HHHHHhhhcC-----------------CCccCHH---------------------HHHHHHHHHHhcCChhHHHHHH
Q 042756           95 F--PLYMRITEES-----------------WFQWNPK---------------------LVAEIIAFLDKQGQREEAETLI  134 (425)
Q Consensus        95 ~--~lf~~m~~~~-----------------~~~~~~~---------------------~~~~ll~~~~~~g~~~~A~~l~  134 (425)
                      +  ..++.|.+.+                 ++.|+-.                     .--.-...+.+.|+++.|.+++
T Consensus       363 i~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieil  442 (840)
T KOG2003|consen  363 IKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEIL  442 (840)
T ss_pred             HhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHH
Confidence            2  1222222211                 1111110                     0001234567889999999998


Q ss_pred             HHHHHhcCCCchhHHHHHHHHHHH-HHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH-----HHHHhcCChhHH
Q 042756          135 LETLSKLGSRERELVLFYCNLIDS-FCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI-----SGLCEMGQPHEA  208 (425)
Q Consensus       135 ~~m~~~~~~~~~~~~~~y~~li~~-~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li-----~~~~~~g~~~~a  208 (425)
                      .-..+...... +.  .-+.|-.. |.+.|+ + +.++-.........        .-||.-.     +.-..+|++++|
T Consensus       443 kv~~~kdnk~~-sa--aa~nl~~l~flqggk-~-~~~aqqyad~aln~--------dryn~~a~~nkgn~~f~ngd~dka  509 (840)
T KOG2003|consen  443 KVFEKKDNKTA-SA--AANNLCALRFLQGGK-D-FADAQQYADIALNI--------DRYNAAALTNKGNIAFANGDLDKA  509 (840)
T ss_pred             HHHHhccchhh-HH--HhhhhHHHHHHhccc-c-hhHHHHHHHHHhcc--------cccCHHHhhcCCceeeecCcHHHH
Confidence            88776533222 11  12233222 223332 1 22222222222111        1333211     112236899999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          209 ENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       209 ~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      .+.|++.....-.-....||+=+ .+-+.|++++|.+.|-.+..-= .-++.+.-.+...|-...+...|++++......
T Consensus       510 ~~~ykeal~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~il-~nn~evl~qianiye~led~aqaie~~~q~~sl  587 (840)
T KOG2003|consen  510 AEFYKEALNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAIL-LNNAEVLVQIANIYELLEDPAQAIELLMQANSL  587 (840)
T ss_pred             HHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc
Confidence            99999987753222233344333 4667899999999988765421 125666667777888888888899888665432


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhhc-----cCCchhhHHHHHhhcc-------hhhHHHHHHHHhCCCCcccceeecc
Q 042756          289 GIPFSVRTYNSVLNSCSTIMSMLQDLN-----SNDFPLSILELTEVLN-------EEEVSVVKELEDSSVLDEAMKWDSG  356 (425)
Q Consensus       289 g~~pd~~t~~~ll~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~l  356 (425)
                       +..|....+.|-..|-+.|+-.++++     -.-+++.++.+..++.       .+.+-..++. ...+.|+.+-|..|
T Consensus       588 -ip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ek-aaliqp~~~kwqlm  665 (840)
T KOG2003|consen  588 -IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEK-AALIQPNQSKWQLM  665 (840)
T ss_pred             -CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHH-HHhcCccHHHHHHH
Confidence             33466788888888888888777765     2234455554333322       1222222221 24456999999999


Q ss_pred             ccch-hcccCcchhHHHHHHHHHHHHHhh
Q 042756          357 ETKL-DLHGMHLGSAYFIILQWMDEMRNR  384 (425)
Q Consensus       357 i~~~-~~~~~~~~a~~~~~~~~~~~m~~~  384 (425)
                      |..| .+.|++.+|     ++++++..+.
T Consensus       666 iasc~rrsgnyqka-----~d~yk~~hrk  689 (840)
T KOG2003|consen  666 IASCFRRSGNYQKA-----FDLYKDIHRK  689 (840)
T ss_pred             HHHHHHhcccHHHH-----HHHHHHHHHh
Confidence            9655 567999999     9999999873

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

Probab=98.45  E-value=0.00012  Score=62.55  Aligned_cols=185  Identities=12%  Similarity=0.068  Sum_probs=145.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      +.--+--+|.+.|+...|.+-+++..+.    +|+...+|..+-..|.+.|..+.+++.++...++.+....      +.
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~----DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~Gd------VL  106 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEH----DPSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGD------VL  106 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh----CcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccc------hh
Confidence            4555778899999999999999998875    4444557888999999999988888887777776554433      88


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      |..-..+|..|++++|...|++....---|. ..||..+--+..+.|+.+.|+..|+.-.+..-. ...+.-.+-.....
T Consensus       107 NNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~  185 (250)
T COG3063         107 NNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYK  185 (250)
T ss_pred             hhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHh
Confidence            9999999999999999999999988643332 458999988999999999999999988775321 34567778888889


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Q 042756          272 HNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~  309 (425)
                      .|++-.|..+++.....+. ++..+.-..|+---..|+
T Consensus       186 ~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd  222 (250)
T COG3063         186 AGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGD  222 (250)
T ss_pred             cccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhcc
Confidence            9999999999999887765 776666655554444444

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

Probab=98.45  E-value=0.00013  Score=68.27  Aligned_cols=194  Identities=9%  Similarity=-0.015  Sum_probs=106.4

Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      ++-+...-+....+.-...+++.|+++|+++.+.... .-+...+|+.++-.-.....   +.-......+.-    ...
T Consensus       258 f~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPY-Rl~dmdlySN~LYv~~~~sk---Ls~LA~~v~~id----KyR  329 (559)
T KOG1155|consen  258 FPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPY-RLDDMDLYSNVLYVKNDKSK---LSYLAQNVSNID----KYR  329 (559)
T ss_pred             CCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCC-cchhHHHHhHHHHHHhhhHH---HHHHHHHHHHhc----cCC
Confidence            5444444444444455678999999999999876332 22334466665544332222   111112221111    111


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-----------
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDG-----------  254 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g-----------  254 (425)
                      |-  |+.++-+-|+-.++.|+|...|++..+.+  |. ...|+-|-.-|....+-..|.+-++...+-.           
T Consensus       330 ~E--TCCiIaNYYSlr~eHEKAv~YFkRALkLN--p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLG  405 (559)
T KOG1155|consen  330 PE--TCCIIANYYSLRSEHEKAVMYFKRALKLN--PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLG  405 (559)
T ss_pred             cc--ceeeehhHHHHHHhHHHHHHHHHHHHhcC--cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhh
Confidence            21  66666666666666666666666666532  22 3344444444444444444444444433311           


Q ss_pred             ---------------------CCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHH
Q 042756          255 ---------------------TRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQ  312 (425)
Q Consensus       255 ---------------------~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~  312 (425)
                                           ++| |...|.+|-.+|.+.++.++|+++|++....| ..+...|..|-+.+-+.++..+
T Consensus       406 QaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~e  484 (559)
T KOG1155|consen  406 QAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNE  484 (559)
T ss_pred             HHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHH
Confidence                                 122 67777777777777777777777777777655 2345666666666666666555


Q ss_pred             h
Q 042756          313 D  313 (425)
Q Consensus       313 ~  313 (425)
                      +
T Consensus       485 A  485 (559)
T KOG1155|consen  485 A  485 (559)
T ss_pred             H
Confidence            4

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.44  E-value=0.00042  Score=64.07  Aligned_cols=230  Identities=11%  Similarity=0.006  Sum_probs=143.7

Q ss_pred             hhHHHHHHHHHHhHHh--cCCC--HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCcc
Q 042756           34 RLTKQGQRFLSSLALA--VTRD--SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQW  109 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~--~~~d--~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~  109 (425)
                      +..+.+..-+.++...  ..|+  ...|..+-..+...|..+.|...+.+.+                     +.+  +-
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al---------------------~l~--P~   96 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQAL---------------------ALR--PD   96 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------HcC--CC
Confidence            3455666667666654  2332  3556666666777776666655555543                     322  13


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++..|+.+-..+...|++++|.+.|+...+.    .|+...+|..+..++...|+++++.+.++...+.   .    |+.
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l----~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~---~----P~~  165 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLEL----DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD---D----PND  165 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---C----CCC
Confidence            6788999999999999999999999998764    2222346777888888899955544444444433   2    222


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC---CC--C-cCHHhHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD---GT--R-VDTVCSN  263 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~---g~--~-~~~~~yn  263 (425)
                      .........+...++.++|...|.+.... ..|+...+ .+  .....|+...+ +.+..+.+.   .+  . .....|.
T Consensus       166 ~~~~~~~~l~~~~~~~~~A~~~l~~~~~~-~~~~~~~~-~~--~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~  240 (296)
T PRK11189        166 PYRALWLYLAESKLDPKQAKENLKQRYEK-LDKEQWGW-NI--VEFYLGKISEE-TLMERLKAGATDNTELAERLCETYF  240 (296)
T ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhh-CCccccHH-HH--HHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            11222222344567899999999776543 23433222 22  23335655544 355555431   11  1 1346899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS  303 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~  303 (425)
                      .+-..+.+.|++++|...|++..+.. .||..-+...+--
T Consensus       241 ~Lg~~~~~~g~~~~A~~~~~~Al~~~-~~~~~e~~~~~~e  279 (296)
T PRK11189        241 YLAKYYLSLGDLDEAAALFKLALANN-VYNFVEHRYALLE  279 (296)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CchHHHHHHHHHH
Confidence            99999999999999999999998764 3465555554433

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.39  E-value=5e-07  Score=53.70  Aligned_cols=32  Identities=25%  Similarity=0.613  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP  222 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  222 (425)
                      +||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            66666666666666666666666666666665

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

Probab=98.39  E-value=0.00057  Score=62.95  Aligned_cols=277  Identities=11%  Similarity=-0.012  Sum_probs=188.9

Q ss_pred             chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           89 RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        89 ~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      |.+..|+++..+-.+.+.  -....|-.-..+--+.|+.+.+-.++.+..+..+.   +....+-+........|+...+
T Consensus        98 G~~~qAEkl~~rnae~~e--~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~---~~l~v~ltrarlll~~~d~~aA  172 (400)
T COG3071          98 GDFQQAEKLLRRNAEHGE--QPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGD---DTLAVELTRARLLLNRRDYPAA  172 (400)
T ss_pred             CcHHHHHHHHHHhhhcCc--chHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCC---chHHHHHHHHHHHHhCCCchhH
Confidence            377788888777544431  12334555556666779999999999998775222   2233566777778888997777


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHcCCCHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG-------FEYKCIIYGYGRLGLLE  241 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-------~ty~~ll~~~~~~g~~~  241 (425)
                      .+-...+.++.+...      .+......+|.+.|++..+..+...|.+.|+--|.       .+|+.++.-....+..+
T Consensus       173 ~~~v~~ll~~~pr~~------~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~  246 (400)
T COG3071         173 RENVDQLLEMTPRHP------EVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSE  246 (400)
T ss_pred             HHHHHHHHHhCcCCh------HHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccch
Confidence            777777777654442      38999999999999999999999999999865443       47888888888888888


Q ss_pred             HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH--H-HHHHHHHHhhccCC
Q 042756          242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS--C-STIMSMLQDLNSND  318 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~--~-~~~~~~~~~~~~~~  318 (425)
                      .-...|+..... .+-+...--+++.-+.++|+.++|.++..+-.+.+..|...++---+..  . -.....++....++
T Consensus       247 gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~  325 (400)
T COG3071         247 GLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHP  325 (400)
T ss_pred             HHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCC
Confidence            777777776542 3446677778888999999999999999998888877762222111110  0 00122233333444


Q ss_pred             chhhHH-HH----HhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          319 FPLSIL-EL----TEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       319 ~~~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      -.+.+. .+    .+-..-..+..+++ ..-...|+..+|+.+-.++.+.|+..+|     .+.+++-..
T Consensus       326 ~~p~L~~tLG~L~~k~~~w~kA~~~le-aAl~~~~s~~~~~~la~~~~~~g~~~~A-----~~~r~e~L~  389 (400)
T COG3071         326 EDPLLLSTLGRLALKNKLWGKASEALE-AALKLRPSASDYAELADALDQLGEPEEA-----EQVRREALL  389 (400)
T ss_pred             CChhHHHHHHHHHHHhhHHHHHHHHHH-HHHhcCCChhhHHHHHHHHHHcCChHHH-----HHHHHHHHH
Confidence            444444 11    11111233443333 2333559999999999999999999999     888888765

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

Probab=98.34  E-value=8.4e-06  Score=61.39  Aligned_cols=81  Identities=17%  Similarity=0.111  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-CcCHHhHHHHHHHHHhcC--------CHHHHHHHHHHHHhCCCCCCHHH
Q 042756          226 EYKCIIYGYGRLGLLEDMERIVNQMESDGT-RVDTVCSNMVLSSYGDHN--------ELSRMVLWLQKMKDSGIPFSVRT  296 (425)
Q Consensus       226 ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~-~~~~~~yn~li~~~~~~g--------~~~~A~~l~~~M~~~g~~pd~~t  296 (425)
                      |-...|..+...+++.....+|+.++.+|+ .|+..+||.++.+.++..        ++-+.+.+|.+|...+++|+..|
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            334556666666788888888888888888 778888888887777543        24456778888888888888888


Q ss_pred             HHHHHHHHHH
Q 042756          297 YNSVLNSCST  306 (425)
Q Consensus       297 ~~~ll~~~~~  306 (425)
                      |+.++.++.+
T Consensus       107 Ynivl~~Llk  116 (120)
T PF08579_consen  107 YNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHH
Confidence            8888887654

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

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

Probab=98.32  E-value=0.00076  Score=66.59  Aligned_cols=249  Identities=8%  Similarity=-0.016  Sum_probs=164.5

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC------------------chhhh
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP------------------RLSSL   93 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~------------------~~~~~   93 (425)
                      -.|..++|+++++.-...+.-...........+.+.|+.++|..++..++.++....                  ...+.
T Consensus        16 e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~   95 (517)
T PF12569_consen   16 EAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEK   95 (517)
T ss_pred             HCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHH
Confidence            356888999999775554555567777788888888999999998888876653211                  12344


Q ss_pred             HHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChh-HHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           94 AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQRE-EAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        94 a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~-~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      ...+|+++...-   |.+.....+.-.+..-..+. .+.+.+..+..+|.|      ++|+.|-..|......+-+.+.+
T Consensus        96 ~~~~y~~l~~~y---p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP------slF~~lk~Ly~d~~K~~~i~~l~  166 (517)
T PF12569_consen   96 LLELYDELAEKY---PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP------SLFSNLKPLYKDPEKAAIIESLV  166 (517)
T ss_pred             HHHHHHHHHHhC---ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc------hHHHHHHHHHcChhHHHHHHHHH
Confidence            455566554432   33322222222222212222 334444444445432      26777777777554433344444


Q ss_pred             HHHHHHhhcCC---------CCccChhHH--HHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCH
Q 042756          173 ARLNQLVNSSS---------SVYVKRQAL--KSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLL  240 (425)
Q Consensus       173 ~~~~~~~~~~~---------~~~p~~~~~--~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~  240 (425)
                      ..+........         .-.|+...|  .-+-..|-..|++++|+++.++..++  .|+ +.-|..--..+-+.|++
T Consensus       167 ~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~  244 (517)
T PF12569_consen  167 EEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDL  244 (517)
T ss_pred             HHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCH
Confidence            44433332211         123555444  55677788999999999999999886  576 55888888899999999


Q ss_pred             HHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 042756          241 EDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF  292 (425)
Q Consensus       241 ~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p  292 (425)
                      ++|.+.++...+.... |...=+-.+..+.++|++++|.+++....+.+..|
T Consensus       245 ~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~  295 (517)
T PF12569_consen  245 KEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDP  295 (517)
T ss_pred             HHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCc
Confidence            9999999998887543 77777788888899999999999999988777644

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 [], [].

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

Probab=98.25  E-value=1.1e-06  Score=50.89  Aligned_cols=30  Identities=20%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 042756          261 CSNMVLSSYGDHNELSRMVLWLQKMKDSGI  290 (425)
Q Consensus       261 ~yn~li~~~~~~g~~~~A~~l~~~M~~~g~  290 (425)
                      +||+||++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            577777777777777777777777766653

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.25  E-value=0.00017  Score=66.66  Aligned_cols=93  Identities=13%  Similarity=0.019  Sum_probs=51.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ..|+.+-..+...|++++|.+.|++..+  +.|+ ..+|..+-.++...|++++|.+.|+...+..  |+..........
T Consensus        99 ~a~~~lg~~~~~~g~~~~A~~~~~~Al~--l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l  174 (296)
T PRK11189         99 DAYNYLGIYLTQAGNFDAAYEAFDSVLE--LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--PNDPYRALWLYL  174 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHH
Confidence            3666666666666666666666666665  2343 4455666666666666666666666665542  332211222222


Q ss_pred             HHhcCCHHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~  286 (425)
                      +...++.++|...|.+..
T Consensus       175 ~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        175 AESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHccCCHHHHHHHHHHHH
Confidence            334556666666665543

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

Probab=98.25  E-value=1.6e-05  Score=75.71  Aligned_cols=137  Identities=14%  Similarity=0.168  Sum_probs=103.1

Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      ++..|.+......+........+++.+....+.+.+.+.+..++...... .+.|.  |..++|+.|.+.|..++++.+.
T Consensus        50 ~~~~l~~k~~~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~-~~~~~--t~ha~vR~~l~~~~~~~~l~~L  126 (429)
T PF10037_consen   50 LYSELDKKFERKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCS-YLLPS--THHALVRQCLELGAEDELLELL  126 (429)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccc-cccCc--cHHHHHHHHHhcCCHHHHHHHH
Confidence            66666654333333333456778888777777555555555554443222 12233  6679999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                      +.=...|+-||.+|||.+|+.+.+.|++..|.++...|...+...+..|+.--+.+|.+.
T Consensus       127 ~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  127 KNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999887777888888888877766

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 [].

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

Probab=98.24  E-value=0.00014  Score=68.45  Aligned_cols=234  Identities=9%  Similarity=-0.014  Sum_probs=158.6

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCH
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNP  111 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~  111 (425)
                      +.|+...|.+-|+...+..+.+...|-.+-..|....+.++.+..|.....-                     +.  -|+
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~l---------------------dp--~n~  394 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYADENQSEKMWKDFNKAEDL---------------------DP--ENP  394 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcccchHHHHHHHHHhhhhccHHHHHHHHHHHhc---------------------CC--CCC
Confidence            4556666777777777662223333777777777777777777666665432                     21  255


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      .+|-.--..+.-.+++++|..=|++-.+-    .|.....|--+-.+.-|.+.   ..++...|.+.....+.+   ..+
T Consensus       395 dvYyHRgQm~flL~q~e~A~aDF~Kai~L----~pe~~~~~iQl~~a~Yr~~k---~~~~m~~Fee~kkkFP~~---~Ev  464 (606)
T KOG0547|consen  395 DVYYHRGQMRFLLQQYEEAIADFQKAISL----DPENAYAYIQLCCALYRQHK---IAESMKTFEEAKKKFPNC---PEV  464 (606)
T ss_pred             chhHhHHHHHHHHHHHHHHHHHHHHHhhc----ChhhhHHHHHHHHHHHHHHH---HHHHHHHHHHHHHhCCCC---chH
Confidence            56666666666778899999888887652    45545556556666667776   666777777666544322   249


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc-----CCC--CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVK-----GLE--PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNM  264 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~--p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~  264 (425)
                      ||..-..+...+++++|.+.|+...+.     ++.  +...+--.++-.- -.+++..|.+++....+..-+ ....|-.
T Consensus       465 y~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~Dpk-ce~A~~t  542 (606)
T KOG0547|consen  465 YNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIELDPK-CEQAYET  542 (606)
T ss_pred             HHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHccCch-HHHHHHH
Confidence            999999999999999999999998763     111  2222333333333 338999999999998876432 5688999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          265 VLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       265 li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      |-..-.+.|++++|+++|++-...     ..|-.-++++|+
T Consensus       543 laq~~lQ~~~i~eAielFEksa~l-----Art~~E~~~a~s  578 (606)
T KOG0547|consen  543 LAQFELQRGKIDEAIELFEKSAQL-----ARTESEMVHAYS  578 (606)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHH-----HHhHHHHHHHHH
Confidence            999999999999999999986532     234444555543

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

Probab=98.22  E-value=1.1e-05  Score=60.68  Aligned_cols=82  Identities=16%  Similarity=0.159  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHcCC--------CHHHHHHHHHHHHHCCCCcCHHh
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGL-EPSGFEYKCIIYGYGRLG--------LLEDMERIVNQMESDGTRVDTVC  261 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~ty~~ll~~~~~~g--------~~~~a~~~~~~m~~~g~~~~~~~  261 (425)
                      |--..|..+...+++.....+|..+++.|+ .|+..+|+.++.+-+++.        ++-....++++|...+++|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            334456666667999999999999999999 899999999999988775        24557889999999999999999


Q ss_pred             HHHHHHHHHhc
Q 042756          262 SNMVLSSYGDH  272 (425)
Q Consensus       262 yn~li~~~~~~  272 (425)
                      ||.++..+.+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            99999988653

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

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

Probab=98.20  E-value=7.3e-05  Score=73.58  Aligned_cols=249  Identities=12%  Similarity=0.029  Sum_probs=167.1

Q ss_pred             ccCCCCCCccccccccchhH-HHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCC
Q 042756            7 MRIPPPWNSRCCRLRQQRLT-LVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDT   85 (425)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~   85 (425)
                      .|.|-++.+.-+...+.+.. .--.+.-|.++.|..+|+++.        .|..+|.+|+..|...+|..+..+-+.   
T Consensus       384 nRlsy~ya~~lpp~Wq~q~~laell~slGitksAl~I~Erle--------mw~~vi~CY~~lg~~~kaeei~~q~le---  452 (777)
T KOG1128|consen  384 NRLSYIYAPHLPPIWQLQRLLAELLLSLGITKSALVIFERLE--------MWDPVILCYLLLGQHGKAEEINRQELE---  452 (777)
T ss_pred             hcccccccCCCCCcchHHHHHHHHHHHcchHHHHHHHHHhHH--------HHHHHHHHHHHhcccchHHHHHHHHhc---
Confidence            44555554433333333222 233455689999999999964        588999999999977777666666442   


Q ss_pred             CCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCc
Q 042756           86 THPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSK  165 (425)
Q Consensus        86 ~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~  165 (425)
                                        ++   |++..|..+........-+++|.++++....+.       .   .++-....+.++ 
T Consensus       453 ------------------k~---~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA-------~---r~~~~~~~~~~~-  500 (777)
T KOG1128|consen  453 ------------------KD---PDPRLYCLLGDVLHDPSLYEKAWELSNYISARA-------Q---RSLALLILSNKD-  500 (777)
T ss_pred             ------------------CC---CcchhHHHhhhhccChHHHHHHHHHhhhhhHHH-------H---Hhhccccccchh-
Confidence                              22   678778777777777777888888888765430       0   111122223566 


Q ss_pred             ccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHH
Q 042756          166 RGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~  244 (425)
                        +.++.+-++....-.+ ..+  .+|-..-.+..+.+++..|.+.|..-..  ..|| ...||++-.+|.+.|+-.+|.
T Consensus       501 --fs~~~~hle~sl~~np-lq~--~~wf~~G~~ALqlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra~  573 (777)
T KOG1128|consen  501 --FSEADKHLERSLEINP-LQL--GTWFGLGCAALQLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRAF  573 (777)
T ss_pred             --HHHHHHHHHHHhhcCc-cch--hHHHhccHHHHHHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHHH
Confidence              4444444444332221 223  3888888889999999999999988776  4676 448999999999999999999


Q ss_pred             HHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHH
Q 042756          245 RIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG-IPFSVRTYNSVLNSCST  306 (425)
Q Consensus       245 ~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g-~~pd~~t~~~ll~~~~~  306 (425)
                      ..+.+..+.. .-+...|..-+....+.|.+++|.+.+.+|.+.. -.-|......++....+
T Consensus       574 ~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~~~~~~d~~vl~~iv~~~~~  635 (777)
T KOG1128|consen  574 RKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLRKKYKDDEVLLIIVRTVLE  635 (777)
T ss_pred             HHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHhhhhcccchhhHHHHHHHHh
Confidence            9999888776 3466778888888889999999999988875421 11255555555554433

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

Probab=98.19  E-value=0.0014  Score=56.20  Aligned_cols=163  Identities=9%  Similarity=0.001  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      .++..+-..|.+.|+.+.|.+-|++..+.... .   -.+.|..---+|..|.   .+++...|.+.+.......| ..+
T Consensus        70 ~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~-~---GdVLNNYG~FLC~qg~---~~eA~q~F~~Al~~P~Y~~~-s~t  141 (250)
T COG3063          70 LAHLVRAHYYQKLGENDLADESYRKALSLAPN-N---GDVLNNYGAFLCAQGR---PEEAMQQFERALADPAYGEP-SDT  141 (250)
T ss_pred             HHHHHHHHHHHHcCChhhHHHHHHHHHhcCCC-c---cchhhhhhHHHHhCCC---hHHHHHHHHHHHhCCCCCCc-chh
Confidence            34445555555555555555555554432111 0   1122333344444554   34444444444433222111 125


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      |..+.-+..+.|+++.|...|++-.+.. +-...+.-.+.....+.|++-.|..+++.....|. ++..+--..|..--+
T Consensus       142 ~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~  219 (250)
T COG3063         142 LENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKR  219 (250)
T ss_pred             hhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHH
Confidence            5555555555666666666666555531 11123455555555566666666666666555544 555555555555555


Q ss_pred             cCCHHHHHHHHHH
Q 042756          272 HNELSRMVLWLQK  284 (425)
Q Consensus       272 ~g~~~~A~~l~~~  284 (425)
                      .|+.+.|-+.=..
T Consensus       220 ~gd~~~a~~Y~~q  232 (250)
T COG3063         220 LGDRAAAQRYQAQ  232 (250)
T ss_pred             hccHHHHHHHHHH
Confidence            6665555444333

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

Probab=98.16  E-value=2.2e-06  Score=49.61  Aligned_cols=30  Identities=47%  Similarity=0.828  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGL  220 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  220 (425)
                      +||+||++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            566666666666666666666666666553

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

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

Probab=98.08  E-value=6.1e-05  Score=71.78  Aligned_cols=120  Identities=12%  Similarity=0.073  Sum_probs=106.3

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKG--LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      +......+++.+....+++++..++.+.+...  ..--..|..++|..|.+.|..+.+..++..=..-||-||..+||.|
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~L  144 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLL  144 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHH
Confidence            44577888888888899999999999998762  2223467789999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI  307 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~  307 (425)
                      |+.+.+.|++..|.++..+|..++...+..|+.-.+.+|.+.
T Consensus       145 md~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  145 MDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999999999888888889999999998876

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 [].

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

Probab=98.08  E-value=0.0018  Score=62.36  Aligned_cols=247  Identities=9%  Similarity=-0.061  Sum_probs=132.4

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccC
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWN  110 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~  110 (425)
                      ...+++++..++++.+.+..++....+..-|.++...|+..+.+.+=.+++...                 +      -.
T Consensus       255 y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-----------------P------~~  311 (611)
T KOG1173|consen  255 YYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-----------------P------SK  311 (611)
T ss_pred             HHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-----------------C------CC
Confidence            344477777777777777756666666666777777776555544444443322                 1      22


Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      +.+|=++--.|.-.|..++|+..|.+-......-.    ..|-.+-+.|+-.|.-|++-.++....+.++..+.  |.  
T Consensus       312 a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fg----paWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hl--P~--  383 (611)
T KOG1173|consen  312 ALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFG----PAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHL--PS--  383 (611)
T ss_pred             CcchhhHHHHHHHhcCcHHHHHHHHHHhhcCcccc----HHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcc--hH--
Confidence            33344455556666777777777777554322211    13556666666666655555565555555544322  21  


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----C--CCcCHHhHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----G--TRVDTVCSN  263 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g--~~~~~~~yn  263 (425)
                      .|  +---|.+.++++.|.++|.+...  +.| |+..++-+--.....+.+.+|..+|+.-...    +  ...-..+++
T Consensus       384 LY--lgmey~~t~n~kLAe~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~  459 (611)
T KOG1173|consen  384 LY--LGMEYMRTNNLKLAEKFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLN  459 (611)
T ss_pred             HH--HHHHHHHhccHHHHHHHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHH
Confidence            22  22234555666666666665543  333 4455555554455555666666666544311    0  001233455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .|-.+|.+.++.++|+..|+...... .-|..||.++--.|...|+++.+
T Consensus       460 NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~A  508 (611)
T KOG1173|consen  460 NLGHAYRKLNKYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKA  508 (611)
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHH
Confidence            55566666666666666666554431 33555555555555555555554

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.02  E-value=0.0018  Score=57.73  Aligned_cols=174  Identities=11%  Similarity=-0.048  Sum_probs=119.1

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .....+-.+...+.+.|++++|...|++....... .+.....+..+..++.+.|+++.+.+.++.+.+..+.....   
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~---  106 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPF-SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDA---  106 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCch---
Confidence            45666777888889999999999999998764322 22222345677788889999655555555555443322111   


Q ss_pred             hhHHHHHHHHHHhc--------CChhHHHHHHHHHHHcCCCCCHH-HH-----------------HHHHHHHHcCCCHHH
Q 042756          189 RQALKSMISGLCEM--------GQPHEAENLIEEMRVKGLEPSGF-EY-----------------KCIIYGYGRLGLLED  242 (425)
Q Consensus       189 ~~~~~~li~~~~~~--------g~~~~a~~~~~~m~~~g~~p~~~-ty-----------------~~ll~~~~~~g~~~~  242 (425)
                      ..++..+-.++.+.        |+.++|.+.|+.....  .|+.. .+                 -.+-..+.+.|++++
T Consensus       107 ~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~  184 (235)
T TIGR03302       107 DYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVA  184 (235)
T ss_pred             HHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHH
Confidence            11344444555543        7889999999999875  33321 11                 134456788899999


Q ss_pred             HHHHHHHHHHCC--CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          243 MERIVNQMESDG--TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       243 a~~~~~~m~~~g--~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      |...++...+..  -......+..+..++...|+.++|..+++.+...
T Consensus       185 A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       185 AINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            999999988752  1224578899999999999999999999888754

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).

>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=97.99  E-value=0.011  Score=58.51  Aligned_cols=271  Identities=11%  Similarity=0.105  Sum_probs=175.8

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcC-----ChHHHHHHHHhhhCCCCC--CCc----------h-hh
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASS-----PQFIALNALSHLLSPDTT--HPR----------L-SS   92 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~-----~~~~a~~~~~~~l~~~~~--~~~----------~-~~   92 (425)
                      +..|+.++|..++..+...-+-|..-|..+..++....     .......++.+.......  .+.          . -.
T Consensus        49 ~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~  128 (517)
T PF12569_consen   49 LKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKE  128 (517)
T ss_pred             HHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHH
Confidence            34479999999999998875555666666666663332     345566666665333211  111          1 22


Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcC-----------CCchhHH--HHHHHHHHHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLG-----------SRERELV--LFYCNLIDSF  159 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~-----------~~~~~~~--~~y~~li~~~  159 (425)
                      .+......+..+| + |+  +|+.|-..|......+-..+++..+.....           ...++..  .++.-+-..|
T Consensus       129 ~~~~yl~~~l~Kg-v-Ps--lF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhy  204 (517)
T PF12569_consen  129 RLDEYLRPQLRKG-V-PS--LFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHY  204 (517)
T ss_pred             HHHHHHHHHHhcC-C-ch--HHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHH
Confidence            3444444555666 4 33  677787878766666667777777654311           0122222  2334445557


Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL  239 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~  239 (425)
                      -..|+   .+++++.+.+.+...+..   +..|-.-.+.|-..|++++|.+..+..+.... -|.+.-+...+.+.++|+
T Consensus       205 d~~g~---~~~Al~~Id~aI~htPt~---~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~LRa~~  277 (517)
T PF12569_consen  205 DYLGD---YEKALEYIDKAIEHTPTL---VELYMTKARILKHAGDLKEAAEAMDEARELDL-ADRYINSKCAKYLLRAGR  277 (517)
T ss_pred             HHhCC---HHHHHHHHHHHHhcCCCc---HHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhHHHHHHHHHHHHHCCC
Confidence            78898   667888888777655322   34888888999999999999999999988643 378888999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCcCHHhH--------HHHHHHHHhcCCHHHHHHHHHHH-------HhCCCCCCHHHHHH---HH
Q 042756          240 LEDMERIVNQMESDGTRVDTVCS--------NMVLSSYGDHNELSRMVLWLQKM-------KDSGIPFSVRTYNS---VL  301 (425)
Q Consensus       240 ~~~a~~~~~~m~~~g~~~~~~~y--------n~li~~~~~~g~~~~A~~l~~~M-------~~~g~~pd~~t~~~---ll  301 (425)
                      +++|.+++......+..|-...+        .-.-.+|.+.|++..|++-|...       .+.  +.|-++|..   .+
T Consensus       278 ~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k~f~~~~~D--QfDFH~Yc~RK~t~  355 (517)
T PF12569_consen  278 IEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLKHFDDFEED--QFDFHSYCLRKMTL  355 (517)
T ss_pred             HHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcc--cccHHHHHHhhccH
Confidence            99999999999887654432222        33457888999988887765554       333  445555531   34


Q ss_pred             HHHHHHHHHHHhh
Q 042756          302 NSCSTIMSMLQDL  314 (425)
Q Consensus       302 ~~~~~~~~~~~~~  314 (425)
                      ++|...-++++.+
T Consensus       356 r~Y~~~L~~ed~l  368 (517)
T PF12569_consen  356 RAYVDMLRWEDKL  368 (517)
T ss_pred             HHHHHHHHHHHHh
Confidence            5555555555543

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 [], [].

>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=97.99  E-value=6.2e-05  Score=63.93  Aligned_cols=91  Identities=13%  Similarity=0.145  Sum_probs=61.7

Q ss_pred             CHHHHHHHHHHHHcC-----CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC----------------CHHHHHHH
Q 042756          223 SGFEYKCIIYGYGRL-----GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN----------------ELSRMVLW  281 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~-----g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g----------------~~~~A~~l  281 (425)
                      |-.+|..+++.|.+.     |.++-....+..|.+.|+..|..+||.|++.+=+..                +.+-|+++
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~l  125 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDL  125 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHH
Confidence            455555555555433     455666666666666666666666666666554321                45678999


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          282 LQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       282 ~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      +++|...|+.||..|+..|++.+.+.+...+.
T Consensus       126 L~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K  157 (228)
T PF06239_consen  126 LEQMENNGVMPDKETEQMLLNIFGRKSHPMKK  157 (228)
T ss_pred             HHHHHHcCCCCcHHHHHHHHHHhccccHHHHH
Confidence            99999999999999999999998776554443

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

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

Probab=97.95  E-value=0.0034  Score=64.15  Aligned_cols=244  Identities=10%  Similarity=-0.001  Sum_probs=151.1

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCC----CC-------------------CchhhhHHHHHHHhhhcCCCc
Q 042756           52 RDSKAASRLISKFVASSPQFIALNALSHLLSPDT----TH-------------------PRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        52 ~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~----~~-------------------~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      +-+...|.+-......|.+..|...|...+....    ..                   .+.++.|.+.|..+.+..   
T Consensus       450 ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh---  526 (1018)
T KOG2002|consen  450 IPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEH---  526 (1018)
T ss_pred             CCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC---
Confidence            5556666666666666777777777776655410    00                   012445556666665543   


Q ss_pred             cCHHHHHHHHHHHHhc-------CChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc
Q 042756          109 WNPKLVAEIIAFLDKQ-------GQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS  181 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~-------g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~  181 (425)
                      |+-      |.+|.+.       +.+.+|...+.+....... .|+   .++.+-+.|.+...+..+.+-+....+....
T Consensus       527 p~Y------Id~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~-np~---arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~  596 (1018)
T KOG2002|consen  527 PGY------IDAYLRLGCMARDKNNLYEASLLLKDALNIDSS-NPN---ARSLLGNLHLKKSEWKPAKKKFETILKKTST  596 (1018)
T ss_pred             chh------HHHHHHhhHHHHhccCcHHHHHHHHHHHhcccC-CcH---HHHHHHHHHHhhhhhcccccHHHHHHhhhcc
Confidence            332      2333322       4555666666665543222 222   3333444666655554455544444443322


Q ss_pred             CCCCccChhHHHHHHHHHHh------------cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          182 SSSVYVKRQALKSMISGLCE------------MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       182 ~~~~~p~~~~~~~li~~~~~------------~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                          .+|..+.-+|-+.|.+            .+..++|+++|.+..... +-|.+.=|-+--.++..|++.+|..+|..
T Consensus       597 ----~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsq  671 (1018)
T KOG2002|consen  597 ----KTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQ  671 (1018)
T ss_pred             ----CCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHH
Confidence                2454333334443322            246678888888877642 23566667777788899999999999999


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHH-HHhCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQK-MKDSGIPFSVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~-M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      ..+... -+..+|-.+-++|+..|++..|++.|+. |.+..-.-+......|-+++-..|.+..++
T Consensus       672 VrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak  736 (1018)
T KOG2002|consen  672 VREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAK  736 (1018)
T ss_pred             HHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHH
Confidence            988654 2456788899999999999999999997 455555667888888888888888776664

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

Probab=97.92  E-value=0.0053  Score=58.32  Aligned_cols=233  Identities=9%  Similarity=-0.038  Sum_probs=129.9

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .....|+.++|.+.++......+.|...+.. ...+...|....                 ..+.+.+.+... ... ..
T Consensus        52 ~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~~~~~~~~~-----------------~~~~~~~~l~~~-~~~-~~  111 (355)
T cd05804          52 SAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLGAFGLGDFSG-----------------MRDHVARVLPLW-APE-NP  111 (355)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHHHHHhccccc-----------------CchhHHHHHhcc-CcC-CC
Confidence            4455667777777777766653334433332 222222221111                 222333333331 111 22


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      ........+-..+...|++++|.+.+++..+....    ....+..+-..|...|+   .+++...+.+....... .|+
T Consensus       112 ~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~----~~~~~~~la~i~~~~g~---~~eA~~~l~~~l~~~~~-~~~  183 (355)
T cd05804         112 DYWYLLGMLAFGLEEAGQYDRAEEAARRALELNPD----DAWAVHAVAHVLEMQGR---FKEGIAFMESWRDTWDC-SSM  183 (355)
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC----CcHHHHHHHHHHHHcCC---HHHHHHHHHhhhhccCC-Ccc
Confidence            23344455667788899999999999998875322    13356778888999999   45555555555443211 123


Q ss_pred             --hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCCHHHH-H--HHHHHHHcCCCHHHHHHH---HHHHHHCCC-CcC
Q 042756          189 --RQALKSMISGLCEMGQPHEAENLIEEMRVKGL-EPSGFEY-K--CIIYGYGRLGLLEDMERI---VNQMESDGT-RVD  258 (425)
Q Consensus       189 --~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~ty-~--~ll~~~~~~g~~~~a~~~---~~~m~~~g~-~~~  258 (425)
                        ...|-.+...+...|++++|.++|++...... .+..... +  .++.-+-..|....+.+.   ...-....- ...
T Consensus       184 ~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~  263 (355)
T cd05804         184 LRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGL  263 (355)
T ss_pred             hhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccc
Confidence              23566788899999999999999999864322 1222211 1  333334444543333322   222111100 111


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          259 TVCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       259 ~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      ....-....++...|+.++|..++..+....
T Consensus       264 ~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~  294 (355)
T cd05804         264 AFNDLHAALALAGAGDKDALDKLLAALKGRA  294 (355)
T ss_pred             hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            2222356677788999999999999987643

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

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

Probab=97.90  E-value=0.00019  Score=65.74  Aligned_cols=82  Identities=13%  Similarity=0.106  Sum_probs=40.8

Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCH-HHHHHHH
Q 042756          204 QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNEL-SRMVLWL  282 (425)
Q Consensus       204 ~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~-~~A~~l~  282 (425)
                      .+.+|..+|+++.+. ..++..+.+.+..++...|++++|++++.+..+..- -+..+.-.+|-.....|+. +.+.+++
T Consensus       182 ~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~gk~~~~~~~~l  259 (290)
T PF04733_consen  182 KYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLGKPTEAAERYL  259 (290)
T ss_dssp             CCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             hHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCChhHHHHHH
Confidence            456666666665443 345555666666666666666666666655443321 1334444455554555544 4455555


Q ss_pred             HHHHh
Q 042756          283 QKMKD  287 (425)
Q Consensus       283 ~~M~~  287 (425)
                      .++..
T Consensus       260 ~qL~~  264 (290)
T PF04733_consen  260 SQLKQ  264 (290)
T ss_dssp             HHCHH
T ss_pred             HHHHH
Confidence            55543

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.

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

Probab=97.89  E-value=0.011  Score=60.08  Aligned_cols=276  Identities=11%  Similarity=0.039  Sum_probs=167.9

Q ss_pred             hhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHHHHHHH
Q 042756           34 RLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAFPLYMR  100 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~~lf~~  100 (425)
                      |+...+...+-......+-|...|-.+-+-....|++..|.-.+.+.+.-.+..-             |....|..-|.+
T Consensus       187 Gd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~  266 (895)
T KOG2076|consen  187 GDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQ  266 (895)
T ss_pred             ccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHH
Confidence            3555555544333222555889999999999999999999999988876554322             234556666776


Q ss_pred             hhhcCC---CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 042756          101 ITEESW---FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQ  177 (425)
Q Consensus       101 m~~~~~---~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~  177 (425)
                      +.....   +.+.....-.+++.|...++-+.|.+.++........  ......++.+...|.+....+.+.........
T Consensus       267 l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~--~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~  344 (895)
T KOG2076|consen  267 LLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKD--EASLEDLNILAELFLKNKQSDKALMKIVDDRN  344 (895)
T ss_pred             HHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccc--cccccHHHHHHHHHHHhHHHHHhhHHHHHHhc
Confidence            655431   1112334445677788888888888888887662111  11112456777777776664433333333322


Q ss_pred             ----------------------HhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC--CHHHHHHHHHH
Q 042756          178 ----------------------LVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP--SGFEYKCIIYG  233 (425)
Q Consensus       178 ----------------------~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~ty~~ll~~  233 (425)
                                            ....+....++..++. ++-++...+..+...-+..-....++.|  +..-|.-+.++
T Consensus       345 r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~r-l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~a  423 (895)
T KOG2076|consen  345 RESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIR-LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADA  423 (895)
T ss_pred             cccCCChhhhhhhhhccccccccccCCCCCCccchhHh-HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHH
Confidence                                  1111112222222311 2223333344444444444444555333  56688889999


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHH
Q 042756          234 YGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR-TYNSVLNSCSTIMSMLQ  312 (425)
Q Consensus       234 ~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~-t~~~ll~~~~~~~~~~~  312 (425)
                      |...|++++|..+|..+.+....-+...|--+-.+|...|..++|.+.|+.....  .||.. .-.+|-+.+-+.|+.++
T Consensus       424 l~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~Ek  501 (895)
T KOG2076|consen  424 LTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL--APDNLDARITLASLYQQLGNHEK  501 (895)
T ss_pred             HHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCchhhhhhHHHHHHhcCCHHH
Confidence            9999999999999999988755557889999999999999999999999988753  45432 22223333455666666


Q ss_pred             hh
Q 042756          313 DL  314 (425)
Q Consensus       313 ~~  314 (425)
                      ++
T Consensus       502 al  503 (895)
T KOG2076|consen  502 AL  503 (895)
T ss_pred             HH
Confidence            64

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

Probab=97.88  E-value=0.00065  Score=60.97  Aligned_cols=228  Identities=11%  Similarity=0.015  Sum_probs=140.0

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHH-
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALK-  193 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~-  193 (425)
                      +-+-.+|.+.|...+|++.|+.-.+...  .++   ||-.|-++|.+..+   -..++..+.+-.+    .+|-.+||- 
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~--~~d---TfllLskvY~ridQ---P~~AL~~~~~gld----~fP~~VT~l~  294 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFP--HPD---TFLLLSKVYQRIDQ---PERALLVIGEGLD----SFPFDVTYLL  294 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCC--chh---HHHHHHHHHHHhcc---HHHHHHHHhhhhh----cCCchhhhhh
Confidence            3467777888888888887777655322  222   67777788887777   3445555544433    334444443 


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g  273 (425)
                      -+-+.+-..++.++|.++|++..+.. .-++....++-..|.-.++.+-|..++.++.+.|+. +...|+.+--+|.-.+
T Consensus       295 g~ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaq  372 (478)
T KOG1129|consen  295 GQARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQ  372 (478)
T ss_pred             hhHHHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhc
Confidence            34455566678888888888776641 124456666677777778888888888888888875 7777888877777888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHH--HHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcccc
Q 042756          274 ELSRMVLWLQKMKDSGIPFSVRT--YNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAM  351 (425)
Q Consensus       274 ~~~~A~~l~~~M~~~g~~pd~~t--~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  351 (425)
                      ++|-++..|.+...---.|+...  |-.+=......|++-.                      +...+++.-..-.-+..
T Consensus       373 Q~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nl----------------------A~rcfrlaL~~d~~h~e  430 (478)
T KOG1129|consen  373 QIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNL----------------------AKRCFRLALTSDAQHGE  430 (478)
T ss_pred             chhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHH----------------------HHHHHHHHhccCcchHH
Confidence            88888887777665433444322  2222111122222211                      11122222111112345


Q ss_pred             eeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          352 KWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       352 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .+|.|----.+.|+.++|     ..+++....
T Consensus       431 alnNLavL~~r~G~i~~A-----rsll~~A~s  457 (478)
T KOG1129|consen  431 ALNNLAVLAARSGDILGA-----RSLLNAAKS  457 (478)
T ss_pred             HHHhHHHHHhhcCchHHH-----HHHHHHhhh
Confidence            666666666788999999     888888765

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

Probab=97.88  E-value=0.033  Score=54.94  Aligned_cols=330  Identities=9%  Similarity=-0.038  Sum_probs=210.0

Q ss_pred             HHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc------hhhhHHH------------H
Q 042756           36 TKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR------LSSLAFP------------L   97 (425)
Q Consensus        36 ~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~------~~~~a~~------------l   97 (425)
                      .+.|..+++..++.++.|...|.+--..=-..|+.+...+++.+.+..-.....      -+.+|..            +
T Consensus       422 YenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAI  501 (913)
T KOG0495|consen  422 YENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAI  501 (913)
T ss_pred             HHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHH
Confidence            344667777777667777888877666666678888888777776433111100      0112221            1


Q ss_pred             HHHhhhcCCC-ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756           98 YMRITEESWF-QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus        98 f~~m~~~~~~-~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      ......-+.- .---.++..--..|.+.+.++-|+.+|....+-..    ...+.|......=-..|..+.++..++...
T Consensus       502 i~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp----~k~slWlra~~~ek~hgt~Esl~Allqkav  577 (913)
T KOG0495|consen  502 IRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFP----CKKSLWLRAAMFEKSHGTRESLEALLQKAV  577 (913)
T ss_pred             HHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhcc----chhHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            1111111100 00123566666777788888888888888776422    222356555555555677554444444443


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ...+.      ....|--..+-+..+|+...|..++.+.-+.+-. +...|-..++.-..+..++.|..+|..-..  ..
T Consensus       578 ~~~pk------ae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~--~s  648 (913)
T KOG0495|consen  578 EQCPK------AEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARS--IS  648 (913)
T ss_pred             HhCCc------chhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhc--cC
Confidence            33222      2237777778888899999999999999886422 567888899999999999999999998766  45


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHHhhc---------cCCchhhHHHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR-TYNSVLNSCSTIMSMLQDLN---------SNDFPLSILEL  326 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~-t~~~ll~~~~~~~~~~~~~~---------~~~~~~~~~~~  326 (425)
                      |+...|.--+...--.|+.++|.+++++-.+.  -|+.. .|-.+=+.+-+.++++.+..         +++.+.++. +
T Consensus       649 gTeRv~mKs~~~er~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWll-L  725 (913)
T KOG0495|consen  649 GTERVWMKSANLERYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLL-L  725 (913)
T ss_pred             CcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHH-H
Confidence            78888888888888889999999999887764  56664 44444455666677766632         333333333 2


Q ss_pred             Hhhcch-hhHHHHHHHHhC---CCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhcc
Q 042756          327 TEVLNE-EEVSVVKELEDS---SVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFN  386 (425)
Q Consensus       327 ~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~  386 (425)
                      .+.-.. .....+..++++   ....|...|-..|+.=.+.|+.+.|     ..+..+..+.++
T Consensus       726 akleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a-----~~lmakALQecp  784 (913)
T KOG0495|consen  726 AKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQA-----ELLMAKALQECP  784 (913)
T ss_pred             HHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHH-----HHHHHHHHHhCC
Confidence            222221 122233344433   3335678899999999999999999     777777766444

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

Probab=97.88  E-value=0.0039  Score=59.07  Aligned_cols=222  Identities=9%  Similarity=0.040  Sum_probs=148.7

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc
Q 042756          123 KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM  202 (425)
Q Consensus       123 ~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~  202 (425)
                      -.|+.-+|.+-|+...+-...+    +..|--+-.+|....+.+.....+....+.-+..    ||  +|..--..+.-.
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~----~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n----~d--vYyHRgQm~flL  407 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAF----NSLYIKRAAAYADENQSEKMWKDFNKAEDLDPEN----PD--VYYHRGQMRFLL  407 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCccc----chHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCC----Cc--hhHhHHHHHHHH
Confidence            4588889999999987642221    2225556667777777444444444443333222    44  888777777778


Q ss_pred             CChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      +++++|..=|++..+  +.| +++.|..+-.+.-|.+.+++++..|++.+++ ++.-..+||-.-..+...++++.|.+-
T Consensus       408 ~q~e~A~aDF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~  484 (606)
T KOG0547|consen  408 QQYEEAIADFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQ  484 (606)
T ss_pred             HHHHHHHHHHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHH
Confidence            899999999998877  455 4678888888889999999999999998875 444588999999999999999999999


Q ss_pred             HHHHHhCCCCCCHH-HHHHHHHHHHHHHHHHHhhccCCchhhHH-HHHhhcchhhHHHHHHHHhCCCCccc---ceeecc
Q 042756          282 LQKMKDSGIPFSVR-TYNSVLNSCSTIMSMLQDLNSNDFPLSIL-ELTEVLNEEEVSVVKELEDSSVLDEA---MKWDSG  356 (425)
Q Consensus       282 ~~~M~~~g~~pd~~-t~~~ll~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~l  356 (425)
                      |+..++.  .|+.. ++...                   .++++ ++.-....++.....+++.+-+..|.   ..|..|
T Consensus       485 YD~ai~L--E~~~~~~~v~~-------------------~plV~Ka~l~~qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tl  543 (606)
T KOG0547|consen  485 YDKAIEL--EPREHLIIVNA-------------------APLVHKALLVLQWKEDINQAENLLRKAIELDPKCEQAYETL  543 (606)
T ss_pred             HHHHHhh--ccccccccccc-------------------hhhhhhhHhhhchhhhHHHHHHHHHHHHccCchHHHHHHHH
Confidence            9997653  33311 11110                   01111 00001112334444455544444443   467788


Q ss_pred             ccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          357 ETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       357 i~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      -.--...|+.++|     +++|++-..
T Consensus       544 aq~~lQ~~~i~eA-----ielFEksa~  565 (606)
T KOG0547|consen  544 AQFELQRGKIDEA-----IELFEKSAQ  565 (606)
T ss_pred             HHHHHHHhhHHHH-----HHHHHHHHH
Confidence            8888899999999     999987644

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

Probab=97.87  E-value=0.011  Score=56.21  Aligned_cols=160  Identities=11%  Similarity=-0.038  Sum_probs=105.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCccc-HHHHHHHHHHHhhcCCCCccCh-hHHHHHH
Q 042756          119 AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRG-FDDTYARLNQLVNSSSSVYVKR-QALKSMI  196 (425)
Q Consensus       119 ~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~-~~~~~~~~~~~~~~~~~~~p~~-~~~~~li  196 (425)
                      ..+...|++++|.+++++..+..  |..  ...+.. ...+...|+..+ ...+...+... .   ...|+. .....+-
T Consensus        51 ~~~~~~g~~~~A~~~~~~~l~~~--P~~--~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~-~---~~~~~~~~~~~~~a  121 (355)
T cd05804          51 LSAWIAGDLPKALALLEQLLDDY--PRD--LLALKL-HLGAFGLGDFSGMRDHVARVLPLW-A---PENPDYWYLLGMLA  121 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC--CCc--HHHHHH-hHHHHHhcccccCchhHHHHHhcc-C---cCCCCcHHHHHHHH
Confidence            34566799999999999987652  121  122332 223333333221 22222222221 1   122332 3444555


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-CcC--HHhHHHHHHHHHhcC
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT-RVD--TVCSNMVLSSYGDHN  273 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~-~~~--~~~yn~li~~~~~~g  273 (425)
                      ..+...|++++|.+.+++..+.. +.+...+..+-..+...|++++|...++......- .|+  ...|..+...+...|
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G  200 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERG  200 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCC
Confidence            67888999999999999999863 33466788888999999999999999998776421 233  245667888999999


Q ss_pred             CHHHHHHHHHHHHhC
Q 042756          274 ELSRMVLWLQKMKDS  288 (425)
Q Consensus       274 ~~~~A~~l~~~M~~~  288 (425)
                      ++++|..+|++....
T Consensus       201 ~~~~A~~~~~~~~~~  215 (355)
T cd05804         201 DYEAALAIYDTHIAP  215 (355)
T ss_pred             CHHHHHHHHHHHhcc
Confidence            999999999998643

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.

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

Probab=97.86  E-value=0.0076  Score=61.71  Aligned_cols=247  Identities=13%  Similarity=0.044  Sum_probs=159.8

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCch-------------hhhHHHHHHHh
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRL-------------SSLAFPLYMRI  101 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~-------------~~~a~~lf~~m  101 (425)
                      .+..|.+.+..+.+..+-=+..|-.+....-..++...|...+.+.+.-+...|..             +..|.+-|..+
T Consensus       511 ~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i  590 (1018)
T KOG2002|consen  511 DTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETI  590 (1018)
T ss_pred             hhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHH
Confidence            56667788888877633334445555422233467888999998888766655531             22344444444


Q ss_pred             hhcCCCccCHHHHHHHHHHHHh------------cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756          102 TEESWFQWNPKLVAEIIAFLDK------------QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus       102 ~~~~~~~~~~~~~~~ll~~~~~------------~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      ..+....+|+++.-.|-+.|.+            .+..++|+++|.+..+.    .|.+...-|=+-..++..|++..+.
T Consensus       591 ~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~----dpkN~yAANGIgiVLA~kg~~~~A~  666 (1018)
T KOG2002|consen  591 LKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRN----DPKNMYAANGIGIVLAEKGRFSEAR  666 (1018)
T ss_pred             HhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhc----CcchhhhccchhhhhhhccCchHHH
Confidence            3332233455554445454432            24467788888887653    3332333344666677888876666


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK-GLEPSGFEYKCIIYGYGRLGLLEDMERIVN  248 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~  248 (425)
                      ++|..+++.....    +|  +|=.+-++|...|++..|+++|+...+. .-.-+..+.+.|-.++-++|.+.+|.+..-
T Consensus       667 dIFsqVrEa~~~~----~d--v~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll  740 (1018)
T KOG2002|consen  667 DIFSQVREATSDF----ED--VWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALL  740 (1018)
T ss_pred             HHHHHHHHHHhhC----Cc--eeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            6666666655432    22  8889999999999999999999987765 444567788999999999999999988877


Q ss_pred             HHHHCCCCcCHHhHHHHHHHH------------------HhcCCHHHHHHHHHHHHhCCCC
Q 042756          249 QMESDGTRVDTVCSNMVLSSY------------------GDHNELSRMVLWLQKMKDSGIP  291 (425)
Q Consensus       249 ~m~~~g~~~~~~~yn~li~~~------------------~~~g~~~~A~~l~~~M~~~g~~  291 (425)
                      ........-..+-||..+-..                  ...+..+.|.++|.+|...+-.
T Consensus       741 ~a~~~~p~~~~v~FN~a~v~kkla~s~lr~~k~t~eev~~a~~~le~a~r~F~~ls~~~d~  801 (1018)
T KOG2002|consen  741 KARHLAPSNTSVKFNLALVLKKLAESILRLEKRTLEEVLEAVKELEEARRLFTELSKNGDK  801 (1018)
T ss_pred             HHHHhCCccchHHhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            666554444556777665433                  1133567788899999876543

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

Probab=97.84  E-value=0.0092  Score=57.62  Aligned_cols=263  Identities=13%  Similarity=0.010  Sum_probs=166.0

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+.+..++++.+.+.+.+  +...+..=|.++...|+..+-..+=.++.+...    +...+|=++-..|-..|....++
T Consensus       259 ~f~~c~kit~~lle~dpf--h~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP----~~a~sW~aVg~YYl~i~k~seAR  332 (611)
T KOG1173|consen  259 RFKECLKITEELLEKDPF--HLPCLPLHIACLYELGKSNKLFLLSHKLVDLYP----SKALSWFAVGCYYLMIGKYSEAR  332 (611)
T ss_pred             hHHHHHHHhHHHHhhCCC--CcchHHHHHHHHHHhcccchHHHHHHHHHHhCC----CCCcchhhHHHHHHHhcCcHHHH
Confidence            456667777776665544  444455556677777777666655556655422    22234556666666667755555


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc--CC-CCCHHHHHHHHHHHHcCCCHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK--GL-EPSGFEYKCIIYGYGRLGLLEDMERI  246 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~-~p~~~ty~~ll~~~~~~g~~~~a~~~  246 (425)
                      ..+..-..+-+.   ..|   .|=..-.+|+-.|+.|.|+..+...-+.  |. .|  .-|..+  -|.+.+.++.|.++
T Consensus       333 ry~SKat~lD~~---fgp---aWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP--~LYlgm--ey~~t~n~kLAe~F  402 (611)
T KOG1173|consen  333 RYFSKATTLDPT---FGP---AWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLP--SLYLGM--EYMRTNNLKLAEKF  402 (611)
T ss_pred             HHHHHHhhcCcc---ccH---HHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcch--HHHHHH--HHHHhccHHHHHHH
Confidence            555544444222   223   7778888888888888888877766543  32 23  233332  47788899999999


Q ss_pred             HHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCC----CCHHHHHHHHHHHHHHHHHHHhhccCCch
Q 042756          247 VNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD--SGIP----FSVRTYNSVLNSCSTIMSMLQDLNSNDFP  320 (425)
Q Consensus       247 ~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~--~g~~----pd~~t~~~ll~~~~~~~~~~~~~~~~~~~  320 (425)
                      |.+..... +-|+...|-+--.....+.+.+|..+|..-..  ..+.    ....|++.|-.+|.+.+..+.+       
T Consensus       403 f~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eA-------  474 (611)
T KOG1173|consen  403 FKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEA-------  474 (611)
T ss_pred             HHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHH-------
Confidence            98765532 23667777776666778889999999988652  1111    1334566666666666655433       


Q ss_pred             hhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeee
Q 042756          321 LSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVC  400 (425)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~  400 (425)
                                     ....+-.-.....+..++.++--.|...|+++.|     ++.|.+..       .+.||..+.+.
T Consensus       475 ---------------I~~~q~aL~l~~k~~~~~asig~iy~llgnld~A-----id~fhKaL-------~l~p~n~~~~~  527 (611)
T KOG1173|consen  475 ---------------IDYYQKALLLSPKDASTHASIGYIYHLLGNLDKA-----IDHFHKAL-------ALKPDNIFISE  527 (611)
T ss_pred             ---------------HHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHH-----HHHHHHHH-------hcCCccHHHHH
Confidence                           2222333334456778888888889999999999     99999865       47888877776


Q ss_pred             ccc
Q 042756          401 GSG  403 (425)
Q Consensus       401 l~~  403 (425)
                      +++
T Consensus       528 lL~  530 (611)
T KOG1173|consen  528 LLK  530 (611)
T ss_pred             HHH
Confidence            664

>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=97.83  E-value=0.00024  Score=60.40  Aligned_cols=88  Identities=17%  Similarity=0.212  Sum_probs=73.9

Q ss_pred             ChhHHHHHHHHHHh-----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC----------------CHHHHHHH
Q 042756          188 KRQALKSMISGLCE-----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG----------------LLEDMERI  246 (425)
Q Consensus       188 ~~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g----------------~~~~a~~~  246 (425)
                      |..+|..+|..|.+     .|..+-....++.|.+-|+.-|..+|+.||+.+=+..                +-+-|.++
T Consensus        46 ~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~l  125 (228)
T PF06239_consen   46 DKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDL  125 (228)
T ss_pred             cHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHH
Confidence            33477777777765     4788999999999999999999999999999976532                24669999


Q ss_pred             HHHHHHCCCCcCHHhHHHHHHHHHhcCCH
Q 042756          247 VNQMESDGTRVDTVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       247 ~~~m~~~g~~~~~~~yn~li~~~~~~g~~  275 (425)
                      +++|+..|+.||..|+..|+..|.+.+.+
T Consensus       126 L~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  126 LEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence            99999999999999999999999877753

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

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

Probab=97.80  E-value=0.007  Score=64.20  Aligned_cols=210  Identities=10%  Similarity=0.006  Sum_probs=149.6

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +...|-.-+.-....+..++|.++..+.|..-..    .++.        +      --.+|.++++.-...|.-+...+
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~----REee--------E------KLNiWiA~lNlEn~yG~eesl~k 1518 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKTINF----REEE--------E------KLNIWIAYLNLENAYGTEESLKK 1518 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCc----chhH--------H------HHHHHHHHHhHHHhhCcHHHHHH
Confidence            3455666666666666666666666665532210    0000        0      11245556666666777888889


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      +|++.++-.   ++  ..+|..|..-|.+....+.+.+.++.+.+.-...      ..+|...+.++.+..+-+.|.+++
T Consensus      1519 VFeRAcqyc---d~--~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~------~~vW~~y~~fLl~~ne~~aa~~lL 1587 (1710)
T KOG1070|consen 1519 VFERACQYC---DA--YTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQT------RKVWIMYADFLLRQNEAEAARELL 1587 (1710)
T ss_pred             HHHHHHHhc---ch--HHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcch------hhHHHHHHHHHhcccHHHHHHHHH
Confidence            999988742   21  2378899999999999766666666665554322      239999999999999999999999


Q ss_pred             HHHHHcCCCCC---HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          213 EEMRVKGLEPS---GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       213 ~~m~~~g~~p~---~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      .+..+.  -|-   ..........-.+.||.+.+..+|+.....-- --...|+..|+.=.++|+.+.+..+|++.+..+
T Consensus      1588 ~rAL~~--lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ayP-KRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~ 1664 (1710)
T KOG1070|consen 1588 KRALKS--LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAYP-KRTDLWSVYIDMEIKHGDIKYVRDLFERVIELK 1664 (1710)
T ss_pred             HHHHhh--cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhCc-cchhHHHHHHHHHHccCCHHHHHHHHHHHHhcC
Confidence            998874  343   33455556667889999999999998887532 256789999999999999999999999999998


Q ss_pred             CCCCH
Q 042756          290 IPFSV  294 (425)
Q Consensus       290 ~~pd~  294 (425)
                      +.|-.
T Consensus      1665 l~~kk 1669 (1710)
T KOG1070|consen 1665 LSIKK 1669 (1710)
T ss_pred             CChhH
Confidence            87743

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

Probab=97.78  E-value=0.019  Score=59.20  Aligned_cols=144  Identities=14%  Similarity=0.109  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI  230 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l  230 (425)
                      +|+.+-.+=.+.|.   +.++.+-+-+.-        |...|--+|....+.|.+|+-.+++...+++.-+|.  .=+.+
T Consensus      1106 vWsqlakAQL~~~~---v~dAieSyikad--------Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~--id~eL 1172 (1666)
T KOG0985|consen 1106 VWSQLAKAQLQGGL---VKDAIESYIKAD--------DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPY--IDSEL 1172 (1666)
T ss_pred             HHHHHHHHHHhcCc---hHHHHHHHHhcC--------CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCcc--chHHH
Confidence            57777777777776   455555443321        223888888888888888888888877777766664  44577


Q ss_pred             HHHHHcCCCHHHHHHHHHH------------HHHCC-------CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 042756          231 IYGYGRLGLLEDMERIVNQ------------MESDG-------TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIP  291 (425)
Q Consensus       231 l~~~~~~g~~~~a~~~~~~------------m~~~g-------~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~  291 (425)
                      |-+|++.+++.+.+++..-            .-+.|       +-.++.-|..|...++..|++..|...-++.-     
T Consensus      1173 i~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAn----- 1247 (1666)
T KOG0985|consen 1173 IFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKAN----- 1247 (1666)
T ss_pred             HHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhcc-----
Confidence            8888888887776655421            00111       01144556777777788888888776655432     


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHh
Q 042756          292 FSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       292 pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                       +..||.-+-.+|...+.+..+
T Consensus      1248 -s~ktWK~VcfaCvd~~EFrlA 1268 (1666)
T KOG0985|consen 1248 -STKTWKEVCFACVDKEEFRLA 1268 (1666)
T ss_pred             -chhHHHHHHHHHhchhhhhHH
Confidence             667888888888887766655

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

Probab=97.78  E-value=0.048  Score=53.74  Aligned_cols=344  Identities=12%  Similarity=0.093  Sum_probs=192.4

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhh----HHHHHHHhhh-------
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSL----AFPLYMRITE-------  103 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~----a~~lf~~m~~-------  103 (425)
                      ..+.+.+++++.++   .++..-+.-|.-+++.++.++|-..+.+.+.++...+.....    ..++++-+.+       
T Consensus       153 lPets~rvyrRYLk---~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~s  229 (835)
T KOG2047|consen  153 LPETSIRVYRRYLK---VAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQS  229 (835)
T ss_pred             ChHHHHHHHHHHHh---cCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcc
Confidence            44556666666653   555567888888999999999999999988765443322111    2222222111       


Q ss_pred             --------cCCCc-cC--HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-----------
Q 042756          104 --------ESWFQ-WN--PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK-----------  161 (425)
Q Consensus       104 --------~~~~~-~~--~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~-----------  161 (425)
                              .|.-. +|  ...|++|...|.+.|.+++|..+|++-.+.-.. .++    |+.+.++|..           
T Consensus       230 lnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~t-vrD----Ft~ifd~Ya~FEE~~~~~~me  304 (835)
T KOG2047|consen  230 LNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTVMT-VRD----FTQIFDAYAQFEESCVAAKME  304 (835)
T ss_pred             cCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhee-hhh----HHHHHHHHHHHHHHHHHHHHh
Confidence                    11000 11  136888999999999999999999997653221 222    3334444432           


Q ss_pred             -----cCCc---ccHHHHHHHHHHHhhcCCCCc---------cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC---CC
Q 042756          162 -----HDSK---RGFDDTYARLNQLVNSSSSVY---------VKRQALKSMISGLCEMGQPHEAENLIEEMRVKG---LE  221 (425)
Q Consensus       162 -----~g~~---~~~~~~~~~~~~~~~~~~~~~---------p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g---~~  221 (425)
                           .|+.   .+++-.+..+...+...+...         -++..|..-++  +..|+..+...+|.+....-   ..
T Consensus       305 ~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~vdP~ka  382 (835)
T KOG2047|consen  305 LADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKTVDPKKA  382 (835)
T ss_pred             hhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHccCcccC
Confidence                 1111   112333444444444332110         01223333333  33677788888888877541   11


Q ss_pred             C-C-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC---HHhHHHHHHHHHhcCCHHHHHHHHHHHHhC--------
Q 042756          222 P-S-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD---TVCSNMVLSSYGDHNELSRMVLWLQKMKDS--------  288 (425)
Q Consensus       222 p-~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~---~~~yn~li~~~~~~g~~~~A~~l~~~M~~~--------  288 (425)
                      | . ..-|..+-+.|-..|+++.|..+|+.-.+-.++.-   ..+|......=.++.+++.|+++.++....        
T Consensus       383 ~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~  462 (835)
T KOG2047|consen  383 VGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEY  462 (835)
T ss_pred             CCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhh
Confidence            1 1 23567777888888888888888888776544332   567777777777888888888887775421        


Q ss_pred             --CCCC-------CHHHHHHHHHHHHHHHHHHHhhc--------cCCchhhHHHHHhhcc-hhhHHHHHHHHhCCCC---
Q 042756          289 --GIPF-------SVRTYNSVLNSCSTIMSMLQDLN--------SNDFPLSILELTEVLN-EEEVSVVKELEDSSVL---  347 (425)
Q Consensus       289 --g~~p-------d~~t~~~ll~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~---  347 (425)
                        |-.|       +...|+..++---..|-++....        .-.-+.++..|..... ..--+..++..++|+.   
T Consensus       463 yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk  542 (835)
T KOG2047|consen  463 YDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLFK  542 (835)
T ss_pred             hcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCC
Confidence              1112       23344444443222222222210        0011112222333322 2233345666788876   


Q ss_pred             -ccc-ceeeccccchhcc---cCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeee
Q 042756          348 -DEA-MKWDSGETKLDLH---GMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVV  399 (425)
Q Consensus       348 -~~~-~~~~~li~~~~~~---~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~  399 (425)
                       |++ ..||..+..+.+.   ..++.|     .++|++..+      |..|...-+.
T Consensus       543 ~p~v~diW~tYLtkfi~rygg~klEra-----RdLFEqaL~------~Cpp~~aKti  588 (835)
T KOG2047|consen  543 WPNVYDIWNTYLTKFIKRYGGTKLERA-----RDLFEQALD------GCPPEHAKTI  588 (835)
T ss_pred             CccHHHHHHHHHHHHHHHhcCCCHHHH-----HHHHHHHHh------cCCHHHHHHH
Confidence             554 3688887776653   356677     899999885      6767665444

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

Probab=97.68  E-value=0.037  Score=51.64  Aligned_cols=263  Identities=9%  Similarity=-0.040  Sum_probs=134.8

Q ss_pred             HhhHHHHHHHHHHhHHh--cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcC-CCc-
Q 042756           33 ARLTKQGQRFLSSLALA--VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEES-WFQ-  108 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~--~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~-~~~-  108 (425)
                      .+.-..|.+.+-.+...  ++-|......+-+.+...|+...+...|.+..+-+.    ..-+++++|-.+.... ... 
T Consensus       209 ~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dp----y~i~~MD~Ya~LL~~eg~~e~  284 (564)
T KOG1174|consen  209 NFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANP----DNVEAMDLYAVLLGQEGGCEQ  284 (564)
T ss_pred             hcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCCh----hhhhhHHHHHHHHHhccCHhh
Confidence            34334444444333333  888999999999999999999999999999866543    2223333333322211 010 


Q ss_pred             -------------cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756          109 -------------WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus       109 -------------~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                                   .+..-|-.-.......++++.|+.+-++-.+.   .++. +..|-.--+++...++.   .++.-.|
T Consensus       285 ~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~---~~r~-~~alilKG~lL~~~~R~---~~A~IaF  357 (564)
T KOG1174|consen  285 DSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDS---EPRN-HEALILKGRLLIALERH---TQAVIAF  357 (564)
T ss_pred             HHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhcc---Cccc-chHHHhccHHHHhccch---HHHHHHH
Confidence                         01111111122223345677777666554432   1221 22232222345566774   4444444


Q ss_pred             HHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH-HHHHHcCCC-HHHHHHHHHHHHHC
Q 042756          176 NQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI-IYGYGRLGL-LEDMERIVNQMESD  253 (425)
Q Consensus       176 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l-l~~~~~~g~-~~~a~~~~~~m~~~  253 (425)
                      +....-.   .-+..+|..|+.+|...|++.+|.-+-+.-... +.-+..+.+-+ -..|.-.-. -++|.++++.-...
T Consensus       358 R~Aq~La---p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~  433 (564)
T KOG1174|consen  358 RTAQMLA---PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKI  433 (564)
T ss_pred             HHHHhcc---hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhcc
Confidence            4433211   013358999999999999988887665544321 11233333332 122222211 24455555543322


Q ss_pred             CCCcC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 042756          254 GTRVD-TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       254 g~~~~-~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~  314 (425)
                        .|+ ...-+.+...+...|..+.++.++++-...  .||..-.+.|-+.+.....+.++|
T Consensus       434 --~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am  491 (564)
T KOG1174|consen  434 --NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAM  491 (564)
T ss_pred             --CCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHH
Confidence              333 333444555555666666666666665432  566666666666655555554444

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

Probab=97.66  E-value=0.055  Score=55.25  Aligned_cols=240  Identities=14%  Similarity=0.068  Sum_probs=155.7

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhc--CChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           27 LVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVAS--SPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~--~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      +|..+-.+.++.|.+..+.+.++ .|+. .|..++.++...  |+.++|+..++.                     ....
T Consensus        16 i~d~ld~~qfkkal~~~~kllkk-~Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~---------------------~~~~   72 (932)
T KOG2053|consen   16 IYDLLDSSQFKKALAKLGKLLKK-HPNA-LYAKVLKALSLFRLGKGDEALKLLEA---------------------LYGL   72 (932)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHH-CCCc-HHHHHHHHHHHHHhcCchhHHHHHhh---------------------hccC
Confidence            89999999999999999998876 4443 366777777654  555555544433                     3333


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS  184 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~  184 (425)
                      . .. |..|...+-..|-+.|+.++|..+|++..+.... . .   --..+..+|.|.+.+....++.-.+.+..++...
T Consensus        73 ~-~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~P~-e-e---ll~~lFmayvR~~~yk~qQkaa~~LyK~~pk~~y  145 (932)
T KOG2053|consen   73 K-GT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQKYPS-E-E---LLYHLFMAYVREKSYKKQQKAALQLYKNFPKRAY  145 (932)
T ss_pred             C-CC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhhCCc-H-H---HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccc
Confidence            2 22 7778888999999999999999999999876433 2 1   2346778888888876666655555554444322


Q ss_pred             CccChhHHHHHHHHHHhcC----------ChhHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCCHHHHHHHHH-HHHH
Q 042756          185 VYVKRQALKSMISGLCEMG----------QPHEAENLIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVN-QMES  252 (425)
Q Consensus       185 ~~p~~~~~~~li~~~~~~g----------~~~~a~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~g~~~~a~~~~~-~m~~  252 (425)
                            .+=++|+-....-          -..-|.+.++.+.+.+ -.-+..-.---+...-..|++++|..++. ..-+
T Consensus       146 ------yfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~  219 (932)
T KOG2053|consen  146 ------YFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAE  219 (932)
T ss_pred             ------hHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence                  4444555554431          1234556666666554 21222222222344556788999999994 4444


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      .-..-+...-|--++.+...+++.+..++-.+....|  +|.  |.+.++++++
T Consensus       220 ~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~--~Dd--y~~~~~sv~k  269 (932)
T KOG2053|consen  220 KLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG--NDD--YKIYTDSVFK  269 (932)
T ss_pred             hccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC--Ccc--hHHHHHHHHH
Confidence            4444456666677888889999999999888888775  343  5555554444

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

Probab=97.61  E-value=0.056  Score=51.38  Aligned_cols=184  Identities=13%  Similarity=0.026  Sum_probs=139.2

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+..|.++|++...-+ . -+...|---+.+=.+..++..|..+++.....   .++... .|-..+..=-..|+..++.
T Consensus        88 e~~RARSv~ERALdvd-~-r~itLWlkYae~Emknk~vNhARNv~dRAvt~---lPRVdq-lWyKY~ymEE~LgNi~gaR  161 (677)
T KOG1915|consen   88 EIQRARSVFERALDVD-Y-RNITLWLKYAEFEMKNKQVNHARNVWDRAVTI---LPRVDQ-LWYKYIYMEEMLGNIAGAR  161 (677)
T ss_pred             HHHHHHHHHHHHHhcc-c-ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh---cchHHH-HHHHHHHHHHHhcccHHHH
Confidence            4567888888876655 2 25556666777778889999999999997764   222222 3445555556678877777


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      ++++..-+       ..||...|++.|+.=.+-.+++.|..++++..-  +.|+..+|--...---+.|.+..|..+|+.
T Consensus       162 qiferW~~-------w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~Vyer  232 (677)
T KOG1915|consen  162 QIFERWME-------WEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSVYER  232 (677)
T ss_pred             HHHHHHHc-------CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            77776654       779999999999999999999999999999987  679999999999999999999999999998


Q ss_pred             HHHC-CC-CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          250 MESD-GT-RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       250 m~~~-g~-~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ..+. |- .-+...|++...-=.++..++.|.-+|+-..+.
T Consensus       233 Aie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~  273 (677)
T KOG1915|consen  233 AIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH  273 (677)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7653 21 123455555555556778888998888887754

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

Probab=97.60  E-value=0.057  Score=50.47  Aligned_cols=267  Identities=9%  Similarity=-0.032  Sum_probs=165.1

Q ss_pred             HHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756           96 PLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus        96 ~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                      ..|--......++.|......+-..+...|+.+.|+..|++....    +|.+...-...--.+.+.|+.+........+
T Consensus       217 ~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~----dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~L  292 (564)
T KOG1174|consen  217 QTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA----NPDNVEAMDLYAVLLGQEGGCEQDSALMDYL  292 (564)
T ss_pred             hHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC----ChhhhhhHHHHHHHHHhccCHhhHHHHHHHH
Confidence            333333333457789999999999999999999999999997643    3322211111222345677766666666666


Q ss_pred             HHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          176 NQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       176 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      +......      ...|-+-.......++++.|+.+-++..+.+  |+ ...|-.=-.++...|++++|.--|+..+...
T Consensus       293 f~~~~~t------a~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~--~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~La  364 (564)
T KOG1174|consen  293 FAKVKYT------ASHWFVHAQLLYDEKKFERALNFVEKCIDSE--PRNHEALILKGRLLIALERHTQAVIAFRTAQMLA  364 (564)
T ss_pred             Hhhhhcc------hhhhhhhhhhhhhhhhHHHHHHHHHHHhccC--cccchHHHhccHHHHhccchHHHHHHHHHHHhcc
Confidence            6653222      2367777777788899999999998887642  22 2233222345677899999999999877642


Q ss_pred             CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH-HHHHH-------HHHHH-HHhhc-cCCchhhHH
Q 042756          255 TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV-LNSCS-------TIMSM-LQDLN-SNDFPLSIL  324 (425)
Q Consensus       255 ~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l-l~~~~-------~~~~~-~~~~~-~~~~~~~~~  324 (425)
                       +.+..+|.-|+.+|...|++.||.-+-+..... +.-+..|...+ ...|.       +...+ ++++. .++|.+.+.
T Consensus       365 -p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~  442 (564)
T KOG1174|consen  365 -PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVN  442 (564)
T ss_pred             -hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHH
Confidence             247899999999999999999998876664321 12233333333 11111       12222 22332 666766665


Q ss_pred             HHHhh---cc--hhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          325 ELTEV---LN--EEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       325 ~~~~~---~~--~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .+..+   .+  .+....++.-+.  ..||...-+.|-.-+.-.+.+.+|     ++.|....+
T Consensus       443 ~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~a-----m~~y~~ALr  499 (564)
T KOG1174|consen  443 LIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKA-----MEYYYKALR  499 (564)
T ss_pred             HHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHH-----HHHHHHHHh
Confidence            33222   22  233333444333  237777777777777777778887     777766554

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.59  E-value=0.058  Score=49.39  Aligned_cols=48  Identities=8%  Similarity=-0.013  Sum_probs=29.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHHHHHHHHHh
Q 042756          265 VLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVL-NSCSTIMSMLQD  313 (425)
Q Consensus       265 li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll-~~~~~~~~~~~~  313 (425)
                      +..+++..|.+.+|+++|-......++ |..+|-+++ ++|.+.+....+
T Consensus       399 ~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lA  447 (557)
T KOG3785|consen  399 LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLA  447 (557)
T ss_pred             HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHH
Confidence            456667788888888888776544443 555665554 445555554444

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.59  E-value=0.0067  Score=49.46  Aligned_cols=104  Identities=6%  Similarity=-0.191  Sum_probs=87.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .+...-.++...|++++|...|++..... +.+...|..+-.++.+.|++++|...|+...... ..+...+..+-.++.
T Consensus        26 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~  103 (144)
T PRK15359         26 TVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            35567778889999999999999988752 3367789999999999999999999999999864 347889999999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 042756          271 DHNELSRMVLWLQKMKDSGIPFSVRTYN  298 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~~g~~pd~~t~~  298 (425)
                      ..|+.++|...|+...+.  .|+...+.
T Consensus       104 ~~g~~~eAi~~~~~Al~~--~p~~~~~~  129 (144)
T PRK15359        104 MMGEPGLAREAFQTAIKM--SYADASWS  129 (144)
T ss_pred             HcCCHHHHHHHHHHHHHh--CCCChHHH
Confidence            999999999999998764  56554443

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

Probab=97.56  E-value=0.012  Score=50.80  Aligned_cols=163  Identities=7%  Similarity=-0.017  Sum_probs=115.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      -+..|...|+++.+..-.+.+..    +..    .|+       ..++   .+++...+.+.....   ..|...|..+-
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~~----~~~----~~~-------~~~~---~~~~i~~l~~~L~~~---P~~~~~w~~Lg   80 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLAD----PLH----QFA-------SQQT---PEAQLQALQDKIRAN---PQNSEQWALLG   80 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHhC----ccc----ccc-------Cchh---HHHHHHHHHHHHHHC---CCCHHHHHHHH
Confidence            45678888998887554422211    110    111       1233   455555555554433   13556999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHH-HHcCCC--HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYG-YGRLGL--LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~-~~~~g~--~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                      ..|...|++++|...|++....  .| +...+..+-.+ +...|+  .++|.+++++..+..-. +...+..+-..+...
T Consensus        81 ~~~~~~g~~~~A~~a~~~Al~l--~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~LA~~~~~~  157 (198)
T PRK10370         81 EYYLWRNDYDNALLAYRQALQL--RGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALMLLASDAFMQ  157 (198)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHc
Confidence            9999999999999999998885  45 56677777776 467777  59999999999987543 778899999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          273 NELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       273 g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      |++++|+..|+++.+.. .|+..-+..+ .+-.
T Consensus       158 g~~~~Ai~~~~~aL~l~-~~~~~r~~~i-~~i~  188 (198)
T PRK10370        158 ADYAQAIELWQKVLDLN-SPRVNRTQLV-ESIN  188 (198)
T ss_pred             CCHHHHHHHHHHHHhhC-CCCccHHHHH-HHHH
Confidence            99999999999998763 5666555444 6533

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

Probab=97.55  E-value=0.0038  Score=50.09  Aligned_cols=110  Identities=10%  Similarity=-0.053  Sum_probs=88.1

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .....+...+.+.|++++|.+.|+.....+ ..+...+..+-..+.+.|++++|..+++...+.+ +.+...|..+-..|
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~   95 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECL   95 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHH
Confidence            356677788888999999999999988753 3367788888999999999999999999887764 34677788888899


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS  303 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~  303 (425)
                      ...|+.++|...|++..+.  .|+...+..+..-
T Consensus        96 ~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~  127 (135)
T TIGR02552        96 LALGEPESALKALDLAIEI--CGENPEYSELKER  127 (135)
T ss_pred             HHcCCHHHHHHHHHHHHHh--ccccchHHHHHHH
Confidence            9999999999999988764  5776665555443

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

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

Probab=97.53  E-value=0.053  Score=57.96  Aligned_cols=220  Identities=10%  Similarity=0.064  Sum_probs=151.7

Q ss_pred             HHHHHHHHhhHHHHHHHHHHhHHhcCCC-----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHH
Q 042756           26 TLVQCLTARLTKQGQRFLSSLALAVTRD-----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMR  100 (425)
Q Consensus        26 ~~~~~l~~~~~~~a~~~~~~m~~~~~~d-----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~  100 (425)
                      ++..-+..+..+.|++++++.+..+.+.     .-.|.++++.-.-.|+.                     +...++|++
T Consensus      1464 YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~e---------------------esl~kVFeR 1522 (1710)
T KOG1070|consen 1464 YMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTE---------------------ESLKKVFER 1522 (1710)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcH---------------------HHHHHHHHH
Confidence            3455567778888999999988763322     23344444444433432                     345556666


Q ss_pred             hhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 042756          101 ITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVN  180 (425)
Q Consensus       101 m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~  180 (425)
                      ..+-.   -.-.+|..|...|.+.+.+++|-++|+.|.++-+. .+   .+|...+..+.+..+   ++++-.++.+.+.
T Consensus      1523 Acqyc---d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q-~~---~vW~~y~~fLl~~ne---~~aa~~lL~rAL~ 1592 (1710)
T KOG1070|consen 1523 ACQYC---DAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQ-TR---KVWIMYADFLLRQNE---AEAARELLKRALK 1592 (1710)
T ss_pred             HHHhc---chHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcc-hh---hHHHHHHHHHhcccH---HHHHHHHHHHHHh
Confidence            55432   12346889999999999999999999999998662 32   378889999998887   5555555555543


Q ss_pred             cCCCCccCh---hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          181 SSSSVYVKR---QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       181 ~~~~~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      .-    |..   ..-.-.+..=.+.|+.+.+..+|+.....- +--...|+..|++-.+.|+.+.++.+|++....++.|
T Consensus      1593 ~l----Pk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1593 SL----PKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             hc----chhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            21    321   122333333456899999999999988752 1134689999999999999999999999999988766


Q ss_pred             C--HHhHHHHHHHHHhcCCHHHHHHH
Q 042756          258 D--TVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       258 ~--~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      -  -..|...+.-=-+.|+-..++.+
T Consensus      1668 kkmKfffKkwLeyEk~~Gde~~vE~V 1693 (1710)
T KOG1070|consen 1668 KKMKFFFKKWLEYEKSHGDEKNVEYV 1693 (1710)
T ss_pred             hHhHHHHHHHHHHHHhcCchhhHHHH
Confidence            4  56777777777777775554444

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

Probab=97.51  E-value=0.0071  Score=55.52  Aligned_cols=195  Identities=19%  Similarity=0.192  Sum_probs=122.4

Q ss_pred             HHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC---------------CchhhhHHHHHHHhhhcC
Q 042756           41 RFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH---------------PRLSSLAFPLYMRITEES  105 (425)
Q Consensus        41 ~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~---------------~~~~~~a~~lf~~m~~~~  105 (425)
                      .++.++.....|.......+..-+...+.-+.+...+.+.+......               .+.+++|++++..-    
T Consensus        53 ~vl~ei~~~~~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~----  128 (290)
T PF04733_consen   53 SVLSEIKKSSSPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG----  128 (290)
T ss_dssp             HHHHHS-TTSSCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT----
T ss_pred             HHHHHhccCCChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc----
Confidence            34455544445666655444333333234445555555554443221               12345555554331    


Q ss_pred             CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh--cCCcccHHHHHHHHHHHhhcCC
Q 042756          106 WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK--HDSKRGFDDTYARLNQLVNSSS  183 (425)
Q Consensus       106 ~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~--~g~~~~~~~~~~~~~~~~~~~~  183 (425)
                         -+.......+..|.+.++++.|.+.++.|.+..   +..   +-..+..++..  .|. +...+++..+.++...  
T Consensus       129 ---~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~---eD~---~l~qLa~awv~l~~g~-e~~~~A~y~f~El~~~--  196 (290)
T PF04733_consen  129 ---GSLELLALAVQILLKMNRPDLAEKELKNMQQID---EDS---ILTQLAEAWVNLATGG-EKYQDAFYIFEELSDK--  196 (290)
T ss_dssp             ---TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS---CCH---HHHHHHHHHHHHHHTT-TCCCHHHHHHHHHHCC--
T ss_pred             ---CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---CcH---HHHHHHHHHHHHHhCc-hhHHHHHHHHHHHHhc--
Confidence               356677788999999999999999999998642   222   22334444433  232 3467888888887543  


Q ss_pred             CCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH-HHHHHHHHHHHHC
Q 042756          184 SVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLL-EDMERIVNQMESD  253 (425)
Q Consensus       184 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~-~~a~~~~~~m~~~  253 (425)
                       ..++..+.|.+..++...|++++|.+++.+..... +-|..|...++.+....|+. +.+.+++.+++..
T Consensus       197 -~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  197 -FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             -S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             -cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence             34667799999999999999999999999977543 22566888888888888887 7788999998864

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.50  E-value=0.029  Score=49.82  Aligned_cols=137  Identities=12%  Similarity=0.023  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc--------CCcccHHHHHHHHHHHhhcCC
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH--------DSKRGFDDTYARLNQLVNSSS  183 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~--------g~~~~~~~~~~~~~~~~~~~~  183 (425)
                      ..+..+..++.+.|++++|...|+++.+.... .+.....+..+-..+.+.        |+   .+++.+.+.+.....+
T Consensus        71 ~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~a~~~~g~~~~~~~~~~~~~~~~---~~~A~~~~~~~~~~~p  146 (235)
T TIGR03302        71 QAQLDLAYAYYKSGDYAEAIAAADRFIRLHPN-HPDADYAYYLRGLSNYNQIDRVDRDQTA---AREAFEAFQELIRRYP  146 (235)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcC-CCchHHHHHHHHHHHHHhcccccCCHHH---HHHHHHHHHHHHHHCC
Confidence            45666788888999999999999998765332 221111233333334332        33   4555555555543321


Q ss_pred             CCccCh-hH--------------HHHHHHHHHhcCChhHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 042756          184 SVYVKR-QA--------------LKSMISGLCEMGQPHEAENLIEEMRVKG--LEPSGFEYKCIIYGYGRLGLLEDMERI  246 (425)
Q Consensus       184 ~~~p~~-~~--------------~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~ty~~ll~~~~~~g~~~~a~~~  246 (425)
                      .. +.. ..              .-.+-..|.+.|++++|...|.+.....  -+.....+..+..++.+.|+.++|..+
T Consensus       147 ~~-~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~  225 (235)
T TIGR03302       147 NS-EYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDA  225 (235)
T ss_pred             CC-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            11 000 00              1134566788999999999999998752  122356889999999999999999999


Q ss_pred             HHHHHHC
Q 042756          247 VNQMESD  253 (425)
Q Consensus       247 ~~~m~~~  253 (425)
                      ++.+..+
T Consensus       226 ~~~l~~~  232 (235)
T TIGR03302       226 AAVLGAN  232 (235)
T ss_pred             HHHHHhh
Confidence            9988765

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

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

Probab=97.48  E-value=0.039  Score=48.42  Aligned_cols=129  Identities=15%  Similarity=0.052  Sum_probs=79.0

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +............+.|++..|...|.+....    .|+....|+.+--+|-+.|+.++++..+....+.....+.     
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l----~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~-----  169 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAARL----APTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPS-----  169 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhcc----CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCch-----
Confidence            3334444666666677777777777775542    2222346666777777777766666666666665444432     


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                       .+|.|.-.|.-.|+++.|..++..-...+- -|..+-..+.-.....|++++|+++-..
T Consensus       170 -~~nNlgms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         170 -IANNLGMSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             -hhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHhhccc
Confidence             666666666667777777777776665432 2455556666666677777777666554

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

Probab=97.46  E-value=0.12  Score=51.07  Aligned_cols=227  Identities=11%  Similarity=0.003  Sum_probs=107.2

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHh--cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chh
Q 042756           27 LVQCLTARLTKQGQRFLSSLALA--VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLS   91 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~--~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~   91 (425)
                      ...|.-.++.+.++++.+.+++.  -++++.+.  .--.+..-|+.++|+..+...+..+...+             ..+
T Consensus        14 ~lk~yE~kQYkkgLK~~~~iL~k~~eHgeslAm--kGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y   91 (700)
T KOG1156|consen   14 ALKCYETKQYKKGLKLIKQILKKFPEHGESLAM--KGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKY   91 (700)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHhCCccchhHHh--ccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhH
Confidence            45666677778888888888777  33444322  22223344677788888777765443211             135


Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDT  171 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~  171 (425)
                      ++|++.|.....-+  +-|..++.-+--.-++.|+++.....-.+..+.    .+.....|..+.-++.-.|....+.+.
T Consensus        92 ~eaiKcy~nAl~~~--~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql----~~~~ra~w~~~Avs~~L~g~y~~A~~i  165 (700)
T KOG1156|consen   92 DEAIKCYRNALKIE--KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQL----RPSQRASWIGFAVAQHLLGEYKMALEI  165 (700)
T ss_pred             HHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh----hhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55555555543322  114444444444444445555444444433331    222233445555555555553333333


Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHH------HhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGL------CEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMER  245 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~------~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~  245 (425)
                      .+.+.+...    ..|+...|.-...-+      .++|..++|.+....-... +.-....-.+--+.+.+.+++++|..
T Consensus       166 l~ef~~t~~----~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~  240 (700)
T KOG1156|consen  166 LEEFEKTQN----TSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ-IVDKLAFEETKADLLMKLGQLEEAVK  240 (700)
T ss_pred             HHHHHHhhc----cCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH-HHHHHHHhhhHHHHHHHHhhHHhHHH
Confidence            333333321    123333444333222      3345555555444433221 11111122333444566666666666


Q ss_pred             HHHHHHHCCCCcCHHhHHHHHHH
Q 042756          246 IVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       246 ~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ++..+..+  .||-.-|+-....
T Consensus       241 ~y~~Ll~r--nPdn~~Yy~~l~~  261 (700)
T KOG1156|consen  241 VYRRLLER--NPDNLDYYEGLEK  261 (700)
T ss_pred             HHHHHHhh--CchhHHHHHHHHH
Confidence            66666655  3555555444433

>PLN02789 farnesyltranstransferase

Probab=97.45  E-value=0.08  Score=49.33  Aligned_cols=204  Identities=8%  Similarity=-0.046  Sum_probs=126.7

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQG-QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g-~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      ..++|+.+.+...+.+.-  +..+|+.--..+.+.| ++++++..++++.+.    .+....+|+.---.+.+.|.. ..
T Consensus        52 ~serAL~lt~~aI~lnP~--~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~----npknyqaW~~R~~~l~~l~~~-~~  124 (320)
T PLN02789         52 RSPRALDLTADVIRLNPG--NYTVWHFRRLCLEALDADLEEELDFAEDVAED----NPKNYQIWHHRRWLAEKLGPD-AA  124 (320)
T ss_pred             CCHHHHHHHHHHHHHCch--hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHH----CCcchHHhHHHHHHHHHcCch-hh
Confidence            344555555555443311  2334444444555566 689999999998765    222223455443344445542 12


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC---CCH----H
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL---GLL----E  241 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~---g~~----~  241 (425)
                      .+......++....+   -|-.+|+..--++.+.|+++++++.++++.+.+.. |...|+.....+.+.   |..    +
T Consensus       125 ~~el~~~~kal~~dp---kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~~~e  200 (320)
T PLN02789        125 NKELEFTRKILSLDA---KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEAMRD  200 (320)
T ss_pred             HHHHHHHHHHHHhCc---ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccccccHH
Confidence            344555555543321   24469999999999999999999999999987533 455666655555443   322    4


Q ss_pred             HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc----CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDH----NELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~----g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      ++.++....+... +-|...|+-+-..|...    ++..+|.+.+.+....+ ..+......|++.|+.
T Consensus       201 ~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        201 SELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             HHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence            5667766666543 23788999999988873    34467888888876643 3366778888888875

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.44  E-value=0.034  Score=57.22  Aligned_cols=146  Identities=10%  Similarity=0.068  Sum_probs=81.6

Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      ...++..+-.|.....+.|..++|+.+++...+.    .|+.......+...+.+.++   .+++....++.....    
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~----~Pd~~~a~~~~a~~L~~~~~---~eeA~~~~~~~l~~~----  150 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQR----FPDSSEAFILMLRGVKRQQG---IEAGRAEIELYFSGG----  150 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh----CCCcHHHHHHHHHHHHHhcc---HHHHHHHHHHHhhcC----
Confidence            3344666666666666666777776666666553    33333445556666666666   344444444443322    


Q ss_pred             cC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHH
Q 042756          187 VK-RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNM  264 (425)
Q Consensus       187 p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~  264 (425)
                      |+ ....+.+-.++.+.|++++|..+|++....  .|+ ..++...-.++-+.|+.++|...|+...+.- .+....||-
T Consensus       151 p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~-~~~~~~~~~  227 (694)
T PRK15179        151 SSSAREILLEAKSWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI-GDGARKLTR  227 (694)
T ss_pred             CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh-CcchHHHHH
Confidence            22 235555566666666666777766666652  232 5566666666666666666666666655431 233445554


Q ss_pred             HH
Q 042756          265 VL  266 (425)
Q Consensus       265 li  266 (425)
                      .+
T Consensus       228 ~~  229 (694)
T PRK15179        228 RL  229 (694)
T ss_pred             HH
Confidence            43

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

Probab=97.39  E-value=0.0079  Score=57.29  Aligned_cols=121  Identities=17%  Similarity=0.143  Sum_probs=64.1

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHH
Q 042756          116 EIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSM  195 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l  195 (425)
                      .++..+...++++.|.++|+++.+..    |.   +...+...+...++   -.++.+.+.+.....+   -|....+.-
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~~----pe---v~~~LA~v~l~~~~---E~~AI~ll~~aL~~~p---~d~~LL~~Q  240 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRERD----PE---VAVLLARVYLLMNE---EVEAIRLLNEALKENP---QDSELLNLQ  240 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhcC----Cc---HHHHHHHHHHhcCc---HHHHHHHHHHHHHhCC---CCHHHHHHH
Confidence            34455555566777777777766542    22   12335555554443   3455555555553321   123344444


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVKGLEPSGF-EYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      ...+.+.++.+.|+.+.+++..  +.|+.+ +|..|..+|.+.|+++.|...++.+.
T Consensus       241 a~fLl~k~~~~lAL~iAk~av~--lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  241 AEFLLSKKKYELALEIAKKAVE--LSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            5555566666666666666555  345433 56666666666666666655555543

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

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

Probab=97.35  E-value=0.0095  Score=48.65  Aligned_cols=129  Identities=12%  Similarity=0.099  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH--HHHH
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG--FEYK  228 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~ty~  228 (425)
                      .|..++..+. .++...+.+.++.+.+.   .+.........=.+-..+...|++++|...|+......-.|+.  ...-
T Consensus        14 ~y~~~~~~~~-~~~~~~~~~~~~~l~~~---~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l   89 (145)
T PF09976_consen   14 LYEQALQALQ-AGDPAKAEAAAEQLAKD---YPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARL   89 (145)
T ss_pred             HHHHHHHHHH-CCCHHHHHHHHHHHHHH---CCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence            5666666664 66654455544444443   2222111123334557788899999999999999997633322  2444


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 042756          229 CIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM  285 (425)
Q Consensus       229 ~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M  285 (425)
                      .+-..+...|++++|...++......+  ....+...-+.|.+.|+.++|...|++.
T Consensus        90 ~LA~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   90 RLARILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            567788999999999999987554433  4557778889999999999999999863

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

Probab=97.35  E-value=0.19  Score=49.81  Aligned_cols=332  Identities=10%  Similarity=-0.026  Sum_probs=194.5

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHHH
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAFP   96 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~~   96 (425)
                      |...+.++.|+.+|....+-++.+...|......=-..|..+....+|.+.+......+             +.+..|..
T Consensus       526 ~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~  605 (913)
T KOG0495|consen  526 CEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARV  605 (913)
T ss_pred             HHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHH
Confidence            34444666777888877766777778888777777777888888888877765544332             23555666


Q ss_pred             HHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756           97 LYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus        97 lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      +++..-+...  -+..++-.-+..-....+++.|+.+|.+.....+..     .+|..-++.---.+.   .+++.++++
T Consensus       606 il~~af~~~p--nseeiwlaavKle~en~e~eraR~llakar~~sgTe-----Rv~mKs~~~er~ld~---~eeA~rllE  675 (913)
T KOG0495|consen  606 ILDQAFEANP--NSEEIWLAAVKLEFENDELERARDLLAKARSISGTE-----RVWMKSANLERYLDN---VEEALRLLE  675 (913)
T ss_pred             HHHHHHHhCC--CcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcc-----hhhHHHhHHHHHhhh---HHHHHHHHH
Confidence            6666555431  255566677777778888888888888876643321     133333333323333   667777776


Q ss_pred             HHhhcCCCCccCh-hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          177 QLVNSSSSVYVKR-QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       177 ~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      +....    +|+- ..|-.+-..+-+.++++.|.+.|..-... ++-.+--|-.+.+.=-+.|.+..|..+++.-.-.+-
T Consensus       676 e~lk~----fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNP  750 (913)
T KOG0495|consen  676 EALKS----FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNP  750 (913)
T ss_pred             HHHHh----CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCC
Confidence            66543    3332 24444444555556666666665543332 222344677777777888899999999998776653


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH---HHHhhc--cCCchhhHHHHHhhc
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS---MLQDLN--SNDFPLSILELTEVL  330 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~---~~~~~~--~~~~~~~~~~~~~~~  330 (425)
                       -+...|-..|..=.+.|..+.|..+..+..+. +.-+..-|.--|-...+.++   ..+++.  .+....++..-.-+-
T Consensus       751 -k~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw  828 (913)
T KOG0495|consen  751 -KNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFW  828 (913)
T ss_pred             -CcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHH
Confidence             37889999999999999999998887776543 33344455544443322211   111111  122222222111111


Q ss_pred             chhhHHHHHHHHhCCCC--cc-cceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          331 NEEEVSVVKELEDSSVL--DE-AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       331 ~~~~~~~~~~~~~~~~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .........+.+.+-+.  || -.+|--+..-+.++|.-++-     .++++.-..
T Consensus       829 ~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~-----kev~~~c~~  879 (913)
T KOG0495|consen  829 SEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQ-----KEVLKKCET  879 (913)
T ss_pred             HHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHH-----HHHHHHHhc
Confidence            11222233333333222  33 25677777777888876666     667766544

>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=97.35  E-value=0.004  Score=45.44  Aligned_cols=96  Identities=14%  Similarity=0.036  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      +|..+...+...|++++|..+|++..+.. ..+...+..+...+...|++++|.+.|+...+... .+..++..+...+.
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~   79 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHH
Confidence            46667778888999999999999987752 22346777888888999999999999998877542 34468888888999


Q ss_pred             hcCCHHHHHHHHHHHHhC
Q 042756          271 DHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~~  288 (425)
                      ..|+.++|...+.+..+.
T Consensus        80 ~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          80 KLGKYEEALEAYEKALEL   97 (100)
T ss_pred             HHHhHHHHHHHHHHHHcc
Confidence            999999999998887643

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.33  E-value=0.013  Score=60.27  Aligned_cols=189  Identities=11%  Similarity=0.060  Sum_probs=132.6

Q ss_pred             HHHHHhcCC-hHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccC-HHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 042756           61 ISKFVASSP-QFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWN-PKLVAEIIAFLDKQGQREEAETLILETL  138 (425)
Q Consensus        61 l~~~~~~~~-~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~-~~~~~~ll~~~~~~g~~~~A~~l~~~m~  138 (425)
                      +..|++.-+ ...++-.+-++....+    .+++|..+++...+-.   |+ ......+...+.+.+++++|+..+++..
T Consensus        75 ~~~~~~~~~~~~~~~~~La~i~~~~g----~~~ea~~~l~~~~~~~---Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l  147 (694)
T PRK15179         75 LLDYVRRYPHTELFQVLVARALEAAH----RSDEGLAVWRGIHQRF---PDSSEAFILMLRGVKRQQGIEAGRAEIELYF  147 (694)
T ss_pred             HHHHHHhccccHHHHHHHHHHHHHcC----CcHHHHHHHHHHHhhC---CCcHHHHHHHHHHHHHhccHHHHHHHHHHHh
Confidence            344555444 3677777777776664    8999999999998765   44 4556678889999999999999999987


Q ss_pred             HhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          139 SKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       139 ~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      +.    .|+.......+-.++.+.|+.+++.++++.+..   .+.   -+..++-.+-.++-+.|+.++|...|++..+.
T Consensus       148 ~~----~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~---~~p---~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        148 SG----GSSSAREILLEAKSWDEIGQSEQADACFERLSR---QHP---EFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             hc----CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHh---cCC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            65    333344567788889999995555555544443   221   12458899999999999999999999999875


Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcCHHhHHHHHHHHHhcC
Q 042756          219 GLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       219 g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~~~~~yn~li~~~~~~g  273 (425)
                       ..|....|+..+      +++..-..+++++.-.    |..........+|.-|.+..
T Consensus       218 -~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (694)
T PRK15179        218 -IGDGARKLTRRL------VDLNADLAALRRLGVEGDGRDVPVSILVLEKMLQEIGRRR  269 (694)
T ss_pred             -hCcchHHHHHHH------HHHHHHHHHHHHcCcccccCCCceeeeeHHHHHHHHhhcC
Confidence             345556666664      3455556666666533    44445667777777777654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.29  E-value=0.29  Score=52.96  Aligned_cols=170  Identities=15%  Similarity=0.046  Sum_probs=108.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCch-hHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          118 IAFLDKQGQREEAETLILETLSKLGSRER-ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       118 l~~~~~~g~~~~A~~l~~~m~~~~~~~~~-~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      -..+...|++++|...+++..+....... ......+.+-..+...|+++.+...+..............+-..+++.+-
T Consensus       459 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la  538 (903)
T PRK04841        459 AQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQS  538 (903)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHH
Confidence            34456789999999999987653211111 11223455566677889966555554444443332211212233556667


Q ss_pred             HHHHhcCChhHHHHHHHHHHHc----CCC--C-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--CCCc--CHHhHHHH
Q 042756          197 SGLCEMGQPHEAENLIEEMRVK----GLE--P-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD--GTRV--DTVCSNMV  265 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~----g~~--p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~--g~~~--~~~~yn~l  265 (425)
                      ..+...|++++|...+++....    +..  | ....+..+-..+...|++++|...+.+....  ...+  ....+..+
T Consensus       539 ~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  618 (903)
T PRK04841        539 EILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAML  618 (903)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHH
Confidence            7788899999999999887653    221  1 2334555566677889999999999876542  1112  24455556


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh
Q 042756          266 LSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ...+...|+.++|...+.+...
T Consensus       619 a~~~~~~G~~~~A~~~l~~a~~  640 (903)
T PRK04841        619 AKISLARGDLDNARRYLNRLEN  640 (903)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            6778899999999999988754

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

Probab=97.25  E-value=0.036  Score=48.61  Aligned_cols=154  Identities=11%  Similarity=0.056  Sum_probs=88.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      .-..+--.|+-+....+.......   ...+ ...-.......++.|+   ..++...+++....   -.+|...||.+-
T Consensus        72 ~a~a~~~~G~a~~~l~~~~~~~~~---~~~d-~~ll~~~gk~~~~~g~---~~~A~~~~rkA~~l---~p~d~~~~~~lg  141 (257)
T COG5010          72 LATALYLRGDADSSLAVLQKSAIA---YPKD-RELLAAQGKNQIRNGN---FGEAVSVLRKAARL---APTDWEAWNLLG  141 (257)
T ss_pred             HHHHHHhcccccchHHHHhhhhcc---Cccc-HHHHHHHHHHHHHhcc---hHHHHHHHHHHhcc---CCCChhhhhHHH
Confidence            444444455555554444443221   1111 1123446666667777   34444444444322   224566777777


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCH
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~  275 (425)
                      -+|.+.|++++|..-|.+..+-  .| +...+|.+--.+.-.||.+.|..++..-...+-. |...-+.|.-.....|++
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~~g~~  218 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALEL--APNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALVVGLQGDF  218 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhhcCCh
Confidence            7777777777777777776663  22 3456666666777777777777777776665432 556666666667777777


Q ss_pred             HHHHHHHH
Q 042756          276 SRMVLWLQ  283 (425)
Q Consensus       276 ~~A~~l~~  283 (425)
                      ++|.++-.
T Consensus       219 ~~A~~i~~  226 (257)
T COG5010         219 REAEDIAV  226 (257)
T ss_pred             HHHHhhcc
Confidence            77765543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.24  E-value=0.014  Score=45.27  Aligned_cols=98  Identities=10%  Similarity=-0.071  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCcCHHhHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGL--EPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG--TRVDTVCSNMVL  266 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~--~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g--~~~~~~~yn~li  266 (425)
                      ++......+.+.|++++|.+.|+++.+..-  ......+..+..++.+.|+++.|.+.|+......  .......+..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            677788888999999999999999987521  1123466778889999999999999999988642  112256688888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhC
Q 042756          267 SSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       267 ~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ..+...|+.++|.+.|++..+.
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHH
Confidence            8899999999999999999876

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.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.24  E-value=0.16  Score=46.59  Aligned_cols=180  Identities=13%  Similarity=0.087  Sum_probs=116.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH--Hhc----CCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          116 EIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSF--CKH----DSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~--~~~----g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      .|+-.|.+.+++++|..+..++.     |..+    |.-++.+.  ...    |..+ -....+.++++..+....--++
T Consensus       290 NL~iYyL~q~dVqeA~~L~Kdl~-----PttP----~EyilKgvv~aalGQe~gSre-HlKiAqqffqlVG~Sa~ecDTI  359 (557)
T KOG3785|consen  290 NLIIYYLNQNDVQEAISLCKDLD-----PTTP----YEYILKGVVFAALGQETGSRE-HLKIAQQFFQLVGESALECDTI  359 (557)
T ss_pred             hheeeecccccHHHHHHHHhhcC-----CCCh----HHHHHHHHHHHHhhhhcCcHH-HHHHHHHHHHHhcccccccccc
Confidence            36777889999999998877753     2222    23344442  222    3322 2344555566654432211112


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHH-HH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL-SS  268 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li-~~  268 (425)
                      ----++-+++.-..++|+++-.++.++.-=..-|.+-|| +..+++..|.+.+|+++|-.+....++ |..+|-+++ ++
T Consensus       360 pGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArC  437 (557)
T KOG3785|consen  360 PGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARC  437 (557)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHH
Confidence            234466677777888999999999988764444555554 668999999999999999988776665 677777655 67


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH-HHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV-LNSCSTIMSM  310 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l-l~~~~~~~~~  310 (425)
                      |.+++.++-|.++|-+|...+   +..+.--+ .+-|-+.+.+
T Consensus       438 yi~nkkP~lAW~~~lk~~t~~---e~fsLLqlIAn~CYk~~eF  477 (557)
T KOG3785|consen  438 YIRNKKPQLAWDMMLKTNTPS---ERFSLLQLIANDCYKANEF  477 (557)
T ss_pred             HHhcCCchHHHHHHHhcCCch---hHHHHHHHHHHHHHHHHHH
Confidence            889999999988877765432   33343333 3456666665

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.21  E-value=0.0075  Score=49.19  Aligned_cols=94  Identities=12%  Similarity=-0.091  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHH
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALK  193 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~  193 (425)
                      +...-..+...|++++|...|+.....    .|.....|..+-.++.+.|+++++.+.++......+      .+...+.
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~----~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p------~~~~a~~   96 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMA----QPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDA------SHPEPVY   96 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHc----CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC------CCcHHHH
Confidence            334556667777777777777776653    222233566677777777774433333333333211      1234677


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      .+-.++.+.|++++|...|++...
T Consensus        97 ~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         97 QTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            777777777777777777777666

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

Probab=97.20  E-value=0.018  Score=54.96  Aligned_cols=93  Identities=11%  Similarity=-0.096  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC-HHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD-TVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~yn~li~~~  269 (425)
                      ..-.+.+.+...++-.+|.++.++.... .+-|......-...+.+.++.+.|.++.+...+.  .|+ -.+|..|..+|
T Consensus       202 v~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Y  278 (395)
T PF09295_consen  202 VAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECY  278 (395)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHH
Confidence            3344555555555555666665555542 1123334444444555666666666666655554  233 33666666666


Q ss_pred             HhcCCHHHHHHHHHHHH
Q 042756          270 GDHNELSRMVLWLQKMK  286 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~  286 (425)
                      ...|++++|+-.++.+.
T Consensus       279 i~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  279 IQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHhcCc
Confidence            66666666665555543

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

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

Probab=97.20  E-value=0.057  Score=53.98  Aligned_cols=221  Identities=7%  Similarity=-0.064  Sum_probs=157.5

Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      ++|-...=..+...+.+.|-+..|..+|+...            .|.-+|..|+..|+..+   +-.+..+...    -.
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erle------------mw~~vi~CY~~lg~~~k---aeei~~q~le----k~  454 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERLE------------MWDPVILCYLLLGQHGK---AEEINRQELE----KD  454 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhHH------------HHHHHHHHHHHhcccch---HHHHHHHHhc----CC
Confidence            44444455567788888999999999998863            57788999999997444   4444444443    23


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL  266 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li  266 (425)
                      ||...|..+.+......-+++|.++++....+       .-..+-....+++++.++.+.|+.-.+.+ ..-..+|-.+-
T Consensus       455 ~d~~lyc~LGDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G  526 (777)
T KOG1128|consen  455 PDPRLYCLLGDVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLG  526 (777)
T ss_pred             CcchhHHHhhhhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhcc
Confidence            67779999999998888999999999876543       11111112234789999999998655432 12456777777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCC
Q 042756          267 SSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSS  345 (425)
Q Consensus       267 ~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (425)
                      -+..+.++++.|.+.|..-..  ..||. ..||.+-.+|.+.++-.++                     -..+.+..+..
T Consensus       527 ~~ALqlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~ra---------------------~~~l~EAlKcn  583 (777)
T KOG1128|consen  527 CAALQLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKKRA---------------------FRKLKEALKCN  583 (777)
T ss_pred             HHHHHHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhHHH---------------------HHHHHHHhhcC
Confidence            777789999999999998764  36766 5899999998887765332                     22334444444


Q ss_pred             CCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          346 VLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       346 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                       .-+...|.-.+..-.+.|.+++|     ++.+.+|..
T Consensus       584 -~~~w~iWENymlvsvdvge~eda-----~~A~~rll~  615 (777)
T KOG1128|consen  584 -YQHWQIWENYMLVSVDVGEFEDA-----IKAYHRLLD  615 (777)
T ss_pred             -CCCCeeeechhhhhhhcccHHHH-----HHHHHHHHH
Confidence             56667888888888899999999     888888765

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

Probab=97.19  E-value=0.084  Score=45.57  Aligned_cols=117  Identities=12%  Similarity=0.025  Sum_probs=65.3

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH-HhcCCc--c
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSF-CKHDSK--R  166 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~-~~~g~~--~  166 (425)
                      ..+++...++...+.+  +.|...|..+-..|...|++++|...|++..+...    +....+..+-.++ ...|+.  +
T Consensus        54 ~~~~~i~~l~~~L~~~--P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P----~~~~~~~~lA~aL~~~~g~~~~~  127 (198)
T PRK10370         54 TPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRG----ENAELYAALATVLYYQAGQHMTP  127 (198)
T ss_pred             hHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC----CCHHHHHHHHHHHHHhcCCCCcH
Confidence            3445555555544433  13666777777777777777777777777665321    1122445555543 455542  3


Q ss_pred             cHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          167 GFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ++.+.++...+..+.      +..++..+-..+.+.|++++|...|+++.+.
T Consensus       128 ~A~~~l~~al~~dP~------~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        128 QTREMIDKALALDAN------EVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHHHhCCC------ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            333333333332221      2236677777777777777777777777664

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

Probab=97.18  E-value=0.058  Score=47.53  Aligned_cols=63  Identities=16%  Similarity=0.180  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          191 ALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       191 ~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      +.+-|-.+|.+    .+.+.+|+-+|++|.++ ..|+..+.+-...++...|++++|+.++++..++.
T Consensus       171 tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd  237 (299)
T KOG3081|consen  171 TLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKD  237 (299)
T ss_pred             HHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhcc
Confidence            55544444444    23555666666666543 45566666666666666666666666666655543

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

Probab=97.14  E-value=0.14  Score=47.07  Aligned_cols=172  Identities=14%  Similarity=0.093  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHh---cCCCchhHHHHHHHHHHHHHhc-CCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSK---LGSRERELVLFYCNLIDSFCKH-DSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~---~~~~~~~~~~~y~~li~~~~~~-g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .|......|-+. ++++|.+.|++....   .+. .......+..+-..|-.. |+++.+.+.+....+.....+...--
T Consensus        77 ~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~-~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a  154 (282)
T PF14938_consen   77 AYEEAANCYKKG-DPDEAIECYEKAIEIYREAGR-FSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSA  154 (282)
T ss_dssp             HHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCc-HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhH
Confidence            344444444333 555555555554331   111 111122333444444444 55444444444333333222211111


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-----CCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHHHC--CCCcC--
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGL-----EPSGF-EYKCIIYGYGRLGLLEDMERIVNQMESD--GTRVD--  258 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-----~p~~~-ty~~ll~~~~~~g~~~~a~~~~~~m~~~--g~~~~--  258 (425)
                      ..++.-+...+.+.|++++|.++|++....-.     +++.. .|-..+-++...||...|.+.|+...+.  ++..+  
T Consensus       155 ~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E  234 (282)
T PF14938_consen  155 AECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSRE  234 (282)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHH
Confidence            23666777778888888888888888765432     22222 2233344556678888888888887643  33222  


Q ss_pred             HHhHHHHHHHHHh--cCCHHHHHHHHHHHH
Q 042756          259 TVCSNMVLSSYGD--HNELSRMVLWLQKMK  286 (425)
Q Consensus       259 ~~~yn~li~~~~~--~g~~~~A~~l~~~M~  286 (425)
                      ...-..||.+|-.  ...+.+|+.-|+.+.
T Consensus       235 ~~~~~~l~~A~~~~D~e~f~~av~~~d~~~  264 (282)
T PF14938_consen  235 YKFLEDLLEAYEEGDVEAFTEAVAEYDSIS  264 (282)
T ss_dssp             HHHHHHHHHHHHTT-CCCHHHHCHHHTTSS
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHcccC
Confidence            3445556666643  234555555555544

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.14  E-value=0.3  Score=52.76  Aligned_cols=265  Identities=8%  Similarity=-0.062  Sum_probs=149.7

Q ss_pred             HHHhhHHHHHHHHHHhHHh-cCCCH----HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcC
Q 042756           31 LTARLTKQGQRFLSSLALA-VTRDS----KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEES  105 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~-~~~d~----~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~  105 (425)
                      ...|++.+|...++..... ...+.    .+.+.+-..+...|+.+.+...+.+.+              ..+...   +
T Consensus       463 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al--------------~~~~~~---g  525 (903)
T PRK04841        463 INDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTE--------------QMARQH---D  525 (903)
T ss_pred             HhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH--------------HHHhhh---c
Confidence            4567888888888876654 22221    233444455555676666666655543              122211   1


Q ss_pred             CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHh----cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc
Q 042756          106 WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSK----LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS  181 (425)
Q Consensus       106 ~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~----~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~  181 (425)
                      ...+-..++..+-..+...|++++|.+.+++....    +....+.....+..+-..+...|+++.+.+.+.........
T Consensus       526 ~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~  605 (903)
T PRK04841        526 VYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSN  605 (903)
T ss_pred             chHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhc
Confidence            11122334556677788899999999998886552    11111111223444555667779966655555544444332


Q ss_pred             CCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCCHHHH--HHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          182 SSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEPSGFEY--KCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       182 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~ty--~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .. .......+..+...+...|+.++|.+.+.+....    +..+.....  ...+..+...|+.+.|.+.+........
T Consensus       606 ~~-~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~  684 (903)
T PRK04841        606 YQ-PQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEF  684 (903)
T ss_pred             cC-chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCC
Confidence            21 1112335556677888899999999999888653    111111011  1123445668999999999877554221


Q ss_pred             CcC---HHhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCCH-HHHHHHHHHHHHHHHHHHh
Q 042756          256 RVD---TVCSNMVLSSYGDHNELSRMVLWLQKMKDS----GIPFSV-RTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       256 ~~~---~~~yn~li~~~~~~g~~~~A~~l~~~M~~~----g~~pd~-~t~~~ll~~~~~~~~~~~~  313 (425)
                      ...   ...+..+..++...|+.++|..++.+....    |..++. .+...+-.++...|+..++
T Consensus       685 ~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A  750 (903)
T PRK04841        685 ANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEA  750 (903)
T ss_pred             ccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHH
Confidence            111   112456677788999999999999987542    322221 3444444455565655444

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

Probab=97.13  E-value=0.034  Score=45.36  Aligned_cols=131  Identities=15%  Similarity=0.087  Sum_probs=76.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..|..++..+. .++...+.+.++.+.+........ ....-.+-..+...|++++   +...+................
T Consensus        13 ~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya-~~A~l~lA~~~~~~g~~~~---A~~~l~~~~~~~~d~~l~~~a   87 (145)
T PF09976_consen   13 ALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYA-ALAALQLAKAAYEQGDYDE---AKAALEKALANAPDPELKPLA   87 (145)
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHH-HHHHHHHHHHHHHCCCHHH---HHHHHHHHHhhCCCHHHHHHH
Confidence            34555666653 677888888888887753332221 1122234456777788444   444444443332111001124


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      .--+-..+...|++++|+..++......  .....+...-+.|.+.|+.++|...|+.
T Consensus        88 ~l~LA~~~~~~~~~d~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   88 RLRLARILLQQGQYDEALATLQQIPDEA--FKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHhccCcc--hHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            4446677778888888888886643322  2334566667778888888888888764

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

Probab=97.11  E-value=0.27  Score=46.94  Aligned_cols=336  Identities=10%  Similarity=0.019  Sum_probs=210.8

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC------------CchhhhHHHHHHH
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH------------PRLSSLAFPLYMR  100 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~------------~~~~~~a~~lf~~  100 (425)
                      -|.+.-|.++|++-.+ ..||..+|++.|+-=.+-...+.|.+++...+.-....            .|.+..|.++|..
T Consensus       154 LgNi~gaRqiferW~~-w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~Vyer  232 (677)
T KOG1915|consen  154 LGNIAGARQIFERWME-WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYER  232 (677)
T ss_pred             hcccHHHHHHHHHHHc-CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            3456667777776443 68899999999888888888888888888875433221            1244556666665


Q ss_pred             hhhcCCCccCHHHHHHHHHHHH----hcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756          101 ITEESWFQWNPKLVAEIIAFLD----KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus       101 m~~~~~~~~~~~~~~~ll~~~~----~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      ..+.-   -|...-..+..+|+    ++..++.|.-+|.-......  .......|..+..-=-+.|+..+.+++..-=+
T Consensus       233 Aie~~---~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~p--k~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KR  307 (677)
T KOG1915|consen  233 AIEFL---GDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIP--KGRAEELYKKYTAFEKQFGDKEGIEDAIVGKR  307 (677)
T ss_pred             HHHHh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHHhcchhhhHHHHhhhh
Confidence            43321   02222223334443    45667778777777655422  22112345556555566788887777654333


Q ss_pred             HHhhcCC--CCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH-------HHHH---HHHHHHHcCCCHHHHH
Q 042756          177 QLVNSSS--SVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG-------FEYK---CIIYGYGRLGLLEDME  244 (425)
Q Consensus       177 ~~~~~~~--~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-------~ty~---~ll~~~~~~g~~~~a~  244 (425)
                      ++..+..  ...-|=.+|--.++.--..|+.+...++|++.... ++|-.       +.|-   -.+-.-....|++.+.
T Consensus       308 k~qYE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr  386 (677)
T KOG1915|consen  308 KFQYEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTR  386 (677)
T ss_pred             hhHHHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence            3321110  01112347778888888889999999999998864 55521       1221   2222234568899999


Q ss_pred             HHHHHHHHCCCCcCHHhHHHHHHHHH----hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhh------
Q 042756          245 RIVNQMESDGTRVDTVCSNMVLSSYG----DHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDL------  314 (425)
Q Consensus       245 ~~~~~m~~~g~~~~~~~yn~li~~~~----~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~------  314 (425)
                      ++++...+ =|+....||.-+=-.|+    ++.++..|.+++...+  |.-|-..+|..-|.-=.+++.++...      
T Consensus       387 ~vyq~~l~-lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYEkf  463 (677)
T KOG1915|consen  387 QVYQACLD-LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYEKF  463 (677)
T ss_pred             HHHHHHHh-hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            99998888 34445666666555554    6778899998888765  77899999888888766666665542      


Q ss_pred             ---ccCCchhhHH--HH-HhhcchhhHHHHHHHHhCCCC--cccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          315 ---NSNDFPLSIL--EL-TEVLNEEEVSVVKELEDSSVL--DEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       315 ---~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                         ++..+.++..  .+ ..+|..+.+..++++--+...  .....|...|.-=...|.+++|     ..+++...+
T Consensus       464 le~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~eka-----R~LYerlL~  535 (677)
T KOG1915|consen  464 LEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKA-----RALYERLLD  535 (677)
T ss_pred             HhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHH-----HHHHHHHHH
Confidence               1222223322  22 445556777777776533322  3346788888888889999999     899998887

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

Probab=97.11  E-value=0.11  Score=54.49  Aligned_cols=30  Identities=17%  Similarity=0.081  Sum_probs=16.0

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhC
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLS   82 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~   82 (425)
                      +...+..|+..+...++++.+..++...+.
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~   59 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLK   59 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            445555555555555555555555554443

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

Probab=97.08  E-value=0.021  Score=45.78  Aligned_cols=63  Identities=10%  Similarity=-0.104  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..|..+-.++.+.|++++|..+|++....+ +.+..++..+-..|...|+++.|.+.|+...+.
T Consensus        52 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        52 RYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            355555555666666666666666554432 223445555555566666666666666655543

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

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

Probab=97.04  E-value=0.32  Score=46.59  Aligned_cols=90  Identities=14%  Similarity=0.110  Sum_probs=42.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      +......+.+.++.++|.+.|+.+...  .|+ ....-.+-.+|.+.|+.++|.++++....+. +-|...|..|-.+|.
T Consensus       343 ~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~  419 (484)
T COG4783         343 LELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYA  419 (484)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHH
Confidence            334444455555555555555555442  333 2233334445555555555555555544332 224455555555555


Q ss_pred             hcCCHHHHHHHHHH
Q 042756          271 DHNELSRMVLWLQK  284 (425)
Q Consensus       271 ~~g~~~~A~~l~~~  284 (425)
                      ..|+..+|..-.-+
T Consensus       420 ~~g~~~~a~~A~AE  433 (484)
T COG4783         420 ELGNRAEALLARAE  433 (484)
T ss_pred             HhCchHHHHHHHHH
Confidence            55544444443333

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

Probab=97.03  E-value=0.14  Score=46.93  Aligned_cols=114  Identities=14%  Similarity=0.080  Sum_probs=72.4

Q ss_pred             HHHHHHHHHHhc-CChhHHHHHHHHHHHc----CCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-----CcC
Q 042756          191 ALKSMISGLCEM-GQPHEAENLIEEMRVK----GLEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGT-----RVD  258 (425)
Q Consensus       191 ~~~~li~~~~~~-g~~~~a~~~~~~m~~~----g~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~-----~~~  258 (425)
                      ++..+-..|-+. |++++|++.|++..+.    | .+.  ..++..+...+.+.|++++|.++|++....-.     +.+
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~  194 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYS  194 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchh
Confidence            555566666666 8899999998887653    3 221  33667788889999999999999998876432     223


Q ss_pred             HH-hHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCC--HHHHHHHHHHHH
Q 042756          259 TV-CSNMVLSSYGDHNELSRMVLWLQKMKDS--GIPFS--VRTYNSVLNSCS  305 (425)
Q Consensus       259 ~~-~yn~li~~~~~~g~~~~A~~l~~~M~~~--g~~pd--~~t~~~ll~~~~  305 (425)
                      +. .|-..+-++...|++..|.+.|++....  ++..+  ......||.+|-
T Consensus       195 ~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~  246 (282)
T PF14938_consen  195 AKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYE  246 (282)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHH
Confidence            32 2223344666788999999999998643  33322  345555565553

>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=96.92  E-value=0.013  Score=46.33  Aligned_cols=78  Identities=17%  Similarity=0.164  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHH---------------HcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-C
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMR---------------VKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD-G  254 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~---------------~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~-g  254 (425)
                      ++.++|.++++.|+++....+.+..=               ...+.||..+..+++.+|+.+|++..|.++.+...+. +
T Consensus         4 ~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~   83 (126)
T PF12921_consen    4 LLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYP   83 (126)
T ss_pred             HHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcC
Confidence            44555555555555555544443321               1123345555555555555555555555555544432 4


Q ss_pred             CCcCHHhHHHHHHH
Q 042756          255 TRVDTVCSNMVLSS  268 (425)
Q Consensus       255 ~~~~~~~yn~li~~  268 (425)
                      ++.+..+|..|+.-
T Consensus        84 I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   84 IPIPKEFWRRLLEW   97 (126)
T ss_pred             CCCCHHHHHHHHHH
Confidence            44444455544443

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

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

Probab=96.91  E-value=0.0019  Score=47.17  Aligned_cols=81  Identities=11%  Similarity=0.064  Sum_probs=55.0

Q ss_pred             cCChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHH
Q 042756          202 MGQPHEAENLIEEMRVKGL-EPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVL  280 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~g~-~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~  280 (425)
                      .|+++.|+.+|+++.+..- .|+...+-.+-.+|.+.|++++|..+++. .+.+.. +....-.+..+|.+.|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~-~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPS-NPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHC-HHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCC-CHHHHHHHHHHHHHhCCHHHHHH
Confidence            5788889999998887632 22444455578888999999999999887 222111 22333355677888999999988


Q ss_pred             HHHH
Q 042756          281 WLQK  284 (425)
Q Consensus       281 l~~~  284 (425)
                      +|++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            8875

>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=0.04  Score=43.56  Aligned_cols=103  Identities=14%  Similarity=0.017  Sum_probs=78.0

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      |..++..+|-++++.|+.+...+++...-.-+......-..       ........|+..+..+++.+|+..|++..|.+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~-------~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~   73 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGD-------YPPSSPLYPTSRLLIAIVHSFGYNGDIFSALK   73 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCc-------cCCCCCCCCCHHHHHHHHHHHHhcccHHHHHH
Confidence            56788999999999999999999998775432111000000       33345578999999999999999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCC
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDS  164 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~  164 (425)
                      +.+...+....+-+.  .+|..|+.-.....+
T Consensus        74 ~vd~fs~~Y~I~i~~--~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   74 LVDFFSRKYPIPIPK--EFWRRLLEWAYVLSS  103 (126)
T ss_pred             HHHHHHHHcCCCCCH--HHHHHHHHHHHHhcC
Confidence            999999987755553  478888887665544

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

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

Probab=96.85  E-value=0.14  Score=53.70  Aligned_cols=159  Identities=9%  Similarity=0.001  Sum_probs=101.5

Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC--
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS--  184 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~--  184 (425)
                      -+.+...+..|+..+-..+++++|.++.++-.+. . |..  ...|-.+-..+.+.++.+.+..+  .+.+.......  
T Consensus        27 ~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~-~-P~~--i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~~~~~~~~  100 (906)
T PRK14720         27 SLSKFKELDDLIDAYKSENLTDEAKDICEEHLKE-H-KKS--ISALYISGILSLSRRPLNDSNLL--NLIDSFSQNLKWA  100 (906)
T ss_pred             CcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh-C-Ccc--eehHHHHHHHHHhhcchhhhhhh--hhhhhcccccchh
Confidence            3456677888999999999999999998865543 1 121  11232233355555553322222  11111111100  


Q ss_pred             -----------CccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          185 -----------VYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       185 -----------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                                 ..-+...+-.+..+|-+.|+.++|..+|++..+.. .-|+.+.|.+-..|+.. ++++|.+++......
T Consensus       101 ~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~  178 (906)
T PRK14720        101 IVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR  178 (906)
T ss_pred             HHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH
Confidence                       00011366677788888899999999999999876 44678899999999999 999999988877664


Q ss_pred             CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          254 GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       254 g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                                     |....++.++.+++.++.+.
T Consensus       179 ---------------~i~~kq~~~~~e~W~k~~~~  198 (906)
T PRK14720        179 ---------------FIKKKQYVGIEEIWSKLVHY  198 (906)
T ss_pred             ---------------HHhhhcchHHHHHHHHHHhc
Confidence                           45555666666666666554

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.84  E-value=0.3  Score=42.90  Aligned_cols=156  Identities=15%  Similarity=0.066  Sum_probs=97.0

Q ss_pred             CChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc
Q 042756          125 GQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM  202 (425)
Q Consensus       125 g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~  202 (425)
                      .+.++.++++.++...  .+...++....|.-++-+....|+.+.+..+++.+.+..+....    +.-..+|  -+-..
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~R----V~~lkam--~lEa~   99 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKR----VGKLKAM--LLEAT   99 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChh----HHHHHHH--HHHHh
Confidence            4567777777776542  11123333445666666666677766677777777665432211    1111111  12335


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWL  282 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~  282 (425)
                      |+.++|+++++...+.. +-|.++|.-=+-..-..|+--+|++-+....+. +.-|...|.-+-..|...|++++|.-++
T Consensus       100 ~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fCl  177 (289)
T KOG3060|consen  100 GNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCL  177 (289)
T ss_pred             hchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHH
Confidence            78888888888888765 335666655444444555555666666666553 3458888888888888888888888888


Q ss_pred             HHHHhC
Q 042756          283 QKMKDS  288 (425)
Q Consensus       283 ~~M~~~  288 (425)
                      ++|.-.
T Consensus       178 EE~ll~  183 (289)
T KOG3060|consen  178 EELLLI  183 (289)
T ss_pred             HHHHHc
Confidence            888753

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

Probab=96.82  E-value=0.32  Score=46.66  Aligned_cols=166  Identities=11%  Similarity=0.109  Sum_probs=106.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      -|..-+. +...|+.++|+..++++...    .|+++.........+.+.++   +.++.+.+.+.....+..   ...+
T Consensus       309 ~YG~A~~-~~~~~~~d~A~~~l~~L~~~----~P~N~~~~~~~~~i~~~~nk---~~~A~e~~~kal~l~P~~---~~l~  377 (484)
T COG4783         309 QYGRALQ-TYLAGQYDEALKLLQPLIAA----QPDNPYYLELAGDILLEANK---AKEAIERLKKALALDPNS---PLLQ  377 (484)
T ss_pred             HHHHHHH-HHHhcccchHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCC---hHHHHHHHHHHHhcCCCc---cHHH
Confidence            4443333 33557888888888887654    33334444556666778887   444444454444433221   1266


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                      -.+-.+|.+.|++.+|.+++++-... .+-|...|..+-.+|...|+..++..-..                  .+|...
T Consensus       378 ~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~A------------------E~~~~~  438 (484)
T COG4783         378 LNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARA------------------EGYALA  438 (484)
T ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHH------------------HHHHhC
Confidence            67778888888888888888877664 34567788888888888888777765443                  345567


Q ss_pred             CCHHHHHHHHHHHHhCC--CCCCHHHHHHHHHHHHHHH
Q 042756          273 NELSRMVLWLQKMKDSG--IPFSVRTYNSVLNSCSTIM  308 (425)
Q Consensus       273 g~~~~A~~l~~~M~~~g--~~pd~~t~~~ll~~~~~~~  308 (425)
                      |+++.|...+....+..  -.|+..=+...|+......
T Consensus       439 G~~~~A~~~l~~A~~~~~~~~~~~aR~dari~~~~~~~  476 (484)
T COG4783         439 GRLEQAIIFLMRASQQVKLGFPDWARADARIDQLRQQN  476 (484)
T ss_pred             CCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHHH
Confidence            88888888877776542  2455555666666655433

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.81  E-value=0.35  Score=43.43  Aligned_cols=154  Identities=11%  Similarity=0.032  Sum_probs=84.8

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhH------------------HHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSREREL------------------VLF  151 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~------------------~~~  151 (425)
                      .++.|++-|....+-+++.|- ..||..+ +..+.|+.+.|++...++.++|....|..                  ...
T Consensus       159 qyEaAvqkFqaAlqvsGyqpl-lAYniAL-aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh  236 (459)
T KOG4340|consen  159 QYEAAVQKFQAALQVSGYQPL-LAYNLAL-AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLH  236 (459)
T ss_pred             cHHHHHHHHHHHHhhcCCCch-hHHHHHH-HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHH
Confidence            467788888877666656543 3666444 44455778888888888877654433221                  011


Q ss_pred             HHHHHHH-------HHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH
Q 042756          152 YCNLIDS-------FCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG  224 (425)
Q Consensus       152 y~~li~~-------~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  224 (425)
                      -+.++.+       +.+.|+   .+.+-+.+.+|++... ...|.+|...+--.-. .+++.+..+-+.-+.+.+- -..
T Consensus       237 ~Sal~eAfNLKaAIeyq~~n---~eAA~eaLtDmPPRaE-~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nP-fP~  310 (459)
T KOG4340|consen  237 QSALVEAFNLKAAIEYQLRN---YEAAQEALTDMPPRAE-EELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNP-FPP  310 (459)
T ss_pred             HHHHHHHhhhhhhhhhhccc---HHHHHHHhhcCCCccc-ccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCC-CCh
Confidence            1223333       233455   4455555666654432 3345556555432222 2334444443444443321 134


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          225 FEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       225 ~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      .||..++-.|||+.-++.|..++.+-.
T Consensus       311 ETFANlLllyCKNeyf~lAADvLAEn~  337 (459)
T KOG4340|consen  311 ETFANLLLLYCKNEYFDLAADVLAENA  337 (459)
T ss_pred             HHHHHHHHHHhhhHHHhHHHHHHhhCc
Confidence            688888888888888888877776543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.79  E-value=0.031  Score=46.86  Aligned_cols=94  Identities=11%  Similarity=-0.057  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP--SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      .|..+...+...|++++|+..|++.....-.|  ...++..+-..+.+.|+.++|.+.++...... +....+++.+...
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~i  115 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAVI  115 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHH
Confidence            67777788888899999999998887653222  23578888888899999999999998877642 2234556666666


Q ss_pred             HH-------hcCCHHHHHHHHHHH
Q 042756          269 YG-------DHNELSRMVLWLQKM  285 (425)
Q Consensus       269 ~~-------~~g~~~~A~~l~~~M  285 (425)
                      |.       ..|++++|...+++-
T Consensus       116 ~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        116 CHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHhhHHHHHcccHHHHHHHHHHH
Confidence            66       778887666666654

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

Probab=96.74  E-value=0.039  Score=50.55  Aligned_cols=145  Identities=5%  Similarity=-0.038  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI  230 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l  230 (425)
                      +|..+++..-+.+..+.+.   .+|.+... ...+..++....++|.-+ ..++.+.|.++|+...+. ..-+...|...
T Consensus         3 v~i~~m~~~~r~~g~~~aR---~vF~~a~~-~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y   76 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAAR---KVFKRARK-DKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEY   76 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHH---HHHHHHHC-CCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHH---HHHHHHHc-CCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHH
Confidence            6788888888877744444   44444432 222433434444444333 256777799999999876 45567788888


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCc---CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 042756          231 IYGYGRLGLLEDMERIVNQMESDGTRV---DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       231 l~~~~~~g~~~~a~~~~~~m~~~g~~~---~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~  304 (425)
                      ++.+.+.|+.+.|..+|+..... +.+   ....|...+.-=.+.|+.+.+.++.+++.+.  -|+..++..+++-|
T Consensus        77 ~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   77 LDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            99999999999999999998865 322   2359999999999999999999999998874  55655555555443

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.

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

Probab=96.70  E-value=0.47  Score=48.45  Aligned_cols=43  Identities=12%  Similarity=0.084  Sum_probs=30.2

Q ss_pred             hhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhh
Q 042756           34 RLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLL   81 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l   81 (425)
                      |..+.|.+-...+     -+-..|..|.+.|.+..+.+.|---+-+|-
T Consensus       742 G~MD~AfksI~~I-----kS~~vW~nmA~McVkT~RLDVAkVClGhm~  784 (1416)
T KOG3617|consen  742 GSMDAAFKSIQFI-----KSDSVWDNMASMCVKTRRLDVAKVCLGHMK  784 (1416)
T ss_pred             ccHHHHHHHHHHH-----hhhHHHHHHHHHhhhhccccHHHHhhhhhh
Confidence            3444454444443     345679999999999998888887777773

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.69  E-value=0.076  Score=44.67  Aligned_cols=84  Identities=14%  Similarity=-0.013  Sum_probs=58.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      ..|..+...+...|++++|...|++.....-.+.  ...+..+...+.+.|++++|...++...+..- -+...+..+..
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~  114 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP-KQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHHH
Confidence            3667777777888888888888888876533222  35777778888888888888888887776421 24555666666


Q ss_pred             HHHhcCC
Q 042756          268 SYGDHNE  274 (425)
Q Consensus       268 ~~~~~g~  274 (425)
                      .|...|+
T Consensus       115 ~~~~~g~  121 (172)
T PRK02603        115 IYHKRGE  121 (172)
T ss_pred             HHHHcCC
Confidence            6666665

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.67  E-value=0.12  Score=39.91  Aligned_cols=102  Identities=14%  Similarity=0.076  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      ++-.+...+.+.|++++|.+.|+++.+...... .....+..+...+.+.|+++   ++...+.+.....+........+
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~---~A~~~~~~~~~~~p~~~~~~~~~   79 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKST-YAPNAHYWLGEAYYAQGKYA---DAAKAFLAVVKKYPKSPKAPDAL   79 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcc-ccHHHHHHHHHHHHhhccHH---HHHHHHHHHHHHCCCCCcccHHH
Confidence            344456666677777777777777765422111 10113344666666666633   33333333322211110112345


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ..+..++.+.|+.++|.+.+++....
T Consensus        80 ~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        80 LKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            56666666667777777777666664

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.

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

Probab=96.66  E-value=0.056  Score=51.38  Aligned_cols=104  Identities=10%  Similarity=-0.077  Sum_probs=79.5

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHH
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELS  276 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~  276 (425)
                      ..+...|++++|++.|++..+.. .-+...|..+-.+|.+.|++++|...++...+..- .+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDP-SLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHhCCHH
Confidence            44566788999999999888742 22466788888888999999999999988877532 25677888888888999999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 042756          277 RMVLWLQKMKDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       277 ~A~~l~~~M~~~g~~pd~~t~~~ll~~~  304 (425)
                      +|...|++..+.  .|+.......+..|
T Consensus        88 eA~~~~~~al~l--~P~~~~~~~~l~~~  113 (356)
T PLN03088         88 TAKAALEKGASL--APGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            999999988764  56666666665554

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

Probab=96.63  E-value=0.31  Score=47.35  Aligned_cols=119  Identities=11%  Similarity=0.043  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHH-HHHCCCCcCHHhHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQ-MESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~-m~~~g~~~~~~~yn~li~~  268 (425)
                      +|...|+.-.+..-+..|..+|.+..+.+..+ ++++++++|.-|| .+|.+-|.++|+. |+..|-  +..--+..++-
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d--~p~yv~~Yldf  444 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGD--SPEYVLKYLDF  444 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCC--ChHHHHHHHHH
Confidence            89999999999999999999999999998877 8889999998777 4678899999995 445432  34445677888


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCH--HHHHHHHHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMKDSGIPFSV--RTYNSVLNSCSTIMSMLQ  312 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~g~~pd~--~t~~~ll~~~~~~~~~~~  312 (425)
                      +...++-..|..+|++....++.||.  ..|..+|+-=+..|++..
T Consensus       445 L~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~s  490 (656)
T KOG1914|consen  445 LSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNS  490 (656)
T ss_pred             HHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHH
Confidence            88899999999999999988777665  689998887666665543

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

Probab=96.53  E-value=1  Score=44.93  Aligned_cols=184  Identities=13%  Similarity=0.098  Sum_probs=106.1

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC---------------chhhhHHHH
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP---------------RLSSLAFPL   97 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~---------------~~~~~a~~l   97 (425)
                      +.+++.++.+...|..       .|-.-+..+.+.+....+..+|...+..-....               +..+-+.++
T Consensus        88 n~c~er~lv~mHkmpR-------Iwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rv  160 (835)
T KOG2047|consen   88 NNCFERCLVFMHKMPR-------IWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRV  160 (835)
T ss_pred             HHHHHHHHHHHhcCCH-------HHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHH
Confidence            4556666655444432       244444444445555555555555443221110               123456666


Q ss_pred             HHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCC---CchhHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 042756           98 YMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGS---RERELVLFYCNLIDSFCKHDSKRGFDDTYAR  174 (425)
Q Consensus        98 f~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~---~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~  174 (425)
                      +++..+-     ++..-+--|..+++.+++++|-+.+.........   ..+++...|.-+-+..++..+.-.-...-.+
T Consensus       161 yrRYLk~-----~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdai  235 (835)
T KOG2047|consen  161 YRRYLKV-----APEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAI  235 (835)
T ss_pred             HHHHHhc-----CHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHH
Confidence            6665432     3334566788999999999999998887542111   1122244567777777766553322223333


Q ss_pred             HHHHhhcCCCCccCh--hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 042756          175 LNQLVNSSSSVYVKR--QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGY  234 (425)
Q Consensus       175 ~~~~~~~~~~~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~  234 (425)
                      ++..    ...++|.  ..|++|-.-|.+.|.+|+|.++|++-.+.-  -+..-|+.+.++|
T Consensus       236 iR~g----i~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Y  291 (835)
T KOG2047|consen  236 IRGG----IRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAY  291 (835)
T ss_pred             HHhh----cccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHH
Confidence            3333    3355664  599999999999999999999999987642  2334455554444

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

Probab=96.49  E-value=0.012  Score=40.74  Aligned_cols=62  Identities=6%  Similarity=0.129  Sum_probs=34.6

Q ss_pred             cCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 042756          236 RLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV  300 (425)
Q Consensus       236 ~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l  300 (425)
                      +.|++++|.++|+.+.+..- -+...+-.+..+|.+.|++++|.+++++....  .|+...|..+
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l   64 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNP-DNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQL   64 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTT-TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHH
Confidence            45666666666666654421 14555556666666666666666666666544  3554444443

...

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

Probab=96.48  E-value=0.35  Score=46.99  Aligned_cols=204  Identities=9%  Similarity=0.074  Sum_probs=127.6

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcC---ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQG---QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR  166 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g---~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~  166 (425)
                      ..+++.++++.....- ..-+..+|..+...=-..-   ..+...+.+++....... .+  ..+|..+|+.--|..-++
T Consensus       308 ~t~e~~~~yEr~I~~l-~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~-~~--tLv~~~~mn~irR~eGlk  383 (656)
T KOG1914|consen  308 LTDEAASIYERAIEGL-LKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDI-DL--TLVYCQYMNFIRRAEGLK  383 (656)
T ss_pred             hHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhcc-CC--ceehhHHHHHHHHhhhHH
Confidence            4566666666644332 2123333333222211111   255566666666554222 22  346888888877766544


Q ss_pred             cHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHH
Q 042756          167 GFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF-EYKCIIYGYGRLGLLEDMER  245 (425)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-ty~~ll~~~~~~g~~~~a~~  245 (425)
                      .+..+|...++.....    =.+.+++++|.-|| .++.+-|.++|+.-..+  -+|.- --...++-+...|+=..|.-
T Consensus       384 aaR~iF~kaR~~~r~~----hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk--f~d~p~yv~~YldfL~~lNdd~N~R~  456 (656)
T KOG1914|consen  384 AARKIFKKAREDKRTR----HHVFVAAALMEYYC-SKDKETAFRIFELGLKK--FGDSPEYVLKYLDFLSHLNDDNNARA  456 (656)
T ss_pred             HHHHHHHHHhhccCCc----chhhHHHHHHHHHh-cCChhHHHHHHHHHHHh--cCCChHHHHHHHHHHHHhCcchhHHH
Confidence            4444444444433222    15569999999888 67788999999986654  23433 33566778888999999999


Q ss_pred             HHHHHHHCCCCcC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCHHHHHHHHHHH
Q 042756          246 IVNQMESDGTRVD--TVCSNMVLSSYGDHNELSRMVLWLQKMKDS---GIPFSVRTYNSVLNSC  304 (425)
Q Consensus       246 ~~~~m~~~g~~~~--~~~yn~li~~~~~~g~~~~A~~l~~~M~~~---g~~pd~~t~~~ll~~~  304 (425)
                      +|+.....++.||  ...|+.+|+-=..-|+...+.++=+++...   ...|...+-..+++-|
T Consensus       457 LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY  520 (656)
T KOG1914|consen  457 LFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRY  520 (656)
T ss_pred             HHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHH
Confidence            9999998876665  589999999999999999999998887532   1333334444444443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.44  E-value=0.6  Score=41.70  Aligned_cols=57  Identities=14%  Similarity=0.085  Sum_probs=41.0

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHC--CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESD--GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~--g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                      +..-|.+.|.+..|..=|+.+.++  +-+......-.++.+|...|..++|.+......
T Consensus       181 ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        181 VAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            345578888888888888888765  333345666678888888888888877665543

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

Probab=96.42  E-value=0.033  Score=40.33  Aligned_cols=94  Identities=15%  Similarity=0.126  Sum_probs=62.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHH
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALK  193 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~  193 (425)
                      +..+...+...|++++|..++++..+.... .   ..++..+...+...++++   ++...+.+.....+   .+..++.
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~---~~~~~~~~~~~~~~~~~~---~a~~~~~~~~~~~~---~~~~~~~   72 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPD-N---ADAYYNLAAAYYKLGKYE---EALEDYEKALELDP---DNAKAYY   72 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCc-c---HHHHHHHHHHHHHHHHHH---HHHHHHHHHHhCCC---cchhHHH
Confidence            445667778889999999999988764221 1   234566777777778744   44444444332221   1224788


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      .+...+...|+.++|...|.+...
T Consensus        73 ~~~~~~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          73 NLGLAYYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHc
Confidence            888888889999999988887765

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.40  E-value=0.43  Score=42.89  Aligned_cols=181  Identities=13%  Similarity=0.026  Sum_probs=116.0

Q ss_pred             hhhhHHHHHHHhhhcCCCcc-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQW-NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~-~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      +++.|++++..-.++.   | +....+.+-.+|-...++..|-+.|+++...  .|....-..|  --..+-+.+.+   
T Consensus        25 ry~DaI~~l~s~~Er~---p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY--~AQSLY~A~i~---   94 (459)
T KOG4340|consen   25 RYADAIQLLGSELERS---PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLY--QAQSLYKACIY---   94 (459)
T ss_pred             hHHHHHHHHHHHHhcC---ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHH--HHHHHHHhccc---
Confidence            6677777777766654   3 5556777888888889999999999998763  1121111111  22334455553   


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHH--hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLC--EMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERI  246 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~--~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~  246 (425)
                      .+++.++..+...     |+...-..-+.+-.  ..+++..+..+.++.-..|   +..+.+..-....+.|+++.|.+=
T Consensus        95 ADALrV~~~~~D~-----~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEaAvqk  166 (459)
T KOG4340|consen   95 ADALRVAFLLLDN-----PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEAAVQK  166 (459)
T ss_pred             HHHHHHHHHhcCC-----HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccccHHHHHHH
Confidence            3455555555432     11112222223322  3578888888888776443   445555555566789999999999


Q ss_pred             HHHHHHC-CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 042756          247 VNQMESD-GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGI  290 (425)
Q Consensus       247 ~~~m~~~-g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~  290 (425)
                      |+...+. |+. ....||.-+.-| +.|+.+.|+++..+.+++|+
T Consensus       167 FqaAlqvsGyq-pllAYniALaHy-~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  167 FQAALQVSGYQ-PLLAYNLALAHY-SSRQYASALKHISEIIERGI  209 (459)
T ss_pred             HHHHHhhcCCC-chhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhh
Confidence            9987765 555 567898877655 56778899999999988775

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

Probab=96.37  E-value=0.029  Score=49.73  Aligned_cols=70  Identities=13%  Similarity=0.093  Sum_probs=44.0

Q ss_pred             CHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC----------------CHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 042756          239 LLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN----------------ELSRMVLWLQKMKDSGIPFSVRTYNSVLN  302 (425)
Q Consensus       239 ~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g----------------~~~~A~~l~~~M~~~g~~pd~~t~~~ll~  302 (425)
                      .++-....++.|.+-|+..|..+|+.||..+=+..                +-+-+++++++|...|+.||..+-..|++
T Consensus        87 HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn  166 (406)
T KOG3941|consen   87 HVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVN  166 (406)
T ss_pred             hHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHH
Confidence            34444444444444455555555555444443221                23457889999999999999999999999


Q ss_pred             HHHHHH
Q 042756          303 SCSTIM  308 (425)
Q Consensus       303 ~~~~~~  308 (425)
                      ++.+-+
T Consensus       167 ~FGr~~  172 (406)
T KOG3941|consen  167 AFGRWN  172 (406)
T ss_pred             Hhcccc
Confidence            887743

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

Probab=96.29  E-value=0.061  Score=49.25  Aligned_cols=146  Identities=13%  Similarity=0.139  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      .+|-.++...-+.+.++.|+++|.+..+.... ... +.+..+++..++ .++.+.+..+++...+.      ..-+...
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~-~~~-vy~~~A~~E~~~-~~d~~~A~~Ife~glk~------f~~~~~~   72 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRC-TYH-VYVAYALMEYYC-NKDPKRARKIFERGLKK------FPSDPDF   72 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS--TH-HHHHHHHHHHHT-CS-HHHHHHHHHHHHHH------HTT-HHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCC-CHH-HHHHHHHHHHHh-CCCHHHHHHHHHHHHHH------CCCCHHH
Confidence            46778888888888999999999998754222 222 233344443332 34433344444443333      2234568


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG---FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~---~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      |...|+.+.+.|+.+.|..+|++.... +.++.   ..|...++-=.+.|+++.+.++.+.+.+.  .|+......+++-
T Consensus        73 ~~~Y~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~r  149 (280)
T PF05843_consen   73 WLEYLDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDR  149 (280)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCC
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHH
Confidence            999999999999999999999999876 33333   49999999999999999999999998874  3454444444444


Q ss_pred             H
Q 042756          269 Y  269 (425)
Q Consensus       269 ~  269 (425)
                      |
T Consensus       150 y  150 (280)
T PF05843_consen  150 Y  150 (280)
T ss_dssp             T
T ss_pred             h
Confidence            4

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.

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

Probab=96.29  E-value=0.52  Score=46.13  Aligned_cols=238  Identities=12%  Similarity=0.033  Sum_probs=109.0

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCC-------------CchhhhHHHH
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTH-------------PRLSSLAFPL   97 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~-------------~~~~~~a~~l   97 (425)
                      +.+|.+..|.=.|+.-.+.-+-+..+|-.|=-.-+..++...+...|.+.+.-+..-             .+.-..|++.
T Consensus       296 m~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al~~  375 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQALKM  375 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHHHH
Confidence            445566666666666555444456666666555555555555666665554432210             0112223333


Q ss_pred             HHH-hhhc---CCCcc---CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-CchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           98 YMR-ITEE---SWFQW---NPKLVAEIIAFLDKQGQREEAETLILETLSKLGS-RERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        98 f~~-m~~~---~~~~~---~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~-~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      ++. +...   ....+   +...-+.  ..+.....+....++|-++...... .+++   ++..|--.|--.|.++.+.
T Consensus       376 L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~Dpd---vQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  376 LDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPD---VQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChh---HHhhhHHHHhcchHHHHHH
Confidence            332 1111   00000   0000000  1222223344555555555433221 2233   3344444455555544444


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      ++|+...+..+.      |...||-|-..++...+.++|+.-|.+.++..=.--.+=||.-| .|...|.+++|.+.|-.
T Consensus       451 Dcf~~AL~v~Pn------d~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgI-S~mNlG~ykEA~~hlL~  523 (579)
T KOG1125|consen  451 DCFEAALQVKPN------DYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGI-SCMNLGAYKEAVKHLLE  523 (579)
T ss_pred             HHHHHHHhcCCc------hHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhh-hhhhhhhHHHHHHHHHH
Confidence            444444443222      22366666666666666666666666666553222223333333 45566666666655553


Q ss_pred             HHH---C------CCCcCHHhHHHHHHHHHhcCCHHHHHH
Q 042756          250 MES---D------GTRVDTVCSNMVLSSYGDHNELSRMVL  280 (425)
Q Consensus       250 m~~---~------g~~~~~~~yn~li~~~~~~g~~~~A~~  280 (425)
                      ...   .      +-.++...|.+|=.++.-.++.|-+.+
T Consensus       524 AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~  563 (579)
T KOG1125|consen  524 ALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQE  563 (579)
T ss_pred             HHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHH
Confidence            321   1      112244566666666666666554433

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

Probab=96.25  E-value=1.5  Score=46.11  Aligned_cols=52  Identities=19%  Similarity=0.253  Sum_probs=35.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR  166 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~  166 (425)
                      |+..|.-++....+.|.+++-...+.-.+++...+.-     =+.||-+|++.++..
T Consensus      1132 Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~i-----d~eLi~AyAkt~rl~ 1183 (1666)
T KOG0985|consen 1132 DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYI-----DSELIFAYAKTNRLT 1183 (1666)
T ss_pred             CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccc-----hHHHHHHHHHhchHH
Confidence            5556777888888888888887766555554443332     256888888888743

>PLN02789 farnesyltranstransferase

Probab=96.23  E-value=1  Score=41.96  Aligned_cols=168  Identities=8%  Similarity=-0.008  Sum_probs=99.4

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCC--hhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCccc
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQ--REEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRG  167 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~--~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~  167 (425)
                      .+++++..++.+.+.+.  -+..+|+.--..+.+.|+  .+++.++++++.+.    .+.+..+|+..--++.+.|++  
T Consensus        87 ~l~eeL~~~~~~i~~np--knyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~----dpkNy~AW~~R~w~l~~l~~~--  158 (320)
T PLN02789         87 DLEEELDFAEDVAEDNP--KNYQIWHHRRWLAEKLGPDAANKELEFTRKILSL----DAKNYHAWSHRQWVLRTLGGW--  158 (320)
T ss_pred             hHHHHHHHHHHHHHHCC--cchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHh----CcccHHHHHHHHHHHHHhhhH--
Confidence            34666777776665542  244455544444455554  36677777777654    333345677777777777774  


Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc---CCh----hHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcC--
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM---GQP----HEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRL--  237 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~---g~~----~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~--  237 (425)
                       +++++.+.+++....   -|...|+.....+.+.   |..    ++.+++..+....  .| |...|+.+-..+...  
T Consensus       159 -~eeL~~~~~~I~~d~---~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~--~P~N~SaW~Yl~~ll~~~~~  232 (320)
T PLN02789        159 -EDELEYCHQLLEEDV---RNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILA--NPRNESPWRYLRGLFKDDKE  232 (320)
T ss_pred             -HHHHHHHHHHHHHCC---CchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHh--CCCCcCHHHHHHHHHhcCCc
Confidence             455555555544321   1233777766655554   222    4566666565553  34 556777777777663  


Q ss_pred             --CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          238 --GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       238 --g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                        +...+|.+++.+..+.++ .+......|++.|+..
T Consensus       233 ~l~~~~~~~~~~~~~~~~~~-~s~~al~~l~d~~~~~  268 (320)
T PLN02789        233 ALVSDPEVSSVCLEVLSKDS-NHVFALSDLLDLLCEG  268 (320)
T ss_pred             ccccchhHHHHHHHhhcccC-CcHHHHHHHHHHHHhh
Confidence              344567788877666543 3677888888888753

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.21  E-value=0.27  Score=49.08  Aligned_cols=72  Identities=7%  Similarity=-0.124  Sum_probs=45.8

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHH
Q 042756          223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYN  298 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~  298 (425)
                      +...|..+--.....|++++|...+++..+.+  |+...|..+-..+...|+.++|...|++....  .|...||.
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P~~pt~~  490 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RPGENTLY  490 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCchHH
Confidence            34555555444555677777777777766654  56667777777777777777777777765432  45444443

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

Probab=96.18  E-value=0.022  Score=39.36  Aligned_cols=63  Identities=17%  Similarity=0.227  Sum_probs=48.8

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHH
Q 042756          200 CEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL  266 (425)
Q Consensus       200 ~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li  266 (425)
                      .+.|++++|+++|++....  .| +...+-.+..+|.+.|++++|.++++.+...  .|+...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            4678899999999999875  34 6677778999999999999999999988876  46655555554

...

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.17  E-value=0.59  Score=47.12  Aligned_cols=166  Identities=10%  Similarity=0.068  Sum_probs=93.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      -|.+-..++++.+|+.+.+.++..+..  ..-|.-+.+.|+..|+++.|+++|-+--         .++--|..|.+.|+
T Consensus       738 aieaai~akew~kai~ildniqdqk~~--s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~k  806 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQKTA--SGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGK  806 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhccc--cccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhcccc
Confidence            345556677888888888877776543  3457777788888888888888876422         35667788888888


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc----cCCchhhHHHHHhhcchhhHHHHHHHHhCCCCccc
Q 042756          275 LSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN----SNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEA  350 (425)
Q Consensus       275 ~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  350 (425)
                      ++.|.++-.+-.  |-......|-+=..-+-+.|++..+.+    .......|..|-+.+..++..   .++++-. |+-
T Consensus       807 w~da~kla~e~~--~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmi---rlv~k~h-~d~  880 (1636)
T KOG3616|consen  807 WEDAFKLAEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMI---RLVEKHH-GDH  880 (1636)
T ss_pred             HHHHHHHHHHhc--CchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHH---HHHHHhC-hhh
Confidence            888887765533  212233334333333444555444422    112223344555555444432   2222211 221


Q ss_pred             --ceeeccccchhcccCcchhHHHHHHHHHHHHH
Q 042756          351 --MKWDSGETKLDLHGMHLGSAYFIILQWMDEMR  382 (425)
Q Consensus       351 --~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~  382 (425)
                        .|-..+-.-|-..|+...|     .+-|-+..
T Consensus       881 l~dt~~~f~~e~e~~g~lkaa-----e~~flea~  909 (1636)
T KOG3616|consen  881 LHDTHKHFAKELEAEGDLKAA-----EEHFLEAG  909 (1636)
T ss_pred             hhHHHHHHHHHHHhccChhHH-----HHHHHhhh
Confidence              2334444556667777777     55554443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.12  E-value=0.52  Score=47.10  Aligned_cols=124  Identities=11%  Similarity=-0.039  Sum_probs=76.7

Q ss_pred             cChhHHHHHHHHHHh--c---CChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcC--------CCHHHHHHHHHHHHH
Q 042756          187 VKRQALKSMISGLCE--M---GQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRL--------GLLEDMERIVNQMES  252 (425)
Q Consensus       187 p~~~~~~~li~~~~~--~---g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~--------g~~~~a~~~~~~m~~  252 (425)
                      .|...|...+.+...  .   ++.+.|.++|++..+  ..|| ...|..+..++...        +++..+.+.......
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~--ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILK--SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            444466666666432  2   346677777777776  3554 33444433332221        123444454444333


Q ss_pred             C-CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 042756          253 D-GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       253 ~-g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      . ....+...|.++--.+...|++++|...|++..+.+  |+...|..+-..+...|+.+.+.
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~  473 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAA  473 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHH
Confidence            2 233455778877666667899999999999988764  78888888888888888877764

>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=96.06  E-value=0.043  Score=44.71  Aligned_cols=70  Identities=11%  Similarity=0.131  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH-----hCCCCCCHHH
Q 042756          226 EYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMK-----DSGIPFSVRT  296 (425)
Q Consensus       226 ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~-----~~g~~pd~~t  296 (425)
                      +...++..+...|+++.|.++...+.... +.|...|-.+|.+|...|+..+|.++|+++.     +-|+.|+..|
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            44445555666666666666666666543 2356667777777777777777777666653     3466666554

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

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.03  E-value=0.32  Score=40.86  Aligned_cols=96  Identities=11%  Similarity=0.003  Sum_probs=61.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ....|..+-..+...|++++|...|++..+....+. .....+..+...+.+.|+++.+.+   .+.+.....+   -+.
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~la~~~~~~g~~~~A~~---~~~~al~~~p---~~~  106 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPN-DRSYILYNMGIIYASNGEHDKALE---YYHQALELNP---KQP  106 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccc-hHHHHHHHHHHHHHHcCCHHHHHH---HHHHHHHhCc---ccH
Confidence            445677788888899999999999999876432211 112357788888999999554444   4444443221   123


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      ..+..+...|...|+...+..-+
T Consensus       107 ~~~~~lg~~~~~~g~~~~a~~~~  129 (172)
T PRK02603        107 SALNNIAVIYHKRGEKAEEAGDQ  129 (172)
T ss_pred             HHHHHHHHHHHHcCChHhHhhCH
Confidence            46777777887777755444333

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

Probab=95.97  E-value=1.4  Score=41.08  Aligned_cols=57  Identities=14%  Similarity=0.172  Sum_probs=25.3

Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      ||..-|-..|.+++..+++++..++...    ...|  .-|-..+.+|.+.|...+|.++...
T Consensus       206 ~dkrfw~lki~aLa~~~~w~eL~~fa~s----kKsP--IGyepFv~~~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  206 PDKRFWWLKIKALAENKDWDELEKFAKS----KKSP--IGYEPFVEACLKYGNKKEASKYIPK  262 (319)
T ss_pred             cHHHHHHHHHHHHHhcCCHHHHHHHHhC----CCCC--CChHHHHHHHHHCCCHHHHHHHHHh
Confidence            4444455555555555555444443221    1122  4444445555555554444444443

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

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.96  E-value=0.38  Score=37.61  Aligned_cols=105  Identities=11%  Similarity=0.116  Sum_probs=76.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC----HHhHHHHHHH
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD----TVCSNMVLSS  268 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~----~~~yn~li~~  268 (425)
                      +-.++-..|+.++|+.+|++-...|+..+  ...+-.+-+++...|++++|..+|+......  |+    ......+-.+
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHH
Confidence            44567778999999999999999887765  3467777888999999999999999887642  33    2222223457


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      +...|+.++|++.+-....    ++...|.--|..|.
T Consensus        85 L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEALA----ETLPRYRRAIRFYA  117 (120)
T ss_pred             HHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence            7889999999998877553    23346666666554

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.89  E-value=0.15  Score=42.57  Aligned_cols=98  Identities=14%  Similarity=0.017  Sum_probs=59.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ....|..+...+...|++++|...|++....... +.....+|..+-..+...|+.+.   +...+.+......   ...
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~-~~~~~~~~~~lg~~~~~~g~~~e---A~~~~~~Al~~~~---~~~  106 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEID-PYDRSYILYNIGLIHTSNGEHTK---ALEYYFQALERNP---FLP  106 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcccc-chhhHHHHHHHHHHHHHcCCHHH---HHHHHHHHHHhCc---CcH
Confidence            3456677777788889999999999988654222 12223467778888888898544   4444444432211   112


Q ss_pred             hHHHHHHHHHH-------hcCChhHHHHHHHH
Q 042756          190 QALKSMISGLC-------EMGQPHEAENLIEE  214 (425)
Q Consensus       190 ~~~~~li~~~~-------~~g~~~~a~~~~~~  214 (425)
                      .+++.+...+.       +.|+++.|...+++
T Consensus       107 ~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        107 QALNNMAVICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHHHHHHHHHHhhHHHHHcccHHHHHHHHHH
Confidence            35666666666       55666555544443

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

Probab=95.89  E-value=0.043  Score=37.54  Aligned_cols=55  Identities=4%  Similarity=-0.011  Sum_probs=34.8

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          232 YGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ..+.+.|++++|.+.|+...+.. +-+...+..+-..+...|++++|..+|++..+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            45566677777777777766654 12556666666666777777777777776654

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.87  E-value=1.3  Score=46.30  Aligned_cols=217  Identities=11%  Similarity=0.001  Sum_probs=130.3

Q ss_pred             cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhH
Q 042756           50 VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREE  129 (425)
Q Consensus        50 ~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~  129 (425)
                      .+.....+..+|+++-.--....++..+-+......    ....|.+.|+..-+-+.-  +..........|++..+++.
T Consensus       471 rK~~~~al~ali~alrld~~~apaf~~LG~iYrd~~----Dm~RA~kCf~KAFeLDat--daeaaaa~adtyae~~~we~  544 (1238)
T KOG1127|consen  471 RKNSALALHALIRALRLDVSLAPAFAFLGQIYRDSD----DMKRAKKCFDKAFELDAT--DAEAAAASADTYAEESTWEE  544 (1238)
T ss_pred             hhhHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHH----HHHHHHHHHHHHhcCCch--hhhhHHHHHHHhhccccHHH
Confidence            344556667777777666666667766666654321    345577777776555422  55567778999999999999


Q ss_pred             HHHHHHHHHHhcCCCchhHHHHHHHHHH--HHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhH
Q 042756          130 AETLILETLSKLGSRERELVLFYCNLID--SFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHE  207 (425)
Q Consensus       130 A~~l~~~m~~~~~~~~~~~~~~y~~li~--~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~  207 (425)
                      |..+.-...+.    .+.....++-.-.  .|-+.+.   ...+...+.......   .-|...|-.+..+|.++|++..
T Consensus       545 a~~I~l~~~qk----a~a~~~k~nW~~rG~yyLea~n---~h~aV~~fQsALR~d---PkD~n~W~gLGeAY~~sGry~~  614 (1238)
T KOG1127|consen  545 AFEICLRAAQK----APAFACKENWVQRGPYYLEAHN---LHGAVCEFQSALRTD---PKDYNLWLGLGEAYPESGRYSH  614 (1238)
T ss_pred             HHHHHHHHhhh----chHHHHHhhhhhccccccCccc---hhhHHHHHHHHhcCC---chhHHHHHHHHHHHHhcCceeh
Confidence            99983332221    1111111222211  2334444   455666666655433   1356799999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHH--HHHcCCCHHHHHHHHHHHHHC------CCCcCHHhHHHHHHHHHhcCCHHHHH
Q 042756          208 AENLIEEMRVKGLEPSGFEYKCIIY--GYGRLGLLEDMERIVNQMESD------GTRVDTVCSNMVLSSYGDHNELSRMV  279 (425)
Q Consensus       208 a~~~~~~m~~~g~~p~~~ty~~ll~--~~~~~g~~~~a~~~~~~m~~~------g~~~~~~~yn~li~~~~~~g~~~~A~  279 (425)
                      |+++|.+...  +.|+ .+|...-.  .-+..|.+++|...+......      +-.--..++--+...+...|-..+|.
T Consensus       615 AlKvF~kAs~--LrP~-s~y~~fk~A~~ecd~GkYkeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kav  691 (1238)
T KOG1127|consen  615 ALKVFTKASL--LRPL-SKYGRFKEAVMECDNGKYKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAV  691 (1238)
T ss_pred             HHHhhhhhHh--cCcH-hHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhh
Confidence            9999998766  4564 34443332  356778888888888776542      11112344444444444455555555


Q ss_pred             HHHHHH
Q 042756          280 LWLQKM  285 (425)
Q Consensus       280 ~l~~~M  285 (425)
                      ..|++-
T Consensus       692 d~~eks  697 (1238)
T KOG1127|consen  692 DFFEKS  697 (1238)
T ss_pred             HHHHHH
Confidence            555543

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

Probab=95.84  E-value=0.066  Score=47.54  Aligned_cols=88  Identities=15%  Similarity=0.193  Sum_probs=71.3

Q ss_pred             ChhHHHHHHHHHHh-----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC----------------HHHHHHH
Q 042756          188 KRQALKSMISGLCE-----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL----------------LEDMERI  246 (425)
Q Consensus       188 ~~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~----------------~~~a~~~  246 (425)
                      |..+|-+++..|..     .+.+|-..-.++.|.+-|++-|..+|+.||+.+-|-.-                -+=+.++
T Consensus        66 dK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~v  145 (406)
T KOG3941|consen   66 DKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKV  145 (406)
T ss_pred             cHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHH
Confidence            33466666666654     36778888888999999999999999999998766532                2338899


Q ss_pred             HHHHHHCCCCcCHHhHHHHHHHHHhcCCH
Q 042756          247 VNQMESDGTRVDTVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       247 ~~~m~~~g~~~~~~~yn~li~~~~~~g~~  275 (425)
                      +++|+..|+.||-.+-..|+.+|.+.+..
T Consensus       146 LeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  146 LEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             HHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence            99999999999999999999999988864

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

Probab=95.84  E-value=0.1  Score=49.65  Aligned_cols=100  Identities=11%  Similarity=0.024  Sum_probs=60.3

Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHH
Q 042756          119 AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISG  198 (425)
Q Consensus       119 ~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~  198 (425)
                      ..+...|++++|.++|++..+...    .....|..+-.+|.+.|+++.   +...+.+.....+   .+...|..+-.+
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P----~~~~a~~~~a~~~~~~g~~~e---Al~~~~~Al~l~P---~~~~a~~~lg~~   79 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDP----NNAELYADRAQANIKLGNFTE---AVADANKAIELDP---SLAKAYLRKGTA   79 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCC----CCHHHHHHHHHHHHHcCCHHH---HHHHHHHHHHhCc---CCHHHHHHHHHH
Confidence            344566788888888888776422    223356667777777787444   4444433332221   123467777777


Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 042756          199 LCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI  230 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l  230 (425)
                      |...|++++|...|++...  +.|+.......
T Consensus        80 ~~~lg~~~eA~~~~~~al~--l~P~~~~~~~~  109 (356)
T PLN03088         80 CMKLEEYQTAKAALEKGAS--LAPGDSRFTKL  109 (356)
T ss_pred             HHHhCCHHHHHHHHHHHHH--hCCCCHHHHHH
Confidence            8888888888888887776  34544444333

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

Probab=95.68  E-value=1.1  Score=44.05  Aligned_cols=154  Identities=10%  Similarity=0.034  Sum_probs=80.2

Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHH
Q 042756          122 DKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISGLC  200 (425)
Q Consensus       122 ~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~  200 (425)
                      .+.|++.+|.-+|+...+.    .|.....|.-|-......++-   ..+...+.+...-    .|+ ....-+|--.|.
T Consensus       296 m~nG~L~~A~LafEAAVkq----dP~haeAW~~LG~~qaENE~E---~~ai~AL~rcl~L----dP~NleaLmaLAVSyt  364 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQ----DPQHAEAWQKLGITQAENENE---QNAISALRRCLEL----DPTNLEALMALAVSYT  364 (579)
T ss_pred             HhcCCchHHHHHHHHHHhh----ChHHHHHHHHhhhHhhhccch---HHHHHHHHHHHhc----CCccHHHHHHHHHHHh
Confidence            5678888888888876654    333344565555555555542   2233333333221    121 223333334444


Q ss_pred             hcCChhHHHHHHHHH-----------------------------------------HH-cCCCCCHHHHHHHHHHHHcCC
Q 042756          201 EMGQPHEAENLIEEM-----------------------------------------RV-KGLEPSGFEYKCIIYGYGRLG  238 (425)
Q Consensus       201 ~~g~~~~a~~~~~~m-----------------------------------------~~-~g~~p~~~ty~~ll~~~~~~g  238 (425)
                      ..|.=..|+..++.-                                         .. .+..+|..++..|--.|--.|
T Consensus       365 Neg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~  444 (579)
T KOG1125|consen  365 NEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSG  444 (579)
T ss_pred             hhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcch
Confidence            444444444444333                                         22 233344455555555555666


Q ss_pred             CHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          239 LLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       239 ~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +++.|...|+...... +-|..+||-|-..++...+.++|+.-|.+..+
T Consensus       445 efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALq  492 (579)
T KOG1125|consen  445 EFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQ  492 (579)
T ss_pred             HHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHh
Confidence            6666666666555432 12456666666666666666666666666554

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

Probab=95.65  E-value=2.7  Score=41.98  Aligned_cols=258  Identities=13%  Similarity=0.020  Sum_probs=151.0

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHh--cCCCHHHHHHHHHHHH------hcCChHHHHHHHHhhhCCCCC------------
Q 042756           27 LVQCLTARLTKQGQRFLSSLALA--VTRDSKAASRLISKFV------ASSPQFIALNALSHLLSPDTT------------   86 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~--~~~d~~~~~~ll~~~~------~~~~~~~a~~~~~~~l~~~~~------------   86 (425)
                      ..+..+.|....|.++++...+.  -.|+...|.....-+-      ++|..+.+++.+..--.+-..            
T Consensus       150 Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~  229 (700)
T KOG1156|consen  150 AVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLL  229 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHH
Confidence            45556677888899999988888  3688877766655443      446666666666543111000            


Q ss_pred             -CCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHH-hcCChhHHH-HHHHHHHHhcCCCchh----------------
Q 042756           87 -HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLD-KQGQREEAE-TLILETLSKLGSRERE----------------  147 (425)
Q Consensus        87 -~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~-~~g~~~~A~-~l~~~m~~~~~~~~~~----------------  147 (425)
                       .-+++++|..+|..+..++   ||..-|...+..+. +..+.-++. .+|....+.......+                
T Consensus       230 ~kl~~lEeA~~~y~~Ll~rn---Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~  306 (700)
T KOG1156|consen  230 MKLGQLEEAVKVYRRLLERN---PDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEI  306 (700)
T ss_pred             HHHhhHHhHHHHHHHHHhhC---chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHH
Confidence             0125789999999998886   67666665444443 443333333 6666554321100000                


Q ss_pred             ------------HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC---------CCCccChhHHH--HHHHHHHhcCC
Q 042756          148 ------------LVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS---------SSVYVKRQALK--SMISGLCEMGQ  204 (425)
Q Consensus       148 ------------~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~---------~~~~p~~~~~~--~li~~~~~~g~  204 (425)
                                  .+.++..+...|-.-...+-.++..-.+.......         ..-.|....|.  .++..|-+.|+
T Consensus       307 vdkyL~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~  386 (700)
T KOG1156|consen  307 VDKYLRPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGD  386 (700)
T ss_pred             HHHHHHHHhhcCCCchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHccc
Confidence                        00133334333332221111122222222211111         01135555444  56778888999


Q ss_pred             hhHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHH
Q 042756          205 PHEAENLIEEMRVKGLEPSGF-EYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQ  283 (425)
Q Consensus       205 ~~~a~~~~~~m~~~g~~p~~~-ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~  283 (425)
                      ++.|..+.+....+  .|+.+ -|-.=-..+..+|++++|...+++..+... +|...=.--..-..+..++++|.++..
T Consensus       387 ~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~INsKcAKYmLrAn~i~eA~~~~s  463 (700)
T KOG1156|consen  387 YEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAINSKCAKYMLRANEIEEAEEVLS  463 (700)
T ss_pred             HHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHHHHHHHHHHHccccHHHHHHHH
Confidence            99999999988764  55533 444445778889999999999998877542 344333345555667889999999988


Q ss_pred             HHHhCCC
Q 042756          284 KMKDSGI  290 (425)
Q Consensus       284 ~M~~~g~  290 (425)
                      ...+.|.
T Consensus       464 kFTr~~~  470 (700)
T KOG1156|consen  464 KFTREGF  470 (700)
T ss_pred             Hhhhccc
Confidence            8887775

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

Probab=95.64  E-value=0.045  Score=39.81  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=44.0

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHHhc
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISGLCEM  202 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~  202 (425)
                      .|+++.|+.+|+++.+.....+ +.. .+-.+-.+|.+.|+   ..+++..+.+. .    ..|+ ....-.+-.+|.+.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~-~~~-~~~~la~~~~~~~~---y~~A~~~~~~~-~----~~~~~~~~~~l~a~~~~~l   71 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNP-NSA-YLYNLAQCYFQQGK---YEEAIELLQKL-K----LDPSNPDIHYLLARCLLKL   71 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTH-HHH-HHHHHHHHHHHTTH---HHHHHHHHHCH-T----HHHCHHHHHHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHHHHCCCCh-hHH-HHHHHHHHHHHCCC---HHHHHHHHHHh-C----CCCCCHHHHHHHHHHHHHh
Confidence            4677778887777776533211 222 23336777777777   44455555441 1    1111 12333446777777


Q ss_pred             CChhHHHHHHHH
Q 042756          203 GQPHEAENLIEE  214 (425)
Q Consensus       203 g~~~~a~~~~~~  214 (425)
                      |++++|+++|++
T Consensus        72 ~~y~eAi~~l~~   83 (84)
T PF12895_consen   72 GKYEEAIKALEK   83 (84)
T ss_dssp             T-HHHHHHHHHH
T ss_pred             CCHHHHHHHHhc
Confidence            888888777764

>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=95.57  E-value=0.09  Score=42.79  Aligned_cols=71  Identities=17%  Similarity=0.192  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCcCHHhH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES-----DGTRVDTVCS  262 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~~y  262 (425)
                      +...++..+...|++++|.++........ +-|...|..+|.+|...|+...|.++|+.+.+     .|+.|+..+-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            66777788888999999999999888752 33677999999999999999999999987753     4888876553

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

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

Probab=95.54  E-value=2.1  Score=39.94  Aligned_cols=103  Identities=15%  Similarity=0.160  Sum_probs=76.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      +.+..|.-+...|+...|.++-.+.+    .||..-|-..+.++++.++|++-+++...      +.+++-|-..+..|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHH
Confidence            66667778888888888888877663    47888888999999999999888876432      235678899999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          271 DHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      +.|+..+|..+..++          ++.--+..|.+.|.+..+
T Consensus       249 ~~~~~~eA~~yI~k~----------~~~~rv~~y~~~~~~~~A  281 (319)
T PF04840_consen  249 KYGNKKEASKYIPKI----------PDEERVEMYLKCGDYKEA  281 (319)
T ss_pred             HCCCHHHHHHHHHhC----------ChHHHHHHHHHCCCHHHH
Confidence            999999888887771          223445556666666554

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

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

Probab=95.50  E-value=1.7  Score=38.66  Aligned_cols=147  Identities=18%  Similarity=0.103  Sum_probs=100.3

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc-CCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH-DSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~-g~~~~~  168 (425)
                      ..++|++......       +......=+..+.+..+++-|.+.++.|.+.    +.+  .|.+-|-.++.+. +.-+++
T Consensus       123 ~~deAl~~~~~~~-------~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i----ded--~tLtQLA~awv~la~ggek~  189 (299)
T KOG3081|consen  123 DFDEALKALHLGE-------NLEAAALNVQILLKMHRFDLAEKELKKMQQI----DED--ATLTQLAQAWVKLATGGEKI  189 (299)
T ss_pred             ChHHHHHHHhccc-------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc----chH--HHHHHHHHHHHHHhccchhh
Confidence            4566666554411       3334444466677888999999999999864    222  2445566666542 112238


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC-HHHHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL-LEDMERIV  247 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~-~~~a~~~~  247 (425)
                      .+++-++.++..+   ..|+..+.|....++...|++++|..++++...+.-. +..|...+|-+--..|. .+...+..
T Consensus       190 qdAfyifeE~s~k---~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~Nliv~a~~~Gkd~~~~~r~l  265 (299)
T KOG3081|consen  190 QDAFYIFEELSEK---TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLANLIVLALHLGKDAEVTERNL  265 (299)
T ss_pred             hhHHHHHHHHhcc---cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCCChHHHHHHH
Confidence            8899999988653   5577779999999999999999999999999987432 45666666655555554 45567777


Q ss_pred             HHHHHC
Q 042756          248 NQMESD  253 (425)
Q Consensus       248 ~~m~~~  253 (425)
                      .+++..
T Consensus       266 ~QLk~~  271 (299)
T KOG3081|consen  266 SQLKLS  271 (299)
T ss_pred             HHHHhc
Confidence            777664

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.49  E-value=0.81  Score=46.21  Aligned_cols=129  Identities=24%  Similarity=0.261  Sum_probs=78.8

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+.+|+.+.+.+..+. .  .+.-|..+..-|+..|+++.|+++|-+-.            .++--|..|.+.|++   +
T Consensus       747 ew~kai~ildniqdqk-~--~s~yy~~iadhyan~~dfe~ae~lf~e~~------------~~~dai~my~k~~kw---~  808 (1636)
T KOG3616|consen  747 EWKKAISILDNIQDQK-T--ASGYYGEIADHYANKGDFEIAEELFTEAD------------LFKDAIDMYGKAGKW---E  808 (1636)
T ss_pred             hhhhhHhHHHHhhhhc-c--ccccchHHHHHhccchhHHHHHHHHHhcc------------hhHHHHHHHhccccH---H
Confidence            4667888888877665 2  33457778888999999999999887731            346678889999984   4


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      +++++..+...    .......|-+--.-.-+.|++.+|.++|-...    .|+     ..|.+|-+.|..++..++.+.
T Consensus       809 da~kla~e~~~----~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~ddmirlv~k  875 (1636)
T KOG3616|consen  809 DAFKLAEECHG----PEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLDDDMIRLVEK  875 (1636)
T ss_pred             HHHHHHHHhcC----chhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcchHHHHHHHH
Confidence            55555544422    22233455555555556666666666554321    122     234455555555555555443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.32  E-value=0.34  Score=43.77  Aligned_cols=102  Identities=9%  Similarity=-0.050  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCcCHHhHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG----FEYKCIIYGYGRLGLLEDMERIVNQMESDG--TRVDTVCSN  263 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g--~~~~~~~yn  263 (425)
                      ..|+.-+.-+.+.|++++|...|+.+...  .|+.    ..+--+-.+|...|++++|...|+.+.+.-  -......+-
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~  221 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHH
Confidence            46777676667789999999999999885  3442    466677788999999999999999998641  111244455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      .+...+...|+.++|.+.|++.++.  .|+..
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~~--yP~s~  251 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIKK--YPGTD  251 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH--CcCCH
Confidence            5566777899999999999998875  45543

>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=95.28  E-value=0.085  Score=37.60  Aligned_cols=59  Identities=22%  Similarity=0.191  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc----C-CCCC-HHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVK----G-LEPS-GFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g-~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      +|+.+-..|...|++++|+..|++..+.    | -.|+ ..++..+-.+|.+.|++++|.+++++
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~   71 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQK   71 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4444555555555555555555544422    1 1121 33444555555555555555555544

...

>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=95.26  E-value=0.12  Score=35.75  Aligned_cols=60  Identities=8%  Similarity=-0.064  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC-CHHHHHHHHHHH
Q 042756          225 FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN-ELSRMVLWLQKM  285 (425)
Q Consensus       225 ~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g-~~~~A~~l~~~M  285 (425)
                      .+|..+-..+...|++++|...|+...+.. +-+...|..+-.+|...| ++++|++.|++.
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            344444444445555555555555444432 113444444444555554 355555554443

...

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

Probab=95.21  E-value=0.1  Score=35.66  Aligned_cols=56  Identities=13%  Similarity=0.026  Sum_probs=44.1

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      -..+.+.|++++|.+.|++..+..  | +...+..+-.++...|++++|..+|+...+.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            456778889999999999988864  5 4567778888888999999999998888654

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=95.18  E-value=4.3  Score=41.43  Aligned_cols=177  Identities=11%  Similarity=0.027  Sum_probs=106.1

Q ss_pred             HHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 042756           98 YMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQ  177 (425)
Q Consensus        98 f~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~  177 (425)
                      +.++.... +.|++.+|..+.-+..+.|+++.+-+.|++....-.. .   ...|..+-..|...|.   -..+..+++.
T Consensus       311 ~~k~r~~~-~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-~---~e~w~~~als~saag~---~s~Av~ll~~  382 (799)
T KOG4162|consen  311 LRKLRLKK-FQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-E---HERWYQLALSYSAAGS---DSKAVNLLRE  382 (799)
T ss_pred             HHHHHHhh-hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-h---HHHHHHHHHHHHHhcc---chHHHHHHHh
Confidence            34444444 7799999999999999999999999999987632111 1   1134444444444444   2334444444


Q ss_pred             HhhcCCCCccCh-----------------------------------------hHHHHHHHHHHhc-----------CCh
Q 042756          178 LVNSSSSVYVKR-----------------------------------------QALKSMISGLCEM-----------GQP  205 (425)
Q Consensus       178 ~~~~~~~~~p~~-----------------------------------------~~~~~li~~~~~~-----------g~~  205 (425)
                      ......  .|+.                                         ..|-.+--+|...           ...
T Consensus       383 ~~~~~~--~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h  460 (799)
T KOG4162|consen  383 SLKKSE--QPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALH  460 (799)
T ss_pred             hccccc--CCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHH
Confidence            433221  1211                                         1222222222211           122


Q ss_pred             hHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 042756          206 HEAENLIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQK  284 (425)
Q Consensus       206 ~~a~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~  284 (425)
                      .++++.+++..+.+ -.|+..-|-++  -|+-.++++.|.+...+..+.+-.-+...|.-|.-.+...+++.+|+.+.+.
T Consensus       461 ~kslqale~av~~d~~dp~~if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~  538 (799)
T KOG4162|consen  461 KKSLQALEEAVQFDPTDPLVIFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDA  538 (799)
T ss_pred             HHHHHHHHHHHhcCCCCchHHHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHH
Confidence            34444444444332 23433333333  3666788999999999888876667899999999999999999999998887


Q ss_pred             HH
Q 042756          285 MK  286 (425)
Q Consensus       285 M~  286 (425)
                      ..
T Consensus       539 al  540 (799)
T KOG4162|consen  539 AL  540 (799)
T ss_pred             HH
Confidence            53

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.12  E-value=1.1  Score=41.24  Aligned_cols=68  Identities=13%  Similarity=0.138  Sum_probs=35.0

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHh--c----CChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDK--Q----GQREEAETLILETLSKLGSRERELVLFYCNLIDS  158 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~--~----g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~  158 (425)
                      .+++.+.+++.|.+.+ +.-+..+|-+.......  .    -...+|.++|+.|++.-.....+.-..+..|+..
T Consensus        77 ~~~~~~~~y~~L~~~g-Fk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~  150 (297)
T PF13170_consen   77 AFKEVLDIYEKLKEAG-FKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM  150 (297)
T ss_pred             HHHHHHHHHHHHHHhc-cCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc
Confidence            4566677777777776 55455444332222222  1    1255677788888775333332222344444433

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=95.04  E-value=2.8  Score=38.65  Aligned_cols=184  Identities=8%  Similarity=0.009  Sum_probs=121.3

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+..|+.....+.+-  .+|++..|..-..+|...|+...|..=+....+-   ...++. .+--+-..+-..|+   ++
T Consensus       170 D~~~ai~~i~~llEi--~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askL---s~DnTe-~~ykis~L~Y~vgd---~~  240 (504)
T KOG0624|consen  170 DCQNAIEMITHLLEI--QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKL---SQDNTE-GHYKISQLLYTVGD---AE  240 (504)
T ss_pred             chhhHHHHHHHHHhc--CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhc---cccchH-HHHHHHHHHHhhhh---HH
Confidence            455566667776653  4599999999999999999999887655554332   222222 22345556667888   67


Q ss_pred             HHHHHHHHHhhcCCCCccChh----HHHHH---------HHHHHhcCChhHHHHHHHHHHHcCCCCCHH---HHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQ----ALKSM---------ISGLCEMGQPHEAENLIEEMRVKGLEPSGF---EYKCIIYG  233 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~----~~~~l---------i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~---ty~~ll~~  233 (425)
                      ..+..+++...-    -||..    .|-.|         +....+.+++.++++-.+...+..-.-..+   .+..+-.+
T Consensus       241 ~sL~~iRECLKl----dpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C  316 (504)
T KOG0624|consen  241 NSLKEIRECLKL----DPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTC  316 (504)
T ss_pred             HHHHHHHHHHcc----CcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeec
Confidence            777777776542    24432    22211         123344677777777777776653221223   34456667


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCcC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          234 YGRLGLLEDMERIVNQMESDGTRVD-TVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       234 ~~~~g~~~~a~~~~~~m~~~g~~~~-~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      +...|.+.+|.+.-.+..+.  .|| +.++.-=..+|.-..+++.|+.=|+...+.
T Consensus       317 ~~~d~~~~eAiqqC~evL~~--d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  317 YREDEQFGEAIQQCKEVLDI--DPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             ccccCCHHHHHHHHHHHHhc--CchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc
Confidence            77888899999988887764  344 778888888898888899999988887764

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=94.95  E-value=0.7  Score=37.79  Aligned_cols=93  Identities=8%  Similarity=-0.096  Sum_probs=71.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .-.+-.-+...|++++|..+|+-...-  -|. ..-|-.+--++-..|++++|...|........ -|...+-.+-.++.
T Consensus        38 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         38 LYRYAMQLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYL  114 (157)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHH
Confidence            334445566789999999999988773  343 34555666677778899999999998887764 47888888888999


Q ss_pred             hcCCHHHHHHHHHHHHh
Q 042756          271 DHNELSRMVLWLQKMKD  287 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~  287 (425)
                      ..|+.+.|.+.|+..+.
T Consensus       115 ~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        115 ACDNVCYAIKALKAVVR  131 (157)
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            99999999999987664

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

Probab=94.78  E-value=1.1  Score=45.95  Aligned_cols=132  Identities=11%  Similarity=0.110  Sum_probs=87.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...|...-..+-..|+.+.|+.+|...+.            |-++++-.|-.|.   .+++..+.++..        |.
T Consensus       911 d~~L~~WWgqYlES~GemdaAl~~Y~~A~D------------~fs~VrI~C~qGk---~~kAa~iA~esg--------d~  967 (1416)
T KOG3617|consen  911 DESLYSWWGQYLESVGEMDAALSFYSSAKD------------YFSMVRIKCIQGK---TDKAARIAEESG--------DK  967 (1416)
T ss_pred             chHHHHHHHHHHhcccchHHHHHHHHHhhh------------hhhheeeEeeccC---chHHHHHHHhcc--------cH
Confidence            556677777777788999999998887542            4578888888888   455555555432        23


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC---------------CCHHHHHHHHHHHHHCC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL---------------GLLEDMERIVNQMESDG  254 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~---------------g~~~~a~~~~~~m~~~g  254 (425)
                      ...-.+-+.|-+.|++.+|..+|.+.         .+|.+.|..|-.+               .+.-.|.++|++.   |
T Consensus       968 AAcYhlaR~YEn~g~v~~Av~FfTrA---------qafsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~---g 1035 (1416)
T KOG3617|consen  968 AACYHLARMYENDGDVVKAVKFFTRA---------QAFSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEEL---G 1035 (1416)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHH---------HHHHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHc---c
Confidence            37778899999999999999999976         4455555443222               2233344444432   2


Q ss_pred             CCcCHHhHHHHHHHHHhcCCHHHHHHH
Q 042756          255 TRVDTVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       255 ~~~~~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      ..     +.--+..|-+.|.+.+|+++
T Consensus      1036 ~~-----~~~AVmLYHkAGm~~kALel 1057 (1416)
T KOG3617|consen 1036 GY-----AHKAVMLYHKAGMIGKALEL 1057 (1416)
T ss_pred             hh-----hhHHHHHHHhhcchHHHHHH
Confidence            11     23345567788888888775

>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=94.77  E-value=0.18  Score=34.88  Aligned_cols=63  Identities=16%  Similarity=0.078  Sum_probs=53.7

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG-LLEDMERIVNQMES  252 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g-~~~~a~~~~~~m~~  252 (425)
                      ..+|..+-..+.+.|++++|+..|++..+.. +-+...|..+-.+|.+.| ++++|.+.|+...+
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            4588999999999999999999999999863 225668889999999999 79999999988765

...

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.73  E-value=1.8  Score=34.78  Aligned_cols=124  Identities=17%  Similarity=0.121  Sum_probs=83.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      ++..+.+.+.......+++.+...+. ..+   ..++.++..|++...    .+..+.+...   .     +......++
T Consensus        13 vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~---~~~~~li~ly~~~~~----~~ll~~l~~~---~-----~~yd~~~~~   76 (140)
T smart00299       13 VVELFEKRNLLEELIPYLESALKLNS-ENP---ALQTKLIELYAKYDP----QKEIERLDNK---S-----NHYDIEKVG   76 (140)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHccCc-cch---hHHHHHHHHHHHHCH----HHHHHHHHhc---c-----ccCCHHHHH
Confidence            88888888899999999998877642 232   367889999998754    3444444421   1     112556688


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL-GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~-g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      +.|.+.+.++++.-++.++..         |...+..+... ++++.|.+++..-      -+...|..++..+..
T Consensus        77 ~~c~~~~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~l~  137 (140)
T smart00299       77 KLCEKAKLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKALLD  137 (140)
T ss_pred             HHHHHcCcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHHHc
Confidence            888888888888888887633         23334444444 7888888877751      255678777776654

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=94.69  E-value=3  Score=37.23  Aligned_cols=160  Identities=11%  Similarity=0.066  Sum_probs=102.5

Q ss_pred             hhhhHHHHHHHhhhcCCCccCH-HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-------
Q 042756           90 LSSLAFPLYMRITEESWFQWNP-KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK-------  161 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~-~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~-------  161 (425)
                      .++.|.+.|+.+......++-. ...-.+..++.+.+++++|...|++..+.....+ ..  -|...+.+.+.       
T Consensus        47 ~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~-~~--~~a~Y~~g~~~~~~~~~~  123 (243)
T PRK10866         47 NWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHP-NI--DYVLYMRGLTNMALDDSA  123 (243)
T ss_pred             CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCC-ch--HHHHHHHHHhhhhcchhh
Confidence            6778888888877654221111 1123466788899999999999999987533322 21  23444555431       


Q ss_pred             ----------cCCcccHHHHHHHHHHHhhcCCC--CccChhH------------HHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          162 ----------HDSKRGFDDTYARLNQLVNSSSS--VYVKRQA------------LKSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       162 ----------~g~~~~~~~~~~~~~~~~~~~~~--~~p~~~~------------~~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                                ..|...+.+++..+.+....-+.  ..|+...            --.+.+.|.+.|.+.-|..=|+.+.+
T Consensus       124 ~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~  203 (243)
T PRK10866        124 LQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVNRVEQMLR  203 (243)
T ss_pred             hhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence                      11333355666666666543221  1122211            11344668889999999999999987


Q ss_pred             c--CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          218 K--GLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       218 ~--g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      .  +........-.+..+|.+.|..++|.++...+..
T Consensus       204 ~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        204 DYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            6  4445566788899999999999999988876654

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

Probab=94.64  E-value=0.21  Score=44.88  Aligned_cols=101  Identities=17%  Similarity=0.169  Sum_probs=73.1

Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHH
Q 042756          121 LDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLC  200 (425)
Q Consensus       121 ~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~  200 (425)
                      +.+.+++++|+..|.+..+-    .|.+.+-|..=-.+|++.|..+.+.+..+.....-+..      ..+|..|-.+|.
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l----~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~y------skay~RLG~A~~  160 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIEL----DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHY------SKAYGRLGLAYL  160 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhc----CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHH------HHHHHHHHHHHH
Confidence            66788999999999998763    33334467888889999998544443333332221111      248999999999


Q ss_pred             hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 042756          201 EMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYG  233 (425)
Q Consensus       201 ~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~  233 (425)
                      ..|++++|.+.|++-.+  +.|+..+|-.=|+.
T Consensus       161 ~~gk~~~A~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  161 ALGKYEEAIEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             ccCcHHHHHHHHHhhhc--cCCCcHHHHHHHHH
Confidence            99999999999998877  78888887766544

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

Probab=94.42  E-value=5.8  Score=39.34  Aligned_cols=151  Identities=10%  Similarity=0.048  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHH--------HHHHcCCCC
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE--------EMRVKGLEP  222 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~--------~m~~~g~~p  222 (425)
                      .+.+++....+.... ....+...+.+.....+.  -...+--+++......|+++.|.+++.        .+.+.+-.|
T Consensus       341 ~~~~ll~~~t~~~~~-~~~ka~e~L~~~~~~~p~--~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P  417 (652)
T KOG2376|consen  341 LFPILLQEATKVREK-KHKKAIELLLQFADGHPE--KSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLP  417 (652)
T ss_pred             HHHHHHHHHHHHHHH-HHhhhHHHHHHHhccCCc--hhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccCh
Confidence            456777776655432 244455555544333211  112355566777788999999999999        555555555


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--CCCcC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH
Q 042756          223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESD--GTRVD----TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT  296 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~--g~~~~----~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t  296 (425)
                        .+...+...+.+.++-+.|..++.+-..-  .-.+.    ..++--+...-.+.|+.++|..+++++.+.. .+|..+
T Consensus       418 --~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~  494 (652)
T KOG2376|consen  418 --GTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDL  494 (652)
T ss_pred             --hHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHH
Confidence              67777888888888877787777765431  11122    2334444444567899999999999998753 678999


Q ss_pred             HHHHHHHHHHH
Q 042756          297 YNSVLNSCSTI  307 (425)
Q Consensus       297 ~~~ll~~~~~~  307 (425)
                      ...++.+|++.
T Consensus       495 l~~lV~a~~~~  505 (652)
T KOG2376|consen  495 LVQLVTAYARL  505 (652)
T ss_pred             HHHHHHHHHhc
Confidence            99999999873

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

Probab=94.37  E-value=0.27  Score=34.91  Aligned_cols=60  Identities=13%  Similarity=0.135  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHh---cCCCchhHHHHHHHHHHHHHhcCCcccHHH
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSK---LGSRERELVLFYCNLIDSFCKHDSKRGFDD  170 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~---~~~~~~~~~~~y~~li~~~~~~g~~~~~~~  170 (425)
                      ..+|+.+-..|...|++++|++.|++..+.   .+...+....++..+-..|...|+++++.+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~   67 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALE   67 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            457888999999999999999999987642   222223335566667777777777443333

...

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=94.35  E-value=0.34  Score=33.79  Aligned_cols=56  Identities=7%  Similarity=-0.127  Sum_probs=35.7

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          232 YGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ..|.+.+++++|.++++.+...+- .+...|...-..|.+.|++++|.+.|+...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDP-DDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCc-ccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            355666677777777776666532 25556666666667777777777777776643

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=94.35  E-value=7  Score=39.99  Aligned_cols=340  Identities=9%  Similarity=-0.047  Sum_probs=183.1

Q ss_pred             HHHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc----------------
Q 042756           26 TLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR----------------   89 (425)
Q Consensus        26 ~~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~----------------   89 (425)
                      .++.....|.+..+-+.|++......-....|+.+-..|..+|....|.+++...+.....+++                
T Consensus       329 Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmasklc~e~l~  408 (799)
T KOG4162|consen  329 LTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMASKLCIERLK  408 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHHHHHHhchh
Confidence            3677788889999999999987665566788999999999999999999999988766532221                


Q ss_pred             ----hhhhHHHHHHHhh-hcCCCccCHHHHHHHHHHHHhc-----------CChhHHHHHHHHHHHhcCCCchhHHHHHH
Q 042756           90 ----LSSLAFPLYMRIT-EESWFQWNPKLVAEIIAFLDKQ-----------GQREEAETLILETLSKLGSRERELVLFYC  153 (425)
Q Consensus        90 ----~~~~a~~lf~~m~-~~~~~~~~~~~~~~ll~~~~~~-----------g~~~~A~~l~~~m~~~~~~~~~~~~~~y~  153 (425)
                          -.+.|.++.+... +.+.+.|-  .|-.+--+|...           ....++++.+++-.+.+..++ . +..|-
T Consensus       409 ~~eegldYA~kai~~~~~~~~~l~~~--~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp-~-~if~l  484 (799)
T KOG4162|consen  409 LVEEGLDYAQKAISLLGGQRSHLKPR--GYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDP-L-VIFYL  484 (799)
T ss_pred             hhhhHHHHHHHHHHHhhhhhhhhhhh--HHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCc-h-HHHHH
Confidence                1344445544322 22333333  333333333321           124467777777766544322 2 33444


Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCC-----------
Q 042756          154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK-GLE-----------  221 (425)
Q Consensus       154 ~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~-----------  221 (425)
                      ++-.+..  ++   +.+|.+...+...-++.  -+...|..+.-.+...+++.+|+.+.+.-... |..           
T Consensus       485 alq~A~~--R~---l~sAl~~~~eaL~l~~~--~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~  557 (799)
T KOG4162|consen  485 ALQYAEQ--RQ---LTSALDYAREALALNRG--DSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIE  557 (799)
T ss_pred             HHHHHHH--Hh---HHHHHHHHHHHHHhcCC--ccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhh
Confidence            4444433  34   45555555555444322  23347877777777778888887776655432 220           


Q ss_pred             -------CCHHHHHHHHHHHHc---------C--------------CCHHHHHHHHHHH--------HHCC---------
Q 042756          222 -------PSGFEYKCIIYGYGR---------L--------------GLLEDMERIVNQM--------ESDG---------  254 (425)
Q Consensus       222 -------p~~~ty~~ll~~~~~---------~--------------g~~~~a~~~~~~m--------~~~g---------  254 (425)
                             --..|...++...-+         .              ++..+|.+....+        +..|         
T Consensus       558 ~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~  637 (799)
T KOG4162|consen  558 LTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSST  637 (799)
T ss_pred             hhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCccc
Confidence                   011122222211110         0              0111111111110        1111         


Q ss_pred             CCc--C------HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cC
Q 042756          255 TRV--D------TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SN  317 (425)
Q Consensus       255 ~~~--~------~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~  317 (425)
                      +.|  +      ...|......+.+.+..++|..++.+....- .-....|.-.-..+...|.++.++.         +.
T Consensus       638 ~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~  716 (799)
T KOG4162|consen  638 VLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPD  716 (799)
T ss_pred             ccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCC
Confidence            111  1      2345556667778888888887777765431 1122333333233444555555533         22


Q ss_pred             Cch---hhHHHHHhhcchhhHH---HHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          318 DFP---LSILELTEVLNEEEVS---VVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       318 ~~~---~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .++   .+-..+...|...-+.   .+.+.++.+ .-+...|-.+-..+-+.|+.+.|     .++|....+
T Consensus       717 hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~v~k~~Gd~~~A-----aecf~aa~q  782 (799)
T KOG4162|consen  717 HVPSMTALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGEVFKKLGDSKQA-----AECFQAALQ  782 (799)
T ss_pred             CcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHccchHHH-----HHHHHHHHh
Confidence            222   2222455555433222   233333332 13446788899999999999999     899987765

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=94.33  E-value=0.77  Score=37.55  Aligned_cols=92  Identities=11%  Similarity=-0.074  Sum_probs=67.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      +-.-+...|++++|.++|+....-    ++....-|-.|--.+-..|+++++.+++.....+.++..      ..+-.+-
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~----Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp------~~~~~ag  110 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIY----DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAP------QAPWAAA  110 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh----CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCc------hHHHHHH
Confidence            455566789999999999998764    222233455677777788887777777777666544332      3778888


Q ss_pred             HHHHhcCChhHHHHHHHHHHHc
Q 042756          197 SGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      .++...|+.+.|.+-|+.....
T Consensus       111 ~c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        111 ECYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            8999999999999999877654

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.12  E-value=1.2  Score=42.92  Aligned_cols=63  Identities=13%  Similarity=0.010  Sum_probs=52.9

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG----FEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ...|+.+-.+|.+.|++++|+..|++..+  +.|+.    .+|..+-.+|.+.|++++|...++...+.
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            46888899999999999999999998877  45663    46889999999999999999999887774

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

Probab=94.10  E-value=6.8  Score=38.89  Aligned_cols=141  Identities=12%  Similarity=-0.036  Sum_probs=72.8

Q ss_pred             hhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHH--------HHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          205 PHEAENLIEEMRVKGLEPS--GFEYKCIIYGYGRLGLLEDMERIVN--------QMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       205 ~~~a~~~~~~m~~~g~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~--------~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      ..++.+++...-+.  .|.  ..+--.++......|+++.|.+++.        .+.+.+..|-.  -.+++..|.+.++
T Consensus       357 ~~ka~e~L~~~~~~--~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~--V~aiv~l~~~~~~  432 (652)
T KOG2376|consen  357 HKKAIELLLQFADG--HPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGT--VGAIVALYYKIKD  432 (652)
T ss_pred             HhhhHHHHHHHhcc--CCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhH--HHHHHHHHHhccC
Confidence            45555555555443  222  2344455566777788888877777        55555554443  3455666666666


Q ss_pred             HHHHHHHHHHHHh--CCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcch-hhHHHHHHHHhCCCCcccc
Q 042756          275 LSRMVLWLQKMKD--SGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNE-EEVSVVKELEDSSVLDEAM  351 (425)
Q Consensus       275 ~~~A~~l~~~M~~--~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  351 (425)
                      .+.|..++++.+.  ..-.+......+++.-.+.   |+               .+.|.. ++...++++++. ..+|..
T Consensus       433 ~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~---f~---------------lr~G~~~ea~s~leel~k~-n~~d~~  493 (652)
T KOG2376|consen  433 NDSASAVLDSAIKWWRKQQTGSIALLSLMREAAE---FK---------------LRHGNEEEASSLLEELVKF-NPNDTD  493 (652)
T ss_pred             CccHHHHHHHHHHHHHHhcccchHHHhHHHHHhH---HH---------------HhcCchHHHHHHHHHHHHh-CCchHH
Confidence            6667777766542  1112333333333332221   11               112333 333445555542 235666


Q ss_pred             eeeccccchhcccCcchh
Q 042756          352 KWDSGETKLDLHGMHLGS  369 (425)
Q Consensus       352 ~~~~li~~~~~~~~~~~a  369 (425)
                      +.-.++.+|++.. +++|
T Consensus       494 ~l~~lV~a~~~~d-~eka  510 (652)
T KOG2376|consen  494 LLVQLVTAYARLD-PEKA  510 (652)
T ss_pred             HHHHHHHHHHhcC-HHHH
Confidence            6777777777543 4555

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.04  E-value=2.4  Score=33.48  Aligned_cols=138  Identities=12%  Similarity=0.133  Sum_probs=72.2

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc
Q 042756          123 KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM  202 (425)
Q Consensus       123 ~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~  202 (425)
                      -.|.+++..++..+......      ..-||=+|.-....-+   .+..++.+.....-.. +.| ..-.-.++++|++.
T Consensus        14 ldG~V~qGveii~k~v~Ssn------i~E~NWvICNiiDaa~---C~yvv~~LdsIGkiFD-is~-C~NlKrVi~C~~~~   82 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNSSN------IKEYNWVICNIIDAAD---CDYVVETLDSIGKIFD-ISK-CGNLKRVIECYAKR   82 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHHS-------HHHHTHHHHHHHHH-----HHHHHHHHHHHGGGS--GGG--S-THHHHHHHHHT
T ss_pred             HhchHHHHHHHHHHHcCcCC------ccccceeeeecchhhc---hhHHHHHHHHHhhhcC-chh-hcchHHHHHHHHHh
Confidence            34788888888888775421      1123445555544444   5566666666543321 111 01223445555544


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWL  282 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~  282 (425)
                      |-.                  ..-+...++...++|+-+.-.++..++.+.+ .+++...-.+-.+|.+.|+..++-+++
T Consensus        83 n~~------------------se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell  143 (161)
T PF09205_consen   83 NKL------------------SEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELL  143 (161)
T ss_dssp             T---------------------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             cch------------------HHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHH
Confidence            422                  2334455666777777777777777766422 456666666777777777777777777


Q ss_pred             HHHHhCCC
Q 042756          283 QKMKDSGI  290 (425)
Q Consensus       283 ~~M~~~g~  290 (425)
                      ++.-+.|+
T Consensus       144 ~~ACekG~  151 (161)
T PF09205_consen  144 KEACEKGL  151 (161)
T ss_dssp             HHHHHTT-
T ss_pred             HHHHHhch
Confidence            77777665

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=93.89  E-value=4.5  Score=38.78  Aligned_cols=144  Identities=10%  Similarity=0.050  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH-HH
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEY-KC  229 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty-~~  229 (425)
                      +|...|++.-+..-   +..+-.+|.+....+ .+.+++..++++|..++ .|+..-|.++|+.-...  -||...| +.
T Consensus       399 v~C~~~N~v~r~~G---l~aaR~~F~k~rk~~-~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~k  471 (660)
T COG5107         399 VFCVHLNYVLRKRG---LEAARKLFIKLRKEG-IVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEK  471 (660)
T ss_pred             HHHHHHHHHHHHhh---HHHHHHHHHHHhccC-CCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHH
Confidence            34445555444333   333333333332222 34455566666666555 34555666666554332  3343333 33


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCcC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESDGTRVD--TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~g~~~~--~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~  304 (425)
                      .+.-+.+.++-+.|..+|+.-..+ +..+  ...|..+|+-=..-|+...|..+=++|.+.  .|-..+.....+.|
T Consensus       472 yl~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry  545 (660)
T COG5107         472 YLLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRY  545 (660)
T ss_pred             HHHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHH
Confidence            445555566666666666632221 0011  345666666666666666666665555542  45555555544444

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=93.71  E-value=7.5  Score=39.42  Aligned_cols=41  Identities=10%  Similarity=-0.027  Sum_probs=26.5

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhh
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHL   80 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~   80 (425)
                      -+++|.++.+.     .|-...|..+.......-..+.|...|.+.
T Consensus       678 gledA~qfiEd-----nPHprLWrllAe~Al~Kl~l~tAE~AFVrc  718 (1189)
T KOG2041|consen  678 GLEDAIQFIED-----NPHPRLWRLLAEYALFKLALDTAEHAFVRC  718 (1189)
T ss_pred             chHHHHHHHhc-----CCchHHHHHHHHHHHHHHhhhhHhhhhhhh
Confidence            34455555444     588888888877777666666666666554

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=93.66  E-value=4.3  Score=35.09  Aligned_cols=157  Identities=13%  Similarity=0.083  Sum_probs=71.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      .-..+.+.|++++|.+.|+.+.......+.. ....-.+..++.+.|+++.+...++.+.+.-+.+...     .+-..+
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a-~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~-----~~A~Y~   84 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYA-PQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKA-----DYALYM   84 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTH-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTH-----HHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHH-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcch-----hhHHHH
Confidence            3444556677888888888877653332222 2233456777777777666666666666654444221     222222


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCC---CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLE---PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~---p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g  273 (425)
                      .+.+.-.......     .......   --...|..++.-|-...-..+|.+.+..+.+.    =...--.+..-|.+.|
T Consensus        85 ~g~~~~~~~~~~~-----~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~----la~~e~~ia~~Y~~~~  155 (203)
T PF13525_consen   85 LGLSYYKQIPGIL-----RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR----LAEHELYIARFYYKRG  155 (203)
T ss_dssp             HHHHHHHHHHHHH------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH----HHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHhCccch-----hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHcc
Confidence            2222111111110     0000000   00124444555555555555665555555432    1111122445566677


Q ss_pred             CHHHHHHHHHHHHhC
Q 042756          274 ELSRMVLWLQKMKDS  288 (425)
Q Consensus       274 ~~~~A~~l~~~M~~~  288 (425)
                      .+..|..-|+.+++.
T Consensus       156 ~y~aA~~r~~~v~~~  170 (203)
T PF13525_consen  156 KYKAAIIRFQYVIEN  170 (203)
T ss_dssp             -HHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHH
Confidence            776676666666654

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

Probab=93.66  E-value=1  Score=40.62  Aligned_cols=101  Identities=18%  Similarity=0.121  Sum_probs=82.2

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-CHHhHHHHHHHHHhcCCHH
Q 042756          199 LCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-DTVCSNMVLSSYGDHNELS  276 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~yn~li~~~~~~g~~~  276 (425)
                      +.+.+++++|+..|.+...  +.| |.+-|..=--+|.+.|.++.|.+=.+.-.+-  .| -..+|..|-.+|...|+++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHH
Confidence            5678999999999999987  455 5677778888999999999998877766653  23 3678999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          277 RMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       277 ~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      +|++.|++..+  +.|+-.+|-.=+..-.
T Consensus       167 ~A~~aykKaLe--ldP~Ne~~K~nL~~Ae  193 (304)
T KOG0553|consen  167 EAIEAYKKALE--LDPDNESYKSNLKIAE  193 (304)
T ss_pred             HHHHHHHhhhc--cCCCcHHHHHHHHHHH
Confidence            99999999775  5898888877766543

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=93.52  E-value=5  Score=36.38  Aligned_cols=128  Identities=8%  Similarity=-0.005  Sum_probs=91.3

Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHH---cCCCHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK-GLEPSGFEYKCIIYGYG---RLGLLEDM  243 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~ll~~~~---~~g~~~~a  243 (425)
                      +++....++......+   -|...|-.|-..|.+.|+++.|..-|..-.+. |-.  ...+..+-.++.   ...+-.++
T Consensus       138 ~~~l~a~Le~~L~~nP---~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n--~~~~~g~aeaL~~~a~~~~ta~a  212 (287)
T COG4235         138 MEALIARLETHLQQNP---GDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDN--PEILLGLAEALYYQAGQQMTAKA  212 (287)
T ss_pred             HHHHHHHHHHHHHhCC---CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCC--HHHHHHHHHHHHHhcCCcccHHH
Confidence            4444555555444432   25569999999999999999999999998874 333  344444444433   33346779


Q ss_pred             HHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 042756          244 ERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS  303 (425)
Q Consensus       244 ~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~  303 (425)
                      ..+|++...... -|+.+-.-|-..+...|++.+|...++.|.+.  -|.......+|+.
T Consensus       213 ~~ll~~al~~D~-~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~--lp~~~~rr~~ie~  269 (287)
T COG4235         213 RALLRQALALDP-ANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL--LPADDPRRSLIER  269 (287)
T ss_pred             HHHHHHHHhcCC-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--CCCCCchHHHHHH
Confidence            999999987642 36677777778899999999999999999976  4555566666654

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.19  E-value=5.7  Score=35.16  Aligned_cols=30  Identities=17%  Similarity=0.181  Sum_probs=14.8

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      |...|.-+-..|...|++++|.-.++++.-
T Consensus       153 D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  153 DQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             cHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            333555555555555555555555555444

>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=93.08  E-value=4.2  Score=39.83  Aligned_cols=156  Identities=12%  Similarity=0.052  Sum_probs=94.6

Q ss_pred             HHHHHHhhHHHHHHHHH--HhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHH--HHHhhh
Q 042756           28 VQCLTARLTKQGQRFLS--SLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPL--YMRITE  103 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~--~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~l--f~~m~~  103 (425)
                      -.++++++.+++.++.+  .+...+  +..-.+.+++-+-+.|-.+.|+.+...--       .+++.|+++  ++.-.+
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~~i--~~~~~~~i~~fL~~~G~~e~AL~~~~D~~-------~rFeLAl~lg~L~~A~~  339 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLPNI--PKDQGQSIARFLEKKGYPELALQFVTDPD-------HRFELALQLGNLDIALE  339 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-HH-------HHHHHHHHCT-HHHHHH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcccC--ChhHHHHHHHHHHHCCCHHHHHhhcCChH-------HHhHHHHhcCCHHHHHH
Confidence            44577888888766664  222112  25557889999999999999988765531       134444433  111111


Q ss_pred             cCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCC
Q 042756          104 ESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSS  183 (425)
Q Consensus       104 ~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~  183 (425)
                      --.-..+...|..|-....+.|+++-|++.|.+..            -|..|+-.|.-.|+.+++.+..+....   .+ 
T Consensus       340 ~a~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~------------d~~~L~lLy~~~g~~~~L~kl~~~a~~---~~-  403 (443)
T PF04053_consen  340 IAKELDDPEKWKQLGDEALRQGNIELAEECYQKAK------------DFSGLLLLYSSTGDREKLSKLAKIAEE---RG-  403 (443)
T ss_dssp             HCCCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT-------------HHHHHHHHHHCT-HHHHHHHHHHHHH---TT-
T ss_pred             HHHhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhc------------CccccHHHHHHhCCHHHHHHHHHHHHH---cc-
Confidence            11122477789999999999999999999998853            156788888888985444444333222   22 


Q ss_pred             CCccChhHHHHHHHHHHhcCChhHHHHHHHHH
Q 042756          184 SVYVKRQALKSMISGLCEMGQPHEAENLIEEM  215 (425)
Q Consensus       184 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  215 (425)
                             -+|....++.-.|+.++..+++.+-
T Consensus       404 -------~~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  404 -------DINIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             --------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             -------CHHHHHHHHHHcCCHHHHHHHHHHc
Confidence                   6788888888899999988887653

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.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=92.92  E-value=8.2  Score=38.22  Aligned_cols=166  Identities=12%  Similarity=0.065  Sum_probs=100.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhH---HHHHHHHHHHHHhc--CCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSREREL---VLFYCNLIDSFCKH--DSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~---~~~y~~li~~~~~~--g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ..+++..+=.||-+.+++++.+-.+..+...+-.   ..+|...+..++..  +.. ....+-+.+..+..    .+|+.
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~-~~~~a~~lL~~~~~----~yP~s  266 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDV-PLEEAEELLEEMLK----RYPNS  266 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCC-CHHHHHHHHHHHHH----hCCCc
Confidence            3356666666888999998888655333222211   12455555555544  221 14555555555543    34665


Q ss_pred             hHHHHHH-HHHHhcCChhHHHHHHHHHHHcCC-C--CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          190 QALKSMI-SGLCEMGQPHEAENLIEEMRVKGL-E--PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       190 ~~~~~li-~~~~~~g~~~~a~~~~~~m~~~g~-~--p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      ..|...- +.+...|++++|++.|++...... .  .....+=-+.-.+.-.++|++|.+.|..+.+.. ..+...|.-+
T Consensus       267 ~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~  345 (468)
T PF10300_consen  267 ALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYL  345 (468)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHH
Confidence            5555444 334457999999999997654211 1  122233334455788899999999999998743 2356666666


Q ss_pred             HHHH-HhcCCH-------HHHHHHHHHHH
Q 042756          266 LSSY-GDHNEL-------SRMVLWLQKMK  286 (425)
Q Consensus       266 i~~~-~~~g~~-------~~A~~l~~~M~  286 (425)
                      ..+| ...|+.       ++|.++|.+..
T Consensus       346 ~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  346 AAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            6555 367777       88888888864

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.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=92.70  E-value=0.99  Score=43.43  Aligned_cols=65  Identities=6%  Similarity=-0.125  Sum_probs=57.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCH----HhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          222 PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDT----VCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       222 p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~----~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      .+...++.+-.+|.+.|++++|...|+...+.  .|+.    .+|..+--+|...|+.++|+..|++..+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            35779999999999999999999999997775  4553    46999999999999999999999998875

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.64  E-value=8.3  Score=35.56  Aligned_cols=134  Identities=7%  Similarity=0.028  Sum_probs=82.3

Q ss_pred             hhHHHHHHHHHHHhcCCCchhHHHHHHH--HHHHHHhcCCc-ccHHHHHHHHHHHhhcCCCCc-cChhHHHHHHHHHHhc
Q 042756          127 REEAETLILETLSKLGSRERELVLFYCN--LIDSFCKHDSK-RGFDDTYARLNQLVNSSSSVY-VKRQALKSMISGLCEM  202 (425)
Q Consensus       127 ~~~A~~l~~~m~~~~~~~~~~~~~~y~~--li~~~~~~g~~-~~~~~~~~~~~~~~~~~~~~~-p~~~~~~~li~~~~~~  202 (425)
                      +++...+++.|.+.+.....-   +|-+  +|.......++ +.+..+..++..|....+.++ ++-.++.+|+..  ..
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y---~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~  152 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEY---LYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TS  152 (297)
T ss_pred             HHHHHHHHHHHHHhccCccCh---HHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--cc
Confidence            556777888888876654421   2212  22222222222 225566777777766654443 566788888776  33


Q ss_pred             C----ChhHHHHHHHHHHHcCCCCC-H-HHHHHHHHHHHcCCC--HHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          203 G----QPHEAENLIEEMRVKGLEPS-G-FEYKCIIYGYGRLGL--LEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       203 g----~~~~a~~~~~~m~~~g~~p~-~-~ty~~ll~~~~~~g~--~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      +    -.+.+..+|+.+...|...+ . ...+.++..+-....  +..+.++++.+.+.|+++....|..+
T Consensus       153 ~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  153 EDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             ccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence            3    33677888999999887764 3 344444433333222  45789999999999999888887655

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=92.62  E-value=13  Score=37.58  Aligned_cols=88  Identities=10%  Similarity=0.052  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCH-----------
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDT-----------  259 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~-----------  259 (425)
                      +.-.+-.-+.+...+.-|-++|..|-.         ..+++......++|.+|+.+-+...+.  .||+           
T Consensus       749 ~l~~~a~ylk~l~~~gLAaeIF~k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLAE~  817 (1081)
T KOG1538|consen  749 PLLLCATYLKKLDSPGLAAEIFLKMGD---------LKSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLAEN  817 (1081)
T ss_pred             HHHHHHHHHhhccccchHHHHHHHhcc---------HHHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhhhh
Confidence            555555666667788889999988743         356788899999999999988876553  3332           


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      .-|.--=.+|.+.|+-.||..+++.+....
T Consensus       818 DrFeEAqkAfhkAGr~~EA~~vLeQLtnna  847 (1081)
T KOG1538|consen  818 DRFEEAQKAFHKAGRQREAVQVLEQLTNNA  847 (1081)
T ss_pred             hhHHHHHHHHHHhcchHHHHHHHHHhhhhh
Confidence            223344568889999999999998876443

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=92.62  E-value=3.3  Score=39.72  Aligned_cols=140  Identities=13%  Similarity=0.109  Sum_probs=70.8

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCch--hHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHH
Q 042756          123 KQGQREEAETLILETLSKLGSRER--ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLC  200 (425)
Q Consensus       123 ~~g~~~~A~~l~~~m~~~~~~~~~--~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~  200 (425)
                      +.+++.+|+++|.++-+.....+.  .-...-+.+|+||.... .+.++.....+++..++.        .|-.+..+..
T Consensus        18 kq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~n-ld~Me~~l~~l~~~~~~s--------~~l~LF~~L~   88 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNN-LDLMEKQLMELRQQFGKS--------AYLPLFKALV   88 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhh-HHHHHHHHHHHHHhcCCc--------hHHHHHHHHH
Confidence            456677777777666543221110  00112345666666443 222333333343332211        4444444432


Q ss_pred             --hcCChhHHHHHHHHHHHc--CCCC------------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcCHH
Q 042756          201 --EMGQPHEAENLIEEMRVK--GLEP------------SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRVDTV  260 (425)
Q Consensus       201 --~~g~~~~a~~~~~~m~~~--g~~p------------~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~~~~  260 (425)
                        +.+.+++|.+.+..-.++  +-.|            |..-=++.+..+...|++.+++.+++.|..+    ....+..
T Consensus        89 ~Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d  168 (549)
T PF07079_consen   89 AYKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSD  168 (549)
T ss_pred             HHHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHH
Confidence              356666776666665544  2221            2222244556667777777777777766654    3336677


Q ss_pred             hHHHHHHHHHh
Q 042756          261 CSNMVLSSYGD  271 (425)
Q Consensus       261 ~yn~li~~~~~  271 (425)
                      +||-++-.+.+
T Consensus       169 ~yd~~vlmlsr  179 (549)
T PF07079_consen  169 MYDRAVLMLSR  179 (549)
T ss_pred             HHHHHHHHHhH
Confidence            77775555544

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=92.48  E-value=1.7  Score=39.32  Aligned_cols=78  Identities=9%  Similarity=-0.027  Sum_probs=59.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHHHHH
Q 042756          225 FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD-----SGIPFSVRTYNS  299 (425)
Q Consensus       225 ~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~-----~g~~pd~~t~~~  299 (425)
                      .++..++..+...|+.+.+...++++.... +.+...|..+|.+|.+.|+...|+..|+.+.+     .|+.|-..+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            466777777888888888888888887654 34778888888888888888888888887753     678887777666


Q ss_pred             HHHH
Q 042756          300 VLNS  303 (425)
Q Consensus       300 ll~~  303 (425)
                      ....
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            6555

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.46  E-value=4.1  Score=36.85  Aligned_cols=100  Identities=9%  Similarity=-0.062  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCC-CHHHHH
Q 042756          151 FYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKG-LEP-SGFEYK  228 (425)
Q Consensus       151 ~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p-~~~ty~  228 (425)
                      .|..-+..+.+.|+++++..+++.+.+..+... ..|+  .+--+-.+|...|++++|...|+.+...- -.| ....+-
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~-~a~~--A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~  221 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDST-YQPN--ANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCc-chHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHH
Confidence            344444444444554433334443333333221 1122  44445555555666666666666655421 000 122333


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          229 CIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       229 ~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      .+...+...|+.+.|.++|+...+.
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3344455566666666666665554

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.32  E-value=1.1  Score=31.16  Aligned_cols=57  Identities=11%  Similarity=-0.095  Sum_probs=44.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      ..|.+.+++++|.++++++...+ +.+...+...-.++.+.|++++|.+.|+...+.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            46788889999999999988852 2245677777788889999999999999888653

>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=92.09  E-value=2.4  Score=35.79  Aligned_cols=97  Identities=15%  Similarity=0.104  Sum_probs=69.7

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHcCCCHHHHHHHHHHHHHC---CCCcCHHhHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG--FEYKCIIYGYGRLGLLEDMERIVNQMESD---GTRVDTVCSNM  264 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~ty~~ll~~~~~~g~~~~a~~~~~~m~~~---g~~~~~~~yn~  264 (425)
                      ..+..+...|++.|+.++|++.|.++.+....|..  ..+-.+|....-.+++..+..........   |-.++...--.
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            37888999999999999999999999987655543  36778888899999999988888766543   22222221112


Q ss_pred             HHHHH--HhcCCHHHHHHHHHHHH
Q 042756          265 VLSSY--GDHNELSRMVLWLQKMK  286 (425)
Q Consensus       265 li~~~--~~~g~~~~A~~l~~~M~  286 (425)
                      ...|+  ...|++.+|-++|-+..
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccC
Confidence            22222  35788999999888765

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.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=91.84  E-value=1.9  Score=34.60  Aligned_cols=86  Identities=19%  Similarity=0.125  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..|+.- ....+.|++++|.+.|+.+..+....+.. ...--.|+.+|.+.++++.+..+++.|.++-+.+..+     .
T Consensus        12 ~ly~~a-~~~l~~~~Y~~A~~~le~L~~ryP~g~ya-~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~v-----d   84 (142)
T PF13512_consen   12 ELYQEA-QEALQKGNYEEAIKQLEALDTRYPFGEYA-EQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNV-----D   84 (142)
T ss_pred             HHHHHH-HHHHHhCCHHHHHHHHHHHHhcCCCCccc-HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCc-----c
Confidence            344433 33445689999999999998865544433 2345678899999999888888888888887776554     6


Q ss_pred             HHHHHHHHHhcCC
Q 042756          192 LKSMISGLCEMGQ  204 (425)
Q Consensus       192 ~~~li~~~~~~g~  204 (425)
                      |--.+.+++.-..
T Consensus        85 Ya~Y~~gL~~~~~   97 (142)
T PF13512_consen   85 YAYYMRGLSYYEQ   97 (142)
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777665443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=91.80  E-value=5.1  Score=31.30  Aligned_cols=111  Identities=19%  Similarity=0.156  Sum_probs=58.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      +-.++-..|+.++|+.+|++-...+.. .......+-.+-..+...|+   .+++...+.+.....+.-.-+....-.+-
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~-~~~~~~a~i~lastlr~LG~---~deA~~~L~~~~~~~p~~~~~~~l~~f~A   82 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLS-GADRRRALIQLASTLRNLGR---YDEALALLEEALEEFPDDELNAALRVFLA   82 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCC-chHHHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHHCCCccccHHHHHHHH
Confidence            345566778888888888887765433 22222234445556667777   45555555555433211000111122222


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYG  235 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~  235 (425)
                      -++...|+.++|++.+-....    ++...|.--|..|+
T Consensus        83 l~L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   83 LALYNLGRPKEALEWLLEALA----ETLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence            355667777777777765543    23335555555544

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=91.70  E-value=1.9  Score=41.20  Aligned_cols=117  Identities=14%  Similarity=0.069  Sum_probs=88.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhH-HHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKG-LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCS-NMVLS  267 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~y-n~li~  267 (425)
                      .+|.+.|++-.+..-++.|..+|-+....| +.++++.++++|.-++ .||...|.++|+.=...  .||...| +-.+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl~  474 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYLL  474 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHHH
Confidence            389999999999999999999999999999 6789999999998776 57788899999854332  2454444 55667


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFS--VRTYNSVLNSCSTIMSM  310 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd--~~t~~~ll~~~~~~~~~  310 (425)
                      -+.+-++-+.|..+|+.-++. +.-+  ...|..+|+-=+..|++
T Consensus       475 fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~l  518 (660)
T COG5107         475 FLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSL  518 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcch
Confidence            778889989999999965432 2222  45777777765665554

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.46  E-value=7.6  Score=39.66  Aligned_cols=52  Identities=15%  Similarity=0.132  Sum_probs=35.0

Q ss_pred             HHHhhHHHHHHHHHHhHHh-----cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhC
Q 042756           31 LTARLTKQGQRFLSSLALA-----VTRDSKAASRLISKFVASSPQFIALNALSHLLS   82 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~-----~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~   82 (425)
                      ...|+.+-|..+++.=...     .-.+...+...+.....+|+++....++.++..
T Consensus       518 y~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~  574 (829)
T KOG2280|consen  518 YQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKN  574 (829)
T ss_pred             HhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHH
Confidence            4456677777666543222     112456677888888889999999988888744

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.40  E-value=7.2  Score=34.79  Aligned_cols=235  Identities=11%  Similarity=0.021  Sum_probs=141.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC----------CC----chhhhHHHHHHH-hhhcCCCccCHHHHHHHH
Q 042756           54 SKAASRLISKFVASSPQFIALNALSHLLSPDTT----------HP----RLSSLAFPLYMR-ITEESWFQWNPKLVAEII  118 (425)
Q Consensus        54 ~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~----------~~----~~~~~a~~lf~~-m~~~~~~~~~~~~~~~ll  118 (425)
                      ...|+.-+..+.+-...+.+..-+...-.-++.          .|    ..+.-+++++.- +...-+.+|+.-.--..+
T Consensus        69 lq~wT~r~~~l~kLR~~~~a~~EL~~f~~lD~pdl~Yey~p~iyp~rrGSmVPFsmR~lhAe~~~~lgnpqesLdRl~~L  148 (366)
T KOG2796|consen   69 LQLWTVRLALLVKLRLFQNAEMELEPFGNLDQPDLYYEYYPHVYPGRRGSMVPFSMRILHAELQQYLGNPQESLDRLHKL  148 (366)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHhhhhhhccCCCcceeeeeccccCCCCcCccccHHHHHHHHHHHHhcCCcHHHHHHHHHH
Confidence            455666677777776666666665554222221          11    134555555443 444333445543221222


Q ss_pred             HHHH-------hcCCh-hHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          119 AFLD-------KQGQR-EEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       119 ~~~~-------~~g~~-~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ..+.       +.|.. +...+++++-..          .+-+.++..+.-.+.+.   -....+.+.....  ..-+..
T Consensus       149 ~~~V~~ii~~~e~~~~~ESsv~lW~KRl~----------~Vmy~~~~~llG~kEy~---iS~d~~~~vi~~~--~e~~p~  213 (366)
T KOG2796|consen  149 KTVVSKILANLEQGLAEESSIRLWRKRLG----------RVMYSMANCLLGMKEYV---LSVDAYHSVIKYY--PEQEPQ  213 (366)
T ss_pred             HHHHHHHHHHHHhccchhhHHHHHHHHHH----------HHHHHHHHHHhcchhhh---hhHHHHHHHHHhC--CcccHH
Confidence            2222       22333 555566655322          12345666655555532   2333333433333  334445


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH-----HHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII-----YGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll-----~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      .-..+.+.-.+.|+.+.|...|++..+..-+.|..+++.++     ..|.-.+++.+|...|.+.....- .|...-|.-
T Consensus       214 L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~-~~~~a~NnK  292 (366)
T KOG2796|consen  214 LLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDP-RNAVANNNK  292 (366)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCC-CchhhhchH
Confidence            88999999999999999999999888775556666666554     346667789999999988876532 255666665


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      .-+..-.|+...|++....|...  .|...+-++++--++.
T Consensus       293 ALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~~~nL~t  331 (366)
T KOG2796|consen  293 ALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESVLFNLTT  331 (366)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhHHHHHHH
Confidence            55566679999999999999875  6777777766655554

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=91.19  E-value=9.2  Score=33.01  Aligned_cols=166  Identities=12%  Similarity=0.030  Sum_probs=98.9

Q ss_pred             hhhhHHHHHHHhhhcCC-CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCC----
Q 042756           90 LSSLAFPLYMRITEESW-FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDS----  164 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~-~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~----  164 (425)
                      .+++|.+.|+.+...-. ........-.+..++-+.|+++.|...|++..+.....+ ..  -+...+.+.+....    
T Consensus        20 ~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~-~~--~~A~Y~~g~~~~~~~~~~   96 (203)
T PF13525_consen   20 DYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSP-KA--DYALYMLGLSYYKQIPGI   96 (203)
T ss_dssp             -HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-T-TH--HHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc-ch--hhHHHHHHHHHHHhCccc
Confidence            67777777777765421 122334455688899999999999999999887533322 11  23334444332111    


Q ss_pred             ------cccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC
Q 042756          165 ------KRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG  238 (425)
Q Consensus       165 ------~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g  238 (425)
                            .....+++                 ..+..+|.-|-.....++|......+.+.-    ..---.+.+-|.+.|
T Consensus        97 ~~~~~D~~~~~~A~-----------------~~~~~li~~yP~S~y~~~A~~~l~~l~~~l----a~~e~~ia~~Y~~~~  155 (203)
T PF13525_consen   97 LRSDRDQTSTRKAI-----------------EEFEELIKRYPNSEYAEEAKKRLAELRNRL----AEHELYIARFYYKRG  155 (203)
T ss_dssp             H-TT---HHHHHHH-----------------HHHHHHHHH-TTSTTHHHHHHHHHHHHHHH----HHHHHHHHHHHHCTT
T ss_pred             hhcccChHHHHHHH-----------------HHHHHHHHHCcCchHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHcc
Confidence                  11112222                 266777777777777788877776665430    111123567799999


Q ss_pred             CHHHHHHHHHHHHHC--CCCcCHHhHHHHHHHHHhcCCHHHHH
Q 042756          239 LLEDMERIVNQMESD--GTRVDTVCSNMVLSSYGDHNELSRMV  279 (425)
Q Consensus       239 ~~~~a~~~~~~m~~~--g~~~~~~~yn~li~~~~~~g~~~~A~  279 (425)
                      .+..|..-++.+.+.  +........-.|+.+|-+.|..+.|.
T Consensus       156 ~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  156 KYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             -HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             cHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            999999999999876  22222355678888999999877543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=91.17  E-value=6.7  Score=31.39  Aligned_cols=125  Identities=10%  Similarity=0.169  Sum_probs=84.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 042756          153 CNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIY  232 (425)
Q Consensus       153 ~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~  232 (425)
                      ..+|..+.+.+.   ...++..+......+.   .+....|.+|..|++.+ .++.++.+..      .++.+....++.
T Consensus        11 ~~vv~~~~~~~~---~~~l~~yLe~~~~~~~---~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~   77 (140)
T smart00299       11 SEVVELFEKRNL---LEELIPYLESALKLNS---ENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGK   77 (140)
T ss_pred             HHHHHHHHhCCc---HHHHHHHHHHHHccCc---cchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHH
Confidence            457777776666   5677777777766542   34459999999999874 3455555553      234566777888


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc-CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          233 GYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH-NELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       233 ~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~-g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      .|-+.+.++++.-++..+..         |.-.+..+... ++++.|.+++.+-      -+...|..+++.+.
T Consensus        78 ~c~~~~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~l  136 (140)
T smart00299       78 LCEKAKLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKALL  136 (140)
T ss_pred             HHHHcCcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHHH
Confidence            99999999988888877644         33344444444 7888888887761      25567777776553

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=91.01  E-value=6.9  Score=41.38  Aligned_cols=180  Identities=8%  Similarity=-0.038  Sum_probs=106.9

Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDT  171 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~  171 (425)
                      ..++..|-+..+.+ .. -...|..|-..|...-+...|.+.|+..-+-    ++.....+....+.|++..+++.+.  
T Consensus       475 ~~al~ali~alrld-~~-~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeL----Datdaeaaaa~adtyae~~~we~a~--  546 (1238)
T KOG1127|consen  475 ALALHALIRALRLD-VS-LAPAFAFLGQIYRDSDDMKRAKKCFDKAFEL----DATDAEAAAASADTYAEESTWEEAF--  546 (1238)
T ss_pred             HHHHHHHHHHHhcc-cc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CchhhhhHHHHHHHhhccccHHHHH--
Confidence            34444444444433 21 2336777777777777777788888776542    3333445677888888888854433  


Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                       ........... ...-...|--.--.|.+.++.-+|..-|..-.+.  -| |...|..+..+|...|++..|.++|...
T Consensus       547 -~I~l~~~qka~-a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~--dPkD~n~W~gLGeAY~~sGry~~AlKvF~kA  622 (1238)
T KOG1127|consen  547 -EICLRAAQKAP-AFACKENWVQRGPYYLEAHNLHGAVCEFQSALRT--DPKDYNLWLGLGEAYPESGRYSHALKVFTKA  622 (1238)
T ss_pred             -HHHHHHhhhch-HHHHHhhhhhccccccCccchhhHHHHHHHHhcC--CchhHHHHHHHHHHHHhcCceehHHHhhhhh
Confidence             33222221110 0011112223333456677888888888776653  34 5568888899999999999999999877


Q ss_pred             HHCCCCcCHHhHHHHHH--HHHhcCCHHHHHHHHHHHH
Q 042756          251 ESDGTRVDTVCSNMVLS--SYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       251 ~~~g~~~~~~~yn~li~--~~~~~g~~~~A~~l~~~M~  286 (425)
                      ...  .|+ .+|...-.  .-|..|++.+|+..+....
T Consensus       623 s~L--rP~-s~y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  623 SLL--RPL-SKYGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             Hhc--CcH-hHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            654  233 33333322  2356777888877777654

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=91.00  E-value=15  Score=34.99  Aligned_cols=180  Identities=9%  Similarity=-0.034  Sum_probs=108.5

Q ss_pred             HhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh---cCCcccHHHHHHHHH
Q 042756          100 RITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK---HDSKRGFDDTYARLN  176 (425)
Q Consensus       100 ~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~---~g~~~~~~~~~~~~~  176 (425)
                      ++......+++.  .-.++-+|-...+++...++++.+..-..........+--...-|+.+   .|+   -++|.+.+.
T Consensus       132 rLd~~~~ls~di--v~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gd---re~Al~il~  206 (374)
T PF13281_consen  132 RLDDPELLSPDI--VINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGD---REKALQILL  206 (374)
T ss_pred             hhCCHhhcChhH--HHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCC---HHHHHHHHH
Confidence            343334444443  334666788999999999999999864221111111122234455666   666   677888877


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHh---------cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC----HHHH
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCE---------MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL----LEDM  243 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~---------~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~----~~~a  243 (425)
                      ..........||  +|..+-..|-.         ...+++|.+.|.+--+.  .||.++=-.+...+...|.    -.+.
T Consensus       207 ~~l~~~~~~~~d--~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el  282 (374)
T PF13281_consen  207 PVLESDENPDPD--TLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEEL  282 (374)
T ss_pred             HHHhccCCCChH--HHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHH
Confidence            755555444444  77777766643         23577888888876553  4665543333333333332    2233


Q ss_pred             HHHH----HHHHHCCC---CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          244 ERIV----NQMESDGT---RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       244 ~~~~----~~m~~~g~---~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      .++-    ...-+.|.   ..|=.-+.++..++.-.|+.++|.+.+++|.+.
T Consensus       283 ~~i~~~l~~llg~kg~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  283 RKIGVKLSSLLGRKGSLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             HHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            3433    22223343   235566778899999999999999999999976

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=89.91  E-value=5.7  Score=32.06  Aligned_cols=50  Identities=14%  Similarity=0.214  Sum_probs=37.0

Q ss_pred             hHHHHHHHHHHhcCC-hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Q 042756          190 QALKSMISGLCEMGQ-PHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL  239 (425)
Q Consensus       190 ~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~  239 (425)
                      .+|++++++.++... ---+..+|+-|++.+.+++..-|..+|+++.+-..
T Consensus        80 ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~~  130 (145)
T PF13762_consen   80 SSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCLIKAALRGYF  130 (145)
T ss_pred             chHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Confidence            378888888876665 45667788888887778888888888887766543

>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=89.88  E-value=4.9  Score=33.88  Aligned_cols=102  Identities=12%  Similarity=0.044  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc--cCh
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY--VKR  189 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~--p~~  189 (425)
                      ..+..+...|++.|+.+.|.+.|.++.+....+... ...+-.+|....-.+++..+.............+....  .-.
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~-id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrl  115 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHK-IDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRL  115 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHH-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence            457778999999999999999999988754443332 34566788888888998888888888887776643210  001


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~  216 (425)
                      .+|..+-  +...|++.+|-+.|-+..
T Consensus       116 k~~~gL~--~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  116 KVYEGLA--NLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHH--HHHhchHHHHHHHHHccC
Confidence            1222221  122466777777666553

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

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

Probab=89.66  E-value=4.3  Score=36.81  Aligned_cols=78  Identities=14%  Similarity=0.085  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCcCHHhHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES-----DGTRVDTVCSNMV  265 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~~yn~l  265 (425)
                      ++..++..+...|+++.+.+.++++...- +-|...|..+|.+|.+.|+...|...++.+.+     .|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            88888999999999999999999998752 33778999999999999999999999887765     5999998888887


Q ss_pred             HHHH
Q 042756          266 LSSY  269 (425)
Q Consensus       266 i~~~  269 (425)
                      ....
T Consensus       234 ~~~~  237 (280)
T COG3629         234 EEIL  237 (280)
T ss_pred             HHHh
Confidence            7773

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=89.55  E-value=4.8  Score=36.01  Aligned_cols=98  Identities=14%  Similarity=0.141  Sum_probs=50.9

Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCC-HHHHHH
Q 042756          152 YCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK-GLEPS-GFEYKC  229 (425)
Q Consensus       152 y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~-~~ty~~  229 (425)
                      |+.-+..| +.|++..+.++|..+.+..+.+. ..|+  .+-=|-.++...|++++|..+|..+.+. +-.|- ..++-.
T Consensus       145 Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~-~~~n--A~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         145 YNAALDLY-KSGDYAEAEQAFQAFIKKYPNST-YTPN--AYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             HHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCc-ccch--hHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            44444433 34445555555555555544432 3344  4444566666666666666666666543 11221 134444


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +-....+.|+.++|..+|+++.+.
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHH
Confidence            445555666666666666666554

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=89.42  E-value=5.2  Score=32.18  Aligned_cols=76  Identities=13%  Similarity=0.045  Sum_probs=51.6

Q ss_pred             HHhcCChhHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          199 LCEMGQPHEAENLIEEMRVKG--LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~~g--~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      ..+.|++++|.+.|+.+..+=  -+-....--.++.+|.+.|++++|...+++.++..-.-.-+-|-..+.|++.-..
T Consensus        20 ~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~~   97 (142)
T PF13512_consen   20 ALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYEQ   97 (142)
T ss_pred             HHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHH
Confidence            345788888888888887751  1113345666788888888888888888888876433334567777777664443

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.29  E-value=16  Score=32.74  Aligned_cols=98  Identities=10%  Similarity=0.027  Sum_probs=80.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH---
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS---  267 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~---  267 (425)
                      +.++++.++.-.|++.-.+.++++..+..-+-+..-...+...-...||++.|..+|++.++..-+.|..+++.++.   
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            78899999999999999999999999977666788888899999999999999999998887554566666776664   


Q ss_pred             --HHHhcCCHHHHHHHHHHHHhC
Q 042756          268 --SYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       268 --~~~~~g~~~~A~~l~~~M~~~  288 (425)
                        .|.-..++.+|...|++....
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~  281 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRM  281 (366)
T ss_pred             hhheecccchHHHHHHHhhcccc
Confidence              445567888888899887654

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.85  E-value=3.4  Score=37.64  Aligned_cols=96  Identities=17%  Similarity=0.213  Sum_probs=60.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-CccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042756          153 CNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII  231 (425)
Q Consensus       153 ~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll  231 (425)
                      ..+++.-....+   .+++...+.+.....+. ..|+. +-.+++.-+. .-+.++++.+...=.+-|+-||.++++.+|
T Consensus        68 d~~V~v~~~~~~---idd~~~~LyKlRhs~~a~~~~~~-~~~~~irlll-ky~pq~~i~~l~npIqYGiF~dqf~~c~l~  142 (418)
T KOG4570|consen   68 DRLVDVISSREE---IDDAEYYLYKLRHSPNAWYLRNW-TIHTWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQFTFCLLM  142 (418)
T ss_pred             hhhhhccccccc---hhHHHHHHHHHhcCcchhhhccc-cHHHHHHHHH-ccChHHHHHHHhCcchhccccchhhHHHHH
Confidence            344444333333   55555555555433221 11221 2222333333 345778888888888889999999999999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHC
Q 042756          232 YGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +.+.+.+++.+|.++.-.|...
T Consensus       143 D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  143 DSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HHHHhcccHHHHHHHHHHHHHH
Confidence            9999999999888887776654

>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=88.55  E-value=7.5  Score=38.08  Aligned_cols=133  Identities=16%  Similarity=0.181  Sum_probs=91.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ..-.+.++..+-+.|..+.|+++-..-.               .-.....+.|+   ++.|++...+.        .+..
T Consensus       295 ~~~~~~i~~fL~~~G~~e~AL~~~~D~~---------------~rFeLAl~lg~---L~~A~~~a~~~--------~~~~  348 (443)
T PF04053_consen  295 KDQGQSIARFLEKKGYPELALQFVTDPD---------------HRFELALQLGN---LDIALEIAKEL--------DDPE  348 (443)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHSS-HH---------------HHHHHHHHCT----HHHHHHHCCCC--------STHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHhhcCChH---------------HHhHHHHhcCC---HHHHHHHHHhc--------CcHH
Confidence            3446778888888888888887654421               23344556787   55555554332        2445


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .|..|-+...+.|+++-|.+.|.+..         -|..++-.|.-.|+.+...++-+....+|-      +|....++.
T Consensus       349 ~W~~Lg~~AL~~g~~~lAe~c~~k~~---------d~~~L~lLy~~~g~~~~L~kl~~~a~~~~~------~n~af~~~~  413 (443)
T PF04053_consen  349 KWKQLGDEALRQGNIELAEECYQKAK---------DFSGLLLLYSSTGDREKLSKLAKIAEERGD------INIAFQAAL  413 (443)
T ss_dssp             HHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHhhc---------CccccHHHHHHhCCHHHHHHHHHHHHHccC------HHHHHHHHH
Confidence            89999999999999999999998753         467788888888988888888877777652      777777777


Q ss_pred             hcCCHHHHHHHHHH
Q 042756          271 DHNELSRMVLWLQK  284 (425)
Q Consensus       271 ~~g~~~~A~~l~~~  284 (425)
                      -.|++++..+++.+
T Consensus       414 ~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  414 LLGDVEECVDLLIE  427 (443)
T ss_dssp             HHT-HHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHH
Confidence            78888888877765

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.

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

Probab=87.96  E-value=1.3  Score=26.11  Aligned_cols=26  Identities=8%  Similarity=0.187  Sum_probs=20.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          261 CSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       261 ~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                      +|+.|-..|.+.|++++|+++|++..
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            47778888888888888888888843

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=87.89  E-value=16  Score=35.28  Aligned_cols=145  Identities=10%  Similarity=0.062  Sum_probs=98.7

Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH--HHcC
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYG--YGRL  237 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~--~~~~  237 (425)
                      -+.++...+++++..+.+...+++...-..+.-+-+|+||... +++.......+..+.  .| ...|-.+..+  +-+.
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y~~   92 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQ--FG-KSAYLPLFKALVAYKQ   92 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHh--cC-CchHHHHHHHHHHHHh
Confidence            4567777777888777776655543322345667888888854 466666666666553  22 3445555554  4578


Q ss_pred             CCHHHHHHHHHHHHHC--CCCc------------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCCCHHHHHH
Q 042756          238 GLLEDMERIVNQMESD--GTRV------------DTVCSNMVLSSYGDHNELSRMVLWLQKMKD----SGIPFSVRTYNS  299 (425)
Q Consensus       238 g~~~~a~~~~~~m~~~--g~~~------------~~~~yn~li~~~~~~g~~~~A~~l~~~M~~----~g~~pd~~t~~~  299 (425)
                      +++..|.+.+..-.++  +-.|            |-.-=+..++++...|++.++..++++|..    +.+..+..+|+.
T Consensus        93 k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~  172 (549)
T PF07079_consen   93 KEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDR  172 (549)
T ss_pred             hhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHH
Confidence            8899998888877654  3322            445557778889999999999999998864    445689999999


Q ss_pred             HHHHHHHHH
Q 042756          300 VLNSCSTIM  308 (425)
Q Consensus       300 ll~~~~~~~  308 (425)
                      ++-.+++.-
T Consensus       173 ~vlmlsrSY  181 (549)
T PF07079_consen  173 AVLMLSRSY  181 (549)
T ss_pred             HHHHHhHHH
Confidence            776666643

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=87.59  E-value=20  Score=31.91  Aligned_cols=84  Identities=15%  Similarity=0.033  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ...|+--+ .-.+.|++++|.+.|+.+..+....+-. ..+--.++-++-+.++.+.+...++.|.+.-+..+.+     
T Consensus        35 ~~LY~~g~-~~L~~gn~~~A~~~fe~l~~~~p~s~~~-~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~-----  107 (254)
T COG4105          35 SELYNEGL-TELQKGNYEEAIKYFEALDSRHPFSPYS-EQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNA-----  107 (254)
T ss_pred             HHHHHHHH-HHHhcCCHHHHHHHHHHHHHcCCCCccc-HHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCCh-----
Confidence            33454333 3445688888888888887653332222 3333456667778888777777777777766555443     


Q ss_pred             HHHHHHHHHHh
Q 042756          191 ALKSMISGLCE  201 (425)
Q Consensus       191 ~~~~li~~~~~  201 (425)
                      -|-.-|.+++.
T Consensus       108 dY~~YlkgLs~  118 (254)
T COG4105         108 DYAYYLKGLSY  118 (254)
T ss_pred             hHHHHHHHHHH
Confidence            56666666654

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

Probab=87.21  E-value=1.4  Score=25.96  Aligned_cols=24  Identities=17%  Similarity=0.117  Sum_probs=13.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEM  215 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m  215 (425)
                      |+.|-..|.+.|++++|+++|++.
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            455555666666666666666553

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=86.96  E-value=16  Score=33.19  Aligned_cols=102  Identities=15%  Similarity=0.061  Sum_probs=49.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      |...|-.|-..|...|+.+.|..-|.+-.+..+. .++   .+..+-.++....+...-.++-..+.+.....+   -|+
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~-n~~---~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~---~~i  227 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGD-NPE---ILLGLAEALYYQAGQQMTAKARALLRQALALDP---ANI  227 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCC-CHH---HHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCC---ccH
Confidence            5555666666677777777776666665543222 222   233333333222222212333334444332221   123


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      .+..-+-..+...|++.+|...|+.|.+.
T Consensus       228 ral~lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         228 RALSLLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence            34444555556666666666666666654

>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=86.62  E-value=0.33  Score=39.29  Aligned_cols=85  Identities=18%  Similarity=0.160  Sum_probs=54.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g  273 (425)
                      .+|+.+.+.+.++....+++.+...+..-+....+.++..|++.++.+...++++.  .     +..-...++..|-+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~--~-----~~yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT--S-----NNYDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS--S-----SSS-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc--c-----cccCHHHHHHHHHhcc
Confidence            45666777777777777888777766556677778888888888777777777661  1     1122345566666666


Q ss_pred             CHHHHHHHHHHH
Q 042756          274 ELSRMVLWLQKM  285 (425)
Q Consensus       274 ~~~~A~~l~~~M  285 (425)
                      .+++|.-+|.++
T Consensus        85 l~~~a~~Ly~~~   96 (143)
T PF00637_consen   85 LYEEAVYLYSKL   96 (143)
T ss_dssp             SHHHHHHHHHCC
T ss_pred             hHHHHHHHHHHc
Confidence            666666666654

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.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=86.45  E-value=35  Score=33.61  Aligned_cols=165  Identities=10%  Similarity=-0.024  Sum_probs=89.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh----
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR----  189 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~----  189 (425)
                      +..+.++.-+..+++.|.+-++......     ....-++..-.+|...|...   ++...-.+....+.....|.    
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~-----~~it~~~n~aA~~~e~~~~~---~c~~~c~~a~E~gre~rad~klIa  298 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA-----TDITYLNNIAAVYLERGKYA---ECIELCEKAVEVGRELRADYKLIA  298 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh-----hhhHHHHHHHHHHHhccHHH---HhhcchHHHHHHhHHHHHHHHHHH
Confidence            4457777777888888888888776542     11222344555577766632   22222222221111110000    


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH-------------------------HHHHHcCCCHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI-------------------------IYGYGRLGLLEDME  244 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l-------------------------l~~~~~~g~~~~a~  244 (425)
                      ..+.-+-++|.+.++++.+...|.+....-..||..+=...                         -+.+.+.|++..|.
T Consensus       299 k~~~r~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av  378 (539)
T KOG0548|consen  299 KALARLGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAV  378 (539)
T ss_pred             HHHHHhhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHH
Confidence            12222334666678889999999887665444443322111                         12255666666666


Q ss_pred             HHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          245 RIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       245 ~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +.+.+++++. +-|...|..--.+|.+.|.+.+|++--+.-++
T Consensus       379 ~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ie  420 (539)
T KOG0548|consen  379 KHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIE  420 (539)
T ss_pred             HHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            6666666654 23566666666666666666666655444433

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=86.35  E-value=31  Score=32.84  Aligned_cols=133  Identities=11%  Similarity=0.065  Sum_probs=77.5

Q ss_pred             HHHHHHh---cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----c--CCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          117 IIAFLDK---QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----H--DSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       117 ll~~~~~---~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~--g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      ..-++-+   .|+.++|++++..+......+.++   +|..+-..|-.    .  .+.+..+++.+.+.+--...+...|
T Consensus       185 yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d---~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y~  261 (374)
T PF13281_consen  185 YAFALNRRNKPGDREKALQILLPVLESDENPDPD---TLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYYS  261 (374)
T ss_pred             HHHHHhhcccCCCHHHHHHHHHHHHhccCCCChH---HHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcCCccccc
Confidence            3445556   799999999999966655555655   56665555432    2  2333456666666655433322222


Q ss_pred             ChhHHHHHHHHHHhcC-ChhHHHHHH---HH-HHHcC---CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          188 KRQALKSMISGLCEMG-QPHEAENLI---EE-MRVKG---LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g-~~~~a~~~~---~~-m~~~g---~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      .+ -+-+|+....... .-.+..++-   .. ..++|   -..|-..+.+++.++.-.|+.++|.+..+.|...
T Consensus       262 GI-N~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  262 GI-NAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             hH-HHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            11 2222333222211 111222222   22 22334   3357778999999999999999999999999976

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=86.20  E-value=16  Score=29.49  Aligned_cols=79  Identities=13%  Similarity=0.277  Sum_probs=43.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHC------CCCcCHHhHHHHHHHHHhcCC-HHHHHHHHHHHHhCCCCCCHHHHHH
Q 042756          227 YKCIIYGYGRLGLLEDMERIVNQMESD------GTRVDTVCSNMVLSSYGDHNE-LSRMVLWLQKMKDSGIPFSVRTYNS  299 (425)
Q Consensus       227 y~~ll~~~~~~g~~~~a~~~~~~m~~~------g~~~~~~~yn~li~~~~~~g~-~~~A~~l~~~M~~~g~~pd~~t~~~  299 (425)
                      .|+++.-.+..+++.....+++.+.-.      | ..+-..|++++.+.++..- ---+..+|+-|++.+.+++..-|..
T Consensus        42 iN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~-~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~  120 (145)
T PF13762_consen   42 INCILNHLASYQNFSGVVSILEHLHFLNTDNIIG-WLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSC  120 (145)
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhh-hcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            345555555555555555554444211      1 1244566777777655554 3345566666666666677777777


Q ss_pred             HHHHHHH
Q 042756          300 VLNSCST  306 (425)
Q Consensus       300 ll~~~~~  306 (425)
                      ||+++.+
T Consensus       121 li~~~l~  127 (145)
T PF13762_consen  121 LIKAALR  127 (145)
T ss_pred             HHHHHHc
Confidence            7766654

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=86.15  E-value=15  Score=29.13  Aligned_cols=119  Identities=10%  Similarity=0.087  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH---HHHHHHHHcCCCHHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEY---KCIIYGYGRLGLLEDME  244 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty---~~ll~~~~~~g~~~~a~  244 (425)
                      +++..+++.+...+.+.     .-||=+|.-....-+.+-..++++..   |--.|....   ..++.+|++.|.     
T Consensus        18 V~qGveii~k~v~Ssni-----~E~NWvICNiiDaa~C~yvv~~LdsI---GkiFDis~C~NlKrVi~C~~~~n~-----   84 (161)
T PF09205_consen   18 VKQGVEIIEKTVNSSNI-----KEYNWVICNIIDAADCDYVVETLDSI---GKIFDISKCGNLKRVIECYAKRNK-----   84 (161)
T ss_dssp             HHHHHHHHHHHHHHS-H-----HHHTHHHHHHHHH--HHHHHHHHHHH---GGGS-GGG-S-THHHHHHHHHTT------
T ss_pred             HHHHHHHHHHHcCcCCc-----cccceeeeecchhhchhHHHHHHHHH---hhhcCchhhcchHHHHHHHHHhcc-----
Confidence            45556666666544432     24555555444444445555555544   323333222   223333333332     


Q ss_pred             HHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          245 RIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       245 ~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                                   +..-.+.-++.+...|+-+.-.+++.+..+. -.|+......+-++|.+.|+..++
T Consensus        85 -------------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~  139 (161)
T PF09205_consen   85 -------------LSEYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREA  139 (161)
T ss_dssp             ---------------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHH
T ss_pred             -------------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhH
Confidence                         4455677888899999999999999998764 378888999999999998876654

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>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=85.39  E-value=29  Score=31.63  Aligned_cols=230  Identities=10%  Similarity=0.077  Sum_probs=125.3

Q ss_pred             HHHhhHHHHHHHHHHhHHhc-CCCHHH--------HHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHh
Q 042756           31 LTARLTKQGQRFLSSLALAV-TRDSKA--------ASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRI  101 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~-~~d~~~--------~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m  101 (425)
                      ...|+.+.|.-++....... ..++..        ||.=...+.+..+.+.|...+.+              |.++++.-
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~--------------a~~~l~~~   69 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQR--------------AYDILEKP   69 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHH--------------HHHHHHhh
Confidence            45678888888888877662 333333        33333333333244444444433              44444331


Q ss_pred             hhcCCCccCH-----HHHHHHHHHHHhcCChh---HHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHH
Q 042756          102 TEESWFQWNP-----KLVAEIIAFLDKQGQRE---EAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYA  173 (425)
Q Consensus       102 ~~~~~~~~~~-----~~~~~ll~~~~~~g~~~---~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~  173 (425)
                      .+.+...++.     .+...++.+|...+..+   +|.++++.+....+. .+.   +|-.-+..+.+.++   .+++.+
T Consensus        70 ~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~-~~~---~~~L~l~il~~~~~---~~~~~~  142 (278)
T PF08631_consen   70 GKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNALRLLESEYGN-KPE---VFLLKLEILLKSFD---EEEYEE  142 (278)
T ss_pred             hhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC-CcH---HHHHHHHHHhccCC---hhHHHH
Confidence            1112233333     46677888887777644   566777777555443 222   45556677777666   566777


Q ss_pred             HHHHHhhcCCCCccChhHHHHHHHHHHhc--CChhHHHHHHHHHHHcCCCCCHH-HH-HHHHH---HHHcC------CCH
Q 042756          174 RLNQLVNSSSSVYVKRQALKSMISGLCEM--GQPHEAENLIEEMRVKGLEPSGF-EY-KCIIY---GYGRL------GLL  240 (425)
Q Consensus       174 ~~~~~~~~~~~~~p~~~~~~~li~~~~~~--g~~~~a~~~~~~m~~~g~~p~~~-ty-~~ll~---~~~~~------g~~  240 (425)
                      .+.+|..+.....   ..+..++..+...  ...+.|...+..+....+.|... -. ..++.   .....      +.+
T Consensus       143 ~L~~mi~~~~~~e---~~~~~~l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i  219 (278)
T PF08631_consen  143 ILMRMIRSVDHSE---SNFDSILHHIKQLAEKSPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKI  219 (278)
T ss_pred             HHHHHHHhccccc---chHHHHHHHHHHHHhhCcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHH
Confidence            7777766543222   3677777766332  34567778887777766666553 11 11111   12221      126


Q ss_pred             HHHHHHHHHHHHC-CCCcCHHhHHHHH-------HHHHhcCCHHHHHHHHHH
Q 042756          241 EDMERIVNQMESD-GTRVDTVCSNMVL-------SSYGDHNELSRMVLWLQK  284 (425)
Q Consensus       241 ~~a~~~~~~m~~~-g~~~~~~~yn~li-------~~~~~~g~~~~A~~l~~~  284 (425)
                      +...++++..... +-+.+..+-.++.       ..+.+.+++++|.++|+-
T Consensus       220 ~~l~~~~~~v~~~~~~~ls~~~~~a~~~LLW~~~~~~~~~k~y~~A~~w~~~  271 (278)
T PF08631_consen  220 ESLEELLSIVEHSLGKQLSAEAASAIHTLLWNKGKKHYKAKNYDEAIEWYEL  271 (278)
T ss_pred             HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHH
Confidence            6666677754432 3333433333332       334567889999999874

It is also involved in sporulation [].

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=85.08  E-value=45  Score=33.85  Aligned_cols=62  Identities=16%  Similarity=0.227  Sum_probs=46.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH-H----------HHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF-E----------YKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t----------y~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      ...++......+++++|+.+-++.-+  ..||.+ -          |.-.=++|.|+|+-.+|.++++++....+
T Consensus       776 ~ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtnnav  848 (1081)
T KOG1538|consen  776 LKSLVQLHVETQRWDEAFALAEKHPE--FKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLTNNAV  848 (1081)
T ss_pred             HHHHhhheeecccchHhHhhhhhCcc--ccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhhhhh
Confidence            35677788889999999998887655  345443 2          33445789999999999999999877543

>PRK15331 chaperone protein SicA; Provisional

Probab=84.75  E-value=11  Score=31.13  Aligned_cols=87  Identities=6%  Similarity=-0.132  Sum_probs=60.9

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHH
Q 042756          199 LCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRM  278 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A  278 (425)
                      +-..|++++|..+|.-+...+.. |..-+..|-.+|-..+++++|...|...-..+. -|...+--.-.+|...|+.+.|
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            44578888888888888774321 233345555566667888888888887665443 2455555667788888888899


Q ss_pred             HHHHHHHHh
Q 042756          279 VLWLQKMKD  287 (425)
Q Consensus       279 ~~l~~~M~~  287 (425)
                      ...|...++
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            888888776

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=84.68  E-value=3.3  Score=25.51  Aligned_cols=28  Identities=7%  Similarity=-0.024  Sum_probs=19.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          261 CSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       261 ~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      +|..+-..|.+.|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4566667777777777777777777654

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.54  E-value=5.6  Score=39.58  Aligned_cols=150  Identities=10%  Similarity=0.004  Sum_probs=76.3

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCC--CCCCchhhhHHHHHHHhhhcCC
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPD--TTHPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~--~~~~~~~~~a~~lf~~m~~~~~  106 (425)
                      +.+++|+++.|..++..+.      ...-+.+.+-+.+.|-.+.|+++--.--.+-  ...-++++.|.++-.+..    
T Consensus       595 t~vmrrd~~~a~~vLp~I~------k~~rt~va~Fle~~g~~e~AL~~s~D~d~rFelal~lgrl~iA~~la~e~~----  664 (794)
T KOG0276|consen  595 TLVLRRDLEVADGVLPTIP------KEIRTKVAHFLESQGMKEQALELSTDPDQRFELALKLGRLDIAFDLAVEAN----  664 (794)
T ss_pred             HHhhhccccccccccccCc------hhhhhhHHhHhhhccchHhhhhcCCChhhhhhhhhhcCcHHHHHHHHHhhc----
Confidence            4566778888887766653      3344566666777766555554321100000  000013444444433321    


Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                         +..-|..|-.+..+.|++..|.+.|....            -|..|+-.+...|+.+++..+...-.+.   +    
T Consensus       665 ---s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~------------d~~~LlLl~t~~g~~~~l~~la~~~~~~---g----  722 (794)
T KOG0276|consen  665 ---SEVKWRQLGDAALSAGELPLASECFLRAR------------DLGSLLLLYTSSGNAEGLAVLASLAKKQ---G----  722 (794)
T ss_pred             ---chHHHHHHHHHHhhcccchhHHHHHHhhc------------chhhhhhhhhhcCChhHHHHHHHHHHhh---c----
Confidence               22233346666677777777766666532            1455666666666643333332222221   1    


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEE  214 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~  214 (425)
                          ..|.-.-+|...|+++++.+++.+
T Consensus       723 ----~~N~AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  723 ----KNNLAFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             ----ccchHHHHHHHcCCHHHHHHHHHh
Confidence                335555566666777776666554

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.44  E-value=24  Score=36.74  Aligned_cols=114  Identities=11%  Similarity=0.114  Sum_probs=55.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      +|.-|.....+..--.+++.+.+.+......   + ..|+++|.+.++.++..+..+..    ..+... -   -....+
T Consensus       403 Vi~kfLdaq~IknLt~YLe~L~~~gla~~dh---t-tlLLncYiKlkd~~kL~efI~~~----~~g~~~-f---d~e~al  470 (933)
T KOG2114|consen  403 VIKKFLDAQRIKNLTSYLEALHKKGLANSDH---T-TLLLNCYIKLKDVEKLTEFISKC----DKGEWF-F---DVETAL  470 (933)
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHHcccccchh---H-HHHHHHHHHhcchHHHHHHHhcC----CCccee-e---eHHHHH
Confidence            5666655555555555666665555443322   1 46777777777744333332221    111111 0   234555


Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                      ..+.+.+-.++|..+-.....     +......++   -..|++++|.+++..+
T Consensus       471 ~Ilr~snyl~~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  471 EILRKSNYLDEAELLATKFKK-----HEWVLDILL---EDLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHhChHHHHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcC
Confidence            555556666665555544332     122333332   2345555555555544

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

Probab=84.30  E-value=59  Score=34.29  Aligned_cols=197  Identities=11%  Similarity=0.060  Sum_probs=106.9

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCcc
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQW  109 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~  109 (425)
                      .+..|..++|..+++........|..|...+-..|-..+                     ..++|..+|++.....   |
T Consensus        53 l~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~---------------------~~d~~~~~Ye~~~~~~---P  108 (932)
T KOG2053|consen   53 LFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLG---------------------KLDEAVHLYERANQKY---P  108 (932)
T ss_pred             HHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHh---------------------hhhHHHHHHHHHHhhC---C
Confidence            344455666666666655443336666666666666666                     4555555665555443   6


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCC-cccH-----HHHHHH-HHHHhhcC
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDS-KRGF-----DDTYAR-LNQLVNSS  182 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~-~~~~-----~~~~~~-~~~~~~~~  182 (425)
                      +......+..+|.|.+++.+-.+.=-++-+.  .|... ...| +++..+..... .+.+     ....+. ..++.+.+
T Consensus       109 ~eell~~lFmayvR~~~yk~qQkaa~~LyK~--~pk~~-yyfW-sV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~  184 (932)
T KOG2053|consen  109 SEELLYHLFMAYVREKSYKKQQKAALQLYKN--FPKRA-YYFW-SVISLILQSIFSENELLDPILLALAEKMVQKLLEKK  184 (932)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCccc-chHH-HHHHHHHHhccCCcccccchhHHHHHHHHHHHhccC
Confidence            6777777888888888776533333333222  12222 1223 34444433211 1111     112222 22222222


Q ss_pred             CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          183 SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMR-VKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       183 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~-~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                       +..-+..-...-...+-..|..++|++++..=. +.-...+...-+--++.+.+.+++.+..++-.++...|-
T Consensus       185 -gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~  257 (932)
T KOG2053|consen  185 -GKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGN  257 (932)
T ss_pred             -CccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCC
Confidence             111122222233334455788999999994433 333334555666778888888999888888888887763

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.18  E-value=23  Score=32.89  Aligned_cols=156  Identities=9%  Similarity=-0.070  Sum_probs=85.9

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHH
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLV  114 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~  114 (425)
                      ...+|-..++.++...+.|..+++..=+++.-.|+.+...+.+.+++.+=                  ..+ ++..+.+-
T Consensus       118 ~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~w------------------n~d-lp~~sYv~  178 (491)
T KOG2610|consen  118 KHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKW------------------NAD-LPCYSYVH  178 (491)
T ss_pred             cccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhcccc------------------CCC-CcHHHHHH
Confidence            34445556666666666677777777777777776666666666554321                  112 32233333


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCC-CCccChhHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSS-SVYVKRQALK  193 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~  193 (425)
                      +..--++...|-+++|++.-++-.+-.   ..+ .-.-.++-+.+--.|+   ..+..+.+.+....-. ..-.-...|=
T Consensus       179 GmyaFgL~E~g~y~dAEk~A~ralqiN---~~D-~Wa~Ha~aHVlem~~r---~Keg~eFM~~ted~Wr~s~mlasHNyW  251 (491)
T KOG2610|consen  179 GMYAFGLEECGIYDDAEKQADRALQIN---RFD-CWASHAKAHVLEMNGR---HKEGKEFMYKTEDDWRQSWMLASHNYW  251 (491)
T ss_pred             HHHHhhHHHhccchhHHHHHHhhccCC---Ccc-hHHHHHHHHHHHhcch---hhhHHHHHHhcccchhhhhHHHhhhhH
Confidence            334444557899999998877766532   222 1122455555666677   4455555544321110 0000112333


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHH
Q 042756          194 SMISGLCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~  216 (425)
                      ..--.+...++++.|+++|++=.
T Consensus       252 H~Al~~iE~aeye~aleIyD~ei  274 (491)
T KOG2610|consen  252 HTALFHIEGAEYEKALEIYDREI  274 (491)
T ss_pred             HHHHhhhcccchhHHHHHHHHHH
Confidence            33445566789999999998654

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.93  E-value=30  Score=30.66  Aligned_cols=156  Identities=12%  Similarity=0.022  Sum_probs=86.1

Q ss_pred             CChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCC
Q 042756          125 GQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQ  204 (425)
Q Consensus       125 g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~  204 (425)
                      ...+.|--+.++|.+-     +..+..|+.-...|..+|.++.+..+++..-++.++   +                  +
T Consensus        72 KayEqaamLake~~kl-----sEvvdl~eKAs~lY~E~GspdtAAmaleKAak~len---v------------------~  125 (308)
T KOG1585|consen   72 KAYEQAAMLAKELSKL-----SEVVDLYEKASELYVECGSPDTAAMALEKAAKALEN---V------------------K  125 (308)
T ss_pred             HHHHHHHHHHHHHHHh-----HHHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhc---C------------------C
Confidence            3455565666666542     222445777788888888887777777776666544   2                  2


Q ss_pred             hhHHHHHHHHHHHcCCC-----CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC----CcC-HHhHHHHHHHHHhcCC
Q 042756          205 PHEAENLIEEMRVKGLE-----PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT----RVD-TVCSNMVLSSYGDHNE  274 (425)
Q Consensus       205 ~~~a~~~~~~m~~~g~~-----p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~----~~~-~~~yn~li~~~~~~g~  274 (425)
                      +++|+++|.+-..--..     --..-|...-..+++...+++|-..|..-.....    -++ -..|-+.|-.|.-..+
T Consensus       126 Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~D  205 (308)
T KOG1585|consen  126 PDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHD  205 (308)
T ss_pred             HHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHH
Confidence            35555555554321000     0112334444566677777776655543322110    111 1335555556666778


Q ss_pred             HHHHHHHHHHHHhC---CCCCCHHHHHHHHHHHHH
Q 042756          275 LSRMVLWLQKMKDS---GIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       275 ~~~A~~l~~~M~~~---g~~pd~~t~~~ll~~~~~  306 (425)
                      +..|.++|++--+.   .-.-|..+...||.+|-.
T Consensus       206 yv~aekc~r~~~qip~f~~sed~r~lenLL~ayd~  240 (308)
T KOG1585|consen  206 YVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYDE  240 (308)
T ss_pred             HHHHHHHhcchhcCccccChHHHHHHHHHHHHhcc
Confidence            88888888874321   112356777777777744

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.57  E-value=33  Score=30.80  Aligned_cols=96  Identities=17%  Similarity=0.077  Sum_probs=75.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCc-CHHhHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKG----LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG-TRV-DTVCSN  263 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g-~~~-~~~~yn  263 (425)
                      ..|+.-+..|. .|++.+|...|....+..    ..||.  +=-|-.++...|++++|..+|..+.+.- =.| -....-
T Consensus       143 ~~Y~~A~~~~k-sgdy~~A~~~F~~fi~~YP~s~~~~nA--~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdall  219 (262)
T COG1729         143 KLYNAALDLYK-SGDYAEAEQAFQAFIKKYPNSTYTPNA--YYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALL  219 (262)
T ss_pred             HHHHHHHHHHH-cCCHHHHHHHHHHHHHcCCCCcccchh--HHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHH
Confidence            36888887665 666999999999999863    33433  3447889999999999999999998752 111 246777


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      -|-.+..+.|+.++|...|.+..+.
T Consensus       220 Klg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         220 KLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            7888889999999999999999875

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=83.25  E-value=34  Score=31.15  Aligned_cols=136  Identities=5%  Similarity=-0.039  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh-cC-ChhHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHcCCCHHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE-MG-QPHEAENLIEEMRV-KGLEPSGFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~-~g-~~~~a~~~~~~m~~-~g~~p~~~ty~~ll~~~~~~g~~~~a~  244 (425)
                      +.++++.+...-.+ ..+.-|..+-..+++.... .+ ...--.++.+-+.. .|-.++..+..++|+.+++.+++..-.
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 VVEALKLYDGLNPD-ESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLF  222 (292)
T ss_pred             HHHHHHHhhccCcc-cceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHH
Confidence            55666666643332 2244566666666666665 22 22233333333333 356788899999999999999999999


Q ss_pred             HHHHHHHHC-CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH-----HhCCCCCCHHHHHHHHHHH
Q 042756          245 RIVNQMESD-GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM-----KDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       245 ~~~~~m~~~-g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M-----~~~g~~pd~~t~~~ll~~~  304 (425)
                      ++++..... +..-|...|..+|..-...|+..-+.++.++=     ++.|+.-+...-..+-+.+
T Consensus       223 ~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L~~LF  288 (292)
T PF13929_consen  223 QFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQLSELF  288 (292)
T ss_pred             HHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHHHHHH
Confidence            999988765 66678999999999999999998888877763     3567776666655554444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.05  E-value=11  Score=34.63  Aligned_cols=95  Identities=6%  Similarity=0.008  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC---CCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKG---LEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g---~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      +-...+..-....+++.+...+-.++...   ..|+  .+++.-++.    .-+.++++-+...=+.-|+.||-++++.+
T Consensus        66 ~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlll----ky~pq~~i~~l~npIqYGiF~dqf~~c~l  141 (418)
T KOG4570|consen   66 TVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLL----KYDPQKAIYTLVNPIQYGIFPDQFTFCLL  141 (418)
T ss_pred             ehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHH----ccChHHHHHHHhCcchhccccchhhHHHH
Confidence            44555555555678888888888877542   2233  334333332    33567888888888899999999999999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      |+.+.+.+++.+|.++.-.|..+.
T Consensus       142 ~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  142 MDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             HHHHHhcccHHHHHHHHHHHHHHH
Confidence            999999999999999888876543

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=82.99  E-value=3.9  Score=25.18  Aligned_cols=28  Identities=25%  Similarity=0.287  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSK  140 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~  140 (425)
                      ++..+-..|.+.|++++|+++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4666888999999999999999999875

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.96  E-value=27  Score=29.27  Aligned_cols=126  Identities=12%  Similarity=0.165  Sum_probs=75.4

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHH--HHhcCCccc
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDS--FCKHDSKRG  167 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~--~~~~g~~~~  167 (425)
                      ..++|+.-|.++.+.+.-..-.-.---+-...+..|+...|+..|+++-.....|...-  -..-|=.+  +...|.   
T Consensus        73 k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~r--d~ARlraa~lLvD~gs---  147 (221)
T COG4649          73 KTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGR--DLARLRAAYLLVDNGS---  147 (221)
T ss_pred             CchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhh--HHHHHHHHHHHhcccc---
Confidence            46789999999888764332222222234455678999999999999876433333210  01122222  345666   


Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP  222 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  222 (425)
                      .+++...++.+...++..  -...-.+|--+-.+.|++.+|.+.|.++..--..|
T Consensus       148 y~dV~srvepLa~d~n~m--R~sArEALglAa~kagd~a~A~~~F~qia~Da~ap  200 (221)
T COG4649         148 YDDVSSRVEPLAGDGNPM--RHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAP  200 (221)
T ss_pred             HHHHHHHhhhccCCCChh--HHHHHHHHhHHHHhccchHHHHHHHHHHHccccCc
Confidence            455555665554444322  12244566667778899999999999887644444

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

Probab=82.87  E-value=3.2  Score=24.78  Aligned_cols=28  Identities=11%  Similarity=0.157  Sum_probs=22.4

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          259 TVCSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       259 ~~~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                      ..+++.|-..|...|++++|..++++..
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            4578888888888999999999888865

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=82.61  E-value=69  Score=33.83  Aligned_cols=97  Identities=19%  Similarity=0.123  Sum_probs=62.8

Q ss_pred             HHhcCChhHHHHHHHHHHHhcCC----CchhHHHHHHHHHHHHH-hcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHH
Q 042756          121 LDKQGQREEAETLILETLSKLGS----RERELVLFYCNLIDSFC-KHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSM  195 (425)
Q Consensus       121 ~~~~g~~~~A~~l~~~m~~~~~~----~~~~~~~~y~~li~~~~-~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l  195 (425)
                      .....++++|..++.+....-..    ........|+.|-.-.. ..|+++.+.+..+...++.+... ..+....+.++
T Consensus       425 ~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~-~~~r~~~~sv~  503 (894)
T COG2909         425 LASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAA-YRSRIVALSVL  503 (894)
T ss_pred             HHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhccccc-chhhhhhhhhh
Confidence            34567899999999887664332    12222234444433322 34665666666666666555443 44677788888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHc
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ..+..-.|++++|..+..+..+.
T Consensus       504 ~~a~~~~G~~~~Al~~~~~a~~~  526 (894)
T COG2909         504 GEAAHIRGELTQALALMQQAEQM  526 (894)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHH
Confidence            89999999999998888777654

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=82.53  E-value=28  Score=31.69  Aligned_cols=122  Identities=8%  Similarity=0.056  Sum_probs=75.9

Q ss_pred             HHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 042756          157 DSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR  236 (425)
Q Consensus       157 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~  236 (425)
                      ......|+...+...+....+..+++..      .--.+..+|...|+.+.|..++..+-..--.........-|..+.+
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~~~~~~------~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~q  215 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAAPENSE------AKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQ  215 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhCcccch------HHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHH
Confidence            3455666655555555555555444422      5667788888888888888888877544222222333334555556


Q ss_pred             CCCHHHHHHHHHHHHHCCCCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          237 LGLLEDMERIVNQMESDGTRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       237 ~g~~~~a~~~~~~m~~~g~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .....+...+-...-..   | |...--.+-..|...|+.++|.+.+-.+.+
T Consensus       216 aa~~~~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~  264 (304)
T COG3118         216 AAATPEIQDLQRRLAAD---PDDVEAALALADQLHLVGRNEAALEHLLALLR  264 (304)
T ss_pred             HhcCCCHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66655555555555553   4 566666677788888888888887776654

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=81.78  E-value=26  Score=33.32  Aligned_cols=93  Identities=8%  Similarity=-0.110  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      +++.+.-+|.+.+++.+|++.-++.+... ++|....=-=-.+|...|+++.|+..|+.+.+.  .|+-..-+.=|..|.
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~l~  335 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIKLK  335 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHH
Confidence            67777777778888888877777776642 233443333345677777888888888877765  354444444343333


Q ss_pred             -hcCCH-HHHHHHHHHHH
Q 042756          271 -DHNEL-SRMVLWLQKMK  286 (425)
Q Consensus       271 -~~g~~-~~A~~l~~~M~  286 (425)
                       +..+. +...++|..|-
T Consensus       336 ~k~~~~~~kekk~y~~mF  353 (397)
T KOG0543|consen  336 QKIREYEEKEKKMYANMF  353 (397)
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence             33333 33466777774

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.38  E-value=16  Score=38.03  Aligned_cols=140  Identities=14%  Similarity=0.216  Sum_probs=88.3

Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHH
Q 042756          121 LDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLC  200 (425)
Q Consensus       121 ~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~  200 (425)
                      +-+.|++++|..-|-+-..   ..+++      .+|.-|-...+   ..+....+..+...+-   .+...-..||.+|.
T Consensus       378 Ly~Kgdf~~A~~qYI~tI~---~le~s------~Vi~kfLdaq~---IknLt~YLe~L~~~gl---a~~dhttlLLncYi  442 (933)
T KOG2114|consen  378 LYGKGDFDEATDQYIETIG---FLEPS------EVIKKFLDAQR---IKNLTSYLEALHKKGL---ANSDHTTLLLNCYI  442 (933)
T ss_pred             HHhcCCHHHHHHHHHHHcc---cCChH------HHHHHhcCHHH---HHHHHHHHHHHHHccc---ccchhHHHHHHHHH
Confidence            4467899998876655432   23332      35555544444   5566666666655542   23447788999999


Q ss_pred             hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHH
Q 042756          201 EMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVL  280 (425)
Q Consensus       201 ~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~  280 (425)
                      +.++.++..++.+... .|..  .+-....+..|-+.+-.++|..+-.....     +...-+.++   -..|++++|++
T Consensus       443 Klkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~  511 (933)
T KOG2114|consen  443 KLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYLDEAELLATKFKK-----HEWVLDILL---EDLHNYEEALR  511 (933)
T ss_pred             HhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHHHHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHH
Confidence            9999999888877655 4433  12355667777777777777766554433     333334443   45578889988


Q ss_pred             HHHHHH
Q 042756          281 WLQKMK  286 (425)
Q Consensus       281 l~~~M~  286 (425)
                      .+..|.
T Consensus       512 yi~slp  517 (933)
T KOG2114|consen  512 YISSLP  517 (933)
T ss_pred             HHhcCC
Confidence            877763

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=81.30  E-value=11  Score=27.95  Aligned_cols=33  Identities=15%  Similarity=0.170  Sum_probs=14.4

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          219 GLEPSGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       219 g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      .+.|+.....+.++||-+.+|+..|.++|+..+
T Consensus        37 DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          37 DLVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             ccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            344444444444444444444444444444333

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=81.28  E-value=60  Score=32.20  Aligned_cols=191  Identities=13%  Similarity=0.046  Sum_probs=103.5

Q ss_pred             hhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHH
Q 042756           34 RLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKL  113 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~  113 (425)
                      +.+.-+.-+|..+.+.++|..   ..++....=.|+=+..+..+.+.....+........++-                .
T Consensus       171 sgv~~G~G~f~L~lSlLPp~~---~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL----------------~  231 (468)
T PF10300_consen  171 SGVYFGFGLFNLVLSLLPPKV---LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLL----------------W  231 (468)
T ss_pred             HhHHHHHHHHHHHHHhCCHHH---HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHH----------------H
Confidence            334444555666655554433   345555555566556666665544332222222222222                3


Q ss_pred             HHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCchhHHHHHHH-HHHHHHhcCCcccHHHHHHHHHHHhhcCCC-Ccc
Q 042756          114 VAEIIAFLDK----QGQREEAETLILETLSKLGSRERELVLFYCN-LIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYV  187 (425)
Q Consensus       114 ~~~ll~~~~~----~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~-li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p  187 (425)
                      |..++..++.    ..+.+.|.++++.+.++..  ..  . .|.- --+.+...|+   ++++.+.+.+....... ...
T Consensus       232 y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP--~s--~-lfl~~~gR~~~~~g~---~~~Ai~~~~~a~~~q~~~~Ql  303 (468)
T PF10300_consen  232 YHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYP--NS--A-LFLFFEGRLERLKGN---LEEAIESFERAIESQSEWKQL  303 (468)
T ss_pred             HHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCC--Cc--H-HHHHHHHHHHHHhcC---HHHHHHHHHHhccchhhHHhH
Confidence            4444444433    4568899999999987622  21  2 2211 1223445677   66666666654432111 112


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHH-HHHcCCCH-------HHHHHHHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIY-GYGRLGLL-------EDMERIVNQMES  252 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~-~~~~~g~~-------~~a~~~~~~m~~  252 (425)
                      ....+--+.-++.-..++++|.+.|.++.+.+-. +..+|.-+.- ++...|+.       ++|.++|.+...
T Consensus       304 ~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~W-Ska~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  304 HHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKW-SKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHHHHHHHHHHHchHHHHHHHHHHHHhcccc-HHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            2335555666678889999999999999986422 3344443332 23445655       777788776654

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.

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

Probab=81.16  E-value=4.3  Score=24.20  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLS  139 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~  139 (425)
                      ..+++.|-..|...|++++|.+++++..+
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            45788899999999999999999998765

>PRK15331 chaperone protein SicA; Provisional

Probab=80.95  E-value=14  Score=30.60  Aligned_cols=89  Identities=16%  Similarity=-0.009  Sum_probs=60.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHH
Q 042756          119 AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISG  198 (425)
Q Consensus       119 ~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~  198 (425)
                      .-+-..|++++|..+|.-+..-... .+.   -|..|-.++-..+.++.+.+++.....+...++.      .+--.-.+
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~~d~~-n~~---Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~------p~f~agqC  114 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCIYDFY-NPD---YTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYR------PVFFTGQC  114 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcC-cHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCC------ccchHHHH
Confidence            3345679999999999998764332 222   2455666666677766666666666655443322      45566778


Q ss_pred             HHhcCChhHHHHHHHHHHH
Q 042756          199 LCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~  217 (425)
                      |...|+.+.|...|.....
T Consensus       115 ~l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        115 QLLMRKAAKARQCFELVNE  133 (165)
T ss_pred             HHHhCCHHHHHHHHHHHHh
Confidence            8888999999998888776

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=80.69  E-value=49  Score=31.52  Aligned_cols=80  Identities=10%  Similarity=-0.169  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 042756          224 GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNS  303 (425)
Q Consensus       224 ~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~  303 (425)
                      ..++..+.-+|.|.+++..|.+.-+.....+ .+|.-.---=-.+|...|+++.|...|+++++.  .|+-..-..=+..
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~  333 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIK  333 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHH
Confidence            4678888999999999999999999887754 235555555567899999999999999999864  7887777666666


Q ss_pred             HHH
Q 042756          304 CST  306 (425)
Q Consensus       304 ~~~  306 (425)
                      |.+
T Consensus       334 l~~  336 (397)
T KOG0543|consen  334 LKQ  336 (397)
T ss_pred             HHH
Confidence            644

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=80.41  E-value=52  Score=30.99  Aligned_cols=235  Identities=10%  Similarity=0.074  Sum_probs=120.9

Q ss_pred             HHHHhhHHHHHHHHHHhHHh---cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCC
Q 042756           30 CLTARLTKQGQRFLSSLALA---VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~---~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~  106 (425)
                      .+...+..+|+..+.....+   ..--..+|..+..+.++.|.++.++..-..              .++.|.+..... 
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~s--------------qi~~a~~~~ds~-   80 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVS--------------QIDTARELEDSD-   80 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHH--------------HHHHHHHHHHHH-
Confidence            34445666677666665554   233456667777777777765554432211              122233322222 


Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh---hcC
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRE-RELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLV---NSS  182 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~-~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~---~~~  182 (425)
                        .-...|-.+-.++-+.-++.+++++=..-..-.+... ...-..-.++-+++...+.+   +++++-|+...   .+.
T Consensus        81 --~~~ea~lnlar~~e~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~f---q~~Lesfe~A~~~A~~~  155 (518)
T KOG1941|consen   81 --FLLEAYLNLARSNEKLCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVF---QKALESFEKALRYAHNN  155 (518)
T ss_pred             --HHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHH---HHHHHHHHHHHHHhhcc
Confidence              1233455555555555555555553322211111100 00011223455555555553   34444444333   222


Q ss_pred             CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHH----cCCCCCHHHHHHH-----HHHHHcCCCHHHHHHHHHHHHH-
Q 042756          183 SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRV----KGLEPSGFEYKCI-----IYGYGRLGLLEDMERIVNQMES-  252 (425)
Q Consensus       183 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~~~ty~~l-----l~~~~~~g~~~~a~~~~~~m~~-  252 (425)
                      ........+|-.|-+.|.+..++++|.-+.....+    -++.-=..-|..+     --++-..|++.+|.+.-++-.+ 
T Consensus       156 ~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~kl  235 (518)
T KOG1941|consen  156 DDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKL  235 (518)
T ss_pred             CCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence            22223345888899999999999988876655543    2222212233333     2345666777666666665443 


Q ss_pred             ---CCCCc-CHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 042756          253 ---DGTRV-DTVCSNMVLSSYGDHNELSRMVLWLQK  284 (425)
Q Consensus       253 ---~g~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~  284 (425)
                         .|-.+ -+.+.-.+-+.|-..|+.+.|..=|+.
T Consensus       236 al~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~  271 (518)
T KOG1941|consen  236 ALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQ  271 (518)
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHH
Confidence               33222 245556677888889998888776665

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=80.29  E-value=35  Score=28.94  Aligned_cols=128  Identities=13%  Similarity=0.022  Sum_probs=69.3

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      |+..---.|-.+..+.|+..+|+..|++......-.++.   ..-.+-++....+++..+...++.+.+..+.+  -+||
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a---~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~--r~pd  161 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAA---MLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAF--RSPD  161 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHH---HHHHHHHHHHhhccHHHHHHHHHHHhhcCCcc--CCCC
Confidence            344444446677777777777777777765543332322   33455566666666433333333333333222  2354


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMER  245 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~  245 (425)
                        +--.+-+.|...|..+.|..-|+.....  -|+...-.-.-..+.+.|+.+++..
T Consensus       162 --~~Ll~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~a  214 (251)
T COG4700         162 --GHLLFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANA  214 (251)
T ss_pred             --chHHHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHH
Confidence              4445566677777777777777777774  3443333333334556665555443

---

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	425
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
2d9i_A	96	NEDD4-binding protein 2; SMR domain, N4BP2, BCL-3	6e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	7e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-07
2vkc_A	135	NEDD4-binding protein 2; human BCL3 binding protei	8e-07
3fau_A	82	NEDD4-binding protein 2; SMR, small-MUTS related d	9e-07

>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 = 69.1 bits (168), Expect = 1e-12
 Identities = 71/433 (16%), Positives = 132/433 (30%), Gaps = 129/433 (29%)

Query: 1   MISSLHMRIPPPWNSRCCRLRQQRLTLVQCLTARLTK--QGQRFLSSL------------ 46
           M+  L  +I P W SR       +L +   + A L +  + + + + L            
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHS-IQAELRRLLKSKPYENCLLVLLNVQNAKAW 259

Query: 47  --------ALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLY 98
                    L  TR  +    L     A++   I+L+  S  L+PD      S L   L 
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFL----SAATTTHISLDHHSMTLTPDEV---KSLLLKYLD 312

Query: 99  MRITE--ESWFQWNPKLVAEIIAFLD---------KQGQREEAETLILETLSKLGSRE-R 146
            R  +        NP+ ++ I   +          K    ++  T+I  +L+ L   E R
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372

Query: 147 ELVLFYCNL-IDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQP 205
           ++   +  L +           F               S ++    L      +      
Sbjct: 373 KM---FDRLSV-----------FPP-------------SAHIPTILLSL----IWFDVIK 401

Query: 206 HEAENLIEEMRVKGL-EPSGFEYKCIIYG-YGRLGLLEDME-----RIVNQMESDGTRVD 258
            +   ++ ++    L E    E    I   Y  L +  + E      IV+      T   
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 259 TVCSNMVLSSY-----GDH----------NELSRMVL---WLQ-KMKDSGIPFSVRTYNS 299
                  L  Y     G H               + L   +L+ K++             
Sbjct: 462 DDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA-------- 513

Query: 300 VLNSCSTIMSMLQDL---------NSNDFPLSILELTEVLNEEEVSVV--KEL------- 341
             N+  +I++ LQ L         N   +   +  + + L + E +++  K         
Sbjct: 514 -WNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572

Query: 342 --EDSSVLDEAMK 352
             ED ++ +EA K
Sbjct: 573 MAEDEAIFEEAHK 585

>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 = 57.6 bits (138), Expect = 5e-09
 Identities = 59/405 (14%), Positives = 113/405 (27%), Gaps = 146/405 (36%)

Query: 11  PPWN-SRCCRLRQQRLTLVQCLTARLTKQGQRFL--------SSLALAVTRDSKAASRL- 60
             +N SR     Q  L L Q L   L       +        + +AL V    K   ++ 
Sbjct: 127 AKYNVSR----LQPYLKLRQALL-ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 61  -------ISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKL 113
                  +    +       L  L + + P+ T    S  +  + +RI   S      +L
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT--SRSDHSSNIKLRI--HSIQAELRRL 237

Query: 114 VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVL---FYCNLIDSF---CKHDSKRG 167
                    K  +           L         LVL         ++F   CK      
Sbjct: 238 ------LKSKPYEN---------CL---------LVLLNVQNAKAWNAFNLSCK------ 267

Query: 168 FDDTYA--RLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE---EMRVKGLEP 222
                   R  Q+ +  S+      +L      L     P E ++L+    + R + L P
Sbjct: 268 ---ILLTTRFKQVTDFLSAATTTHISLDHHSMTL----TPDEVKSLLLKYLDCRPQDL-P 319

Query: 223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD--HNELSRMVL 280
                                     ++ +         +   LS   +   + L+    
Sbjct: 320 R-------------------------EVLT--------TNPRRLSIIAESIRDGLATWDN 346

Query: 281 WLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDF----------------PLSIL 324
           W     D           +++ S       L  L   ++                P  +L
Sbjct: 347 WKHVNCD--------KLTTIIESS------LNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392

Query: 325 EL--TEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHL 367
            L   +V+  + + VV +L   S++++       E+ + +  ++L
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEK----QPKESTISIPSIYL 433

>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 = 49.5 bits (117), Expect = 1e-06
 Identities = 59/354 (16%), Positives = 118/354 (33%), Gaps = 88/354 (24%)

Query: 114 VAEIIAFLDKQGQREEAETLILETLSKLGSR------ERELVLFYCNLIDSFCKHDSKRG 167
           +  II               +  TL            E  L + Y  L+        +  
Sbjct: 51  IDHII----MSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS 106

Query: 168 FD-DTY-ARLNQLVNSSSSV---YVKR-QALKSMISGLCEMGQPHEAENLIEEMRVKGLE 221
                Y  + ++L N +       V R Q    +   L E+ +P +  N++    + G+ 
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL-RPAK--NVL----IDGVL 159

Query: 222 PSG-----------------FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNM 264
            SG                  ++K  I+ +  L      E ++  ++    ++D      
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFK--IF-WLNLKNCNSPETVLEMLQKLLYQIDPN---- 212

Query: 265 VLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNS-NDFPLS- 322
             +S  DH+   ++ +   + +   +    + Y + L     ++  +Q+  + N F LS 
Sbjct: 213 -WTSRSDHSSNIKLRIHSIQAELRRL-LKSKPYENCL----LVLLNVQNAKAWNAFNLSC 266

Query: 323 -IL------ELTEVLNEEEVSVVKELEDSSVL--DEAM----KW-DSGETKL-----DLH 363
            IL      ++T+ L+    + +     S  L  DE      K+ D     L       +
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326

Query: 364 GMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAM 417
              L     II + + +    ++N KHV            K +T+  ESS+  +
Sbjct: 327 PRRLS----IIAESIRDGLATWDNWKHV---------NCDKLTTII-ESSLNVL 366

>2d9i_A NEDD4-binding protein 2; SMR domain, N4BP2, BCL-3 binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.68.8.1 Length = 96

 Score = 52.2 bits (125), Expect = 6e-09
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 354 DSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESS 413
            SG+  LDLHG+H+  A   +++ +++    F          ++V+ G G HS   G + 
Sbjct: 5   SSGQNVLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGK--PYLSVITGRGNHSQ-GGVAR 61

Query: 414 VKAMVKKMMVR 424
           +K  V K ++ 
Sbjct: 62  IKPAVIKYLIS 72

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 57.1 bits (136), Expect = 7e-09
 Identities = 29/216 (13%), Positives = 57/216 (26%), Gaps = 10/216 (4%)

Query: 194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG-LLEDMERIVNQMES 252
           +++ G    G   E   ++  ++  GL P    Y   +   GR       +ER + QM  
Sbjct: 170 AVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQ 229

Query: 253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQ 312
           +G ++  + + ++LS       L  +                   + +L         + 
Sbjct: 230 EGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVS 289

Query: 313 DLN-------SNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGM 365
                             L +        VSV K    S  +  A K            +
Sbjct: 290 YPKLHLPLKTLQCLFEKQLHMELASRVCVVSVEKPTLPSKEVKHARKTLKTLRDQWEKAL 349

Query: 366 HLGSAYFIILQWMDEMRNRFNNEKH--VIPAEITVV 399
                        +    RF+      ++     V 
Sbjct: 350 CRALRETKNRLEREVYEGRFSLYPFLCLLDEREVVR 385

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 51.7 bits (122), Expect = 3e-07
 Identities = 11/104 (10%), Positives = 25/104 (24%), Gaps = 3/104 (2%)

Query: 204 QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVN---QMESDGTRVDTV 260
                +    +     L                   L     ++            +   
Sbjct: 107 SLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLD 166

Query: 261 CSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC 304
             N V+  +        +V  L  +KD+G+   + +Y + L   
Sbjct: 167 MYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCM 210

>3fau_A NEDD4-binding protein 2; SMR, small-MUTS related domain, nicking endonuclease, alternative splicing, ATP-binding, coiled coil, cytoplasm, hydrolase; 1.90A {Homo sapiens} Length = 82

 Score = 45.6 bits (108), Expect = 9e-07
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 360 LDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVK 419
           LDLHG+H+  A   +++ +++    F          ++V+ G G HS   G + +K  V 
Sbjct: 3   LDLHGLHVDEALEHLMRVLEKKTEEFKQNGGK--PYLSVITGRGNHSQ-GGVARIKPAVI 59

Query: 420 KMMVR 424
           K ++ 
Sbjct: 60  KYLIS 64

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	425
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	99.93
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.92
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.88
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.84
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.81
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.73
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.73
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.63
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.61
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.55
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.55
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.54
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.51
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.51
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.49
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.48
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.48
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.44
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.44
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.43
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.4
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.4
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.39
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.37
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.37
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.34
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.32
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.31
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.3
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.27
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.24
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.22
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.22
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.21
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.21
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.21
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.21
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.19
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.18
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.17
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.15
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.13
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.13
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.13
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.11
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.08
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.07
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.07
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.06
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.06
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.06
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.04
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.03
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.03
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.01
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.01
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.99
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.99
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.98
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.97
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.97
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.97
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.95
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.95
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.93
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.93
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.92
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.91
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.91
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.89
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.86
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.86
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.85
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.82
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.76
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.74
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.71
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.7
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.69
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.69
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.65
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.65
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.62
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.62
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.6
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.54
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.5
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.48
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.41
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.39
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.39
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.36
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.32
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.31
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.3
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.28
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.28
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.27
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.24
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.24
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.19
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.19
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.14
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.13
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.11
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.09
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.06
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.05
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.03
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.03
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.02
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.02
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.01
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.01
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.97
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.96
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.96
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.96
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.96
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.95
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.95
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.93
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.93
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.91
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.9
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.89
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.86
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.85
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.85
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.84
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.83
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.79
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.79
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.77
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.77
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.76
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.74
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.74
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.73
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.72
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.72
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.72
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.72
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.71
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.7
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.69
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.69
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.65
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.63
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.61
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.57
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.56
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.56
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.55
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.55
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.55
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.54
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.52
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.5
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.46
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.45
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.42
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.39
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.38
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.36
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.35
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.34
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.31
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.26
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.23
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.19
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.14
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.11
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.06
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.02
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.01
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.98
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.96
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.94
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.9
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.82
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.82
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.77
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.75
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.75
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.7
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.61
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.59
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.46
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.42
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.41
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.4
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.34
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.29
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.29
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.29
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.29
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.2
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.12
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	95.93
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.84
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	95.68
1klx_A	138	Cysteine rich protein B; structural genomics, heli	95.56
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	95.53
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.53
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	95.39
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.38
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.29
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	95.26
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	95.19
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	94.95
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	94.75
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.73
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	94.6
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	94.33
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	94.09
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	93.23
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	92.45
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	91.96
1pc2_A	152	Mitochondria fission protein; unknown function; NM	91.72
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	91.51
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	91.42
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	90.89
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	90.3
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	90.25
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	89.55
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	89.11
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	88.52
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	88.3
1pc2_A	152	Mitochondria fission protein; unknown function; NM	88.27
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	87.36
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	85.44
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	83.97
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	83.48
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	83.2
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	82.79
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	82.1
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	81.95
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	81.68

>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=2.1e-34  Score=283.51  Aligned_cols=219  Identities=15%  Similarity=0.163  Sum_probs=186.0

Q ss_pred             hhhHHHHHHHhhhcCCCccCH-HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCccc--
Q 042756           91 SSLAFPLYMRITEESWFQWNP-KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRG--  167 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~-~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~--  167 (425)
                      ...+..+++++.+++ ..+.+ .+++.+|.+|++.|++++|+++|++|.+.|..|+   ..+||+||.+|++.+..+.  
T Consensus         6 ~s~~e~L~~~~~~k~-~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd---~~tyn~Li~~c~~~~~~~~~~   81 (501)
T 4g26_A            6 ASPSENLSRKAKKKA-IQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLS---QYHYNVLLYVCSLAEAATESS   81 (501)
T ss_dssp             -------------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCC---HHHHHHHHHHHTTCCCCSSSS
T ss_pred             cchHHHHHHHHHHhc-ccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC---HhHHHHHHHHHHhCCchhhhh
Confidence            345667777777776 33333 4688999999999999999999999999887665   4589999999998876433  


Q ss_pred             ----HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHH
Q 042756          168 ----FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDM  243 (425)
Q Consensus       168 ----~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a  243 (425)
                          ++++++++.+|...+  +.||..|||+||.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|
T Consensus        82 ~~~~l~~A~~lf~~M~~~G--~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A  159 (501)
T 4g26_A           82 PNPGLSRGFDIFKQMIVDK--VVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA  159 (501)
T ss_dssp             CCHHHHHHHHHHHHHHHTT--CCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hcchHHHHHHHHHHHHHhC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHH
Confidence                678999999998877  88999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc
Q 042756          244 ERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN  315 (425)
Q Consensus       244 ~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~  315 (425)
                      .++|++|.+.|+.||..|||+||.+|++.|++++|.++|++|++.|+.|+..||+.++..|+..+....+..
T Consensus       160 ~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~a~~~g~~  231 (501)
T 4g26_A          160 YEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVATKTGVK  231 (501)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHHHHTCCBS
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCcchhhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999998776655543

>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=6.5e-34  Score=280.02  Aligned_cols=187  Identities=16%  Similarity=0.069  Sum_probs=172.5

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC---------HHHHHHHHHHHHHCCCCcCHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL---------LEDMERIVNQMESDGTRVDTV  260 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~---------~~~a~~~~~~m~~~g~~~~~~  260 (425)
                      ..++.+|++|++.|++++|+++|++|.+.|++||.+|||+||.+|++.+.         ++.|.++|++|.+.|+.||..
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~  106 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA  106 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHH
Confidence            46888999999999999999999999999999999999999999987764         688999999999999999999


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHH
Q 042756          261 CSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKE  340 (425)
Q Consensus       261 ~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  340 (425)
                      |||+||.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|+++.+                     ..++.+
T Consensus       107 tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A---------------------~~l~~~  165 (501)
T 4g26_A          107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA---------------------YEVDAH  165 (501)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHH---------------------HHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHH---------------------HHHHHH
Confidence            99999999999999999999999999999999999999999999998887553                     345667


Q ss_pred             HHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccc
Q 042756          341 LEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHST  407 (425)
Q Consensus       341 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~  407 (425)
                      +.+.|+.||..||++||.+|++.|+.++|     .++|++|++     .|..|+..||+.++..++.
T Consensus       166 M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A-----~~ll~~Mr~-----~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          166 MVESEVVPEEPELAALLKVSMDTKNADKV-----YKTLQRLRD-----LVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHTTCCCCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH-----HTSSBCHHHHHHHHHHHHS
T ss_pred             HHhcCCCCCHHHHHHHHHHHhhCCCHHHH-----HHHHHHHHH-----hCCCcCHHHHHHHHHHHhc
Confidence            77899999999999999999999999999     999999999     9999999999999876654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.93  E-value=5.7e-25  Score=222.17  Aligned_cols=376  Identities=9%  Similarity=-0.075  Sum_probs=283.0

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC------------CCchhhhHHH
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT------------HPRLSSLAFP   96 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~------------~~~~~~~a~~   96 (425)
                      .++..|++++|.++|+.+... .||..++..+..+|.+.|+++.|..++.+++.....            ..+.+++|.+
T Consensus        93 ~~~~~g~~~~A~~~~~~~~~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  171 (597)
T 2xpi_A           93 DALMQQQYKCAAFVGEKVLDI-TGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLYNRSSACRYLAAFCLVKLYDWQGALN  171 (597)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-HCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGGGTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHccCchHHHHHHHHHHhh-CCCchHHHHHHHHHHHcCcHHHHHHHHHHHhccccchhHHHHHHHHHHHHhhHHHHHH
Confidence            334557899999999999854 568899999999999999999999999998533211            1235789999


Q ss_pred             HHHHhhhcC--------------CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhH--------------
Q 042756           97 LYMRITEES--------------WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSREREL--------------  148 (425)
Q Consensus        97 lf~~m~~~~--------------~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~--------------  148 (425)
                      +|+++....              ....+..+|+.++.+|.+.|++++|.++|++|.+.... ....              
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~~~  250 (597)
T 2xpi_A          172 LLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAK-CYEAFDQLVSNHLLTADE  250 (597)
T ss_dssp             HHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHTTCSCHHH
T ss_pred             HHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCch-hhHHHHHHHHhhcccchh
Confidence            999532221              13456889999999999999999999999999875322 1110              


Q ss_pred             ---------------------HHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhH
Q 042756          149 ---------------------VLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHE  207 (425)
Q Consensus       149 ---------------------~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~  207 (425)
                                           ..+|+.++..|.+.|+   .+++...+.++...    .++..+|+.++.+|.+.|++++
T Consensus       251 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~---~~~A~~~~~~~~~~----~~~~~~~~~l~~~~~~~g~~~~  323 (597)
T 2xpi_A          251 EWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDE---LRRAEDYLSSINGL----EKSSDLLLCKADTLFVRSRFID  323 (597)
T ss_dssp             HHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHH---HHHHHHHHHTSTTG----GGCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcch---HHHHHHHHHHhhcC----CchHHHHHHHHHHHHHhcCHHH
Confidence                                 0112233455556666   56677777666532    3678899999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          208 AENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       208 a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      |.++|+++.+.+ +.+..+++.++.+|.+.|++++|.++|+.+.+.. ..+..+|+.++..|.+.|++++|.++|+++.+
T Consensus       324 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  401 (597)
T 2xpi_A          324 VLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSST  401 (597)
T ss_dssp             HHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            999999998765 3367789999999999999999999999998643 34788999999999999999999999999987


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cCC---chhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeec
Q 042756          288 SGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SND---FPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDS  355 (425)
Q Consensus       288 ~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (425)
                      .. ..+..+|+.+..+|.+.|++++++.         +..   +..+...+...+..+++....+........+..+|+.
T Consensus       402 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  480 (597)
T 2xpi_A          402 MD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNE  480 (597)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHH
Confidence            42 3357799999999999888877743         111   2223335666677666665554443333456788999


Q ss_pred             cccchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCC--eeeeeeccccccccccchHHHHHHHHHh
Q 042756          356 GETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPA--EITVVCGSGKHSTVRGESSVKAMVKKMM  422 (425)
Q Consensus       356 li~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~--~~t~~~l~~~~~~~~~~~~~~~~~~~~~  422 (425)
                      ++..|.+.|++++|     .++|++|.+..+ ..+..|+  ..+|..+...|...+..+......+++.
T Consensus       481 l~~~~~~~g~~~~A-----~~~~~~~~~~~~-~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  543 (597)
T 2xpi_A          481 LGVVAFNKSDMQTA-----INHFQNALLLVK-KTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGL  543 (597)
T ss_dssp             HHHHHHHTTCHHHH-----HHHHHHHHHHHH-HSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHH-----HHHHHHHHHhhh-ccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            99999999999999     999999987211 0166888  6788888888888777777776666654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.92  E-value=5.8e-24  Score=214.77  Aligned_cols=343  Identities=9%  Similarity=-0.087  Sum_probs=252.7

Q ss_pred             HHHhhHHHHHHHHHHhHHhc----------------CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC--------
Q 042756           31 LTARLTKQGQRFLSSLALAV----------------TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT--------   86 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~----------------~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~--------   86 (425)
                      ...|++++|.++|+++....                .++..+|+.++.+|.+.|+.+.|...|.+++..+..        
T Consensus       161 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l  240 (597)
T 2xpi_A          161 VKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQL  240 (597)
T ss_dssp             HHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHH
Confidence            44567778888887432111                235899999999999999999999999998654321        


Q ss_pred             -------------------------------------------CCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHh
Q 042756           87 -------------------------------------------HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDK  123 (425)
Q Consensus        87 -------------------------------------------~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~  123 (425)
                                                                 ..+.+++|.++|+++.+.   .++..+++.++.+|.+
T Consensus       241 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~~~  317 (597)
T 2xpi_A          241 VSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL---EKSSDLLLCKADTLFV  317 (597)
T ss_dssp             HHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG---GGCHHHHHHHHHHHHH
T ss_pred             HHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC---CchHHHHHHHHHHHHH
Confidence                                                       123567788888888764   3788899999999999


Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcC
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMG  203 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g  203 (425)
                      .|++++|.++|+++.+.... .   ..+|..++.+|.+.|+   .+++...+.++....   ..+..+|+.++.+|.+.|
T Consensus       318 ~g~~~~A~~~~~~~~~~~~~-~---~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~---~~~~~~~~~l~~~~~~~g  387 (597)
T 2xpi_A          318 RSRFIDVLAITTKILEIDPY-N---LDVYPLHLASLHESGE---KNKLYLISNDLVDRH---PEKAVTWLAVGIYYLCVN  387 (597)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT-C---CTTHHHHHHHHHHHTC---HHHHHHHHHHHHHHC---TTSHHHHHHHHHHHHHTT
T ss_pred             hcCHHHHHHHHHHHHHcCcc-c---HHHHHHHHHHHHHhCC---HHHHHHHHHHHHhhC---cccHHHHHHHHHHHHHhc
Confidence            99999999999998875322 2   2367889999999999   455555555554322   235668999999999999


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHH
Q 042756          204 QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQ  283 (425)
Q Consensus       204 ~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~  283 (425)
                      ++++|.++|+++.+.. +.+..+|+.++.+|.+.|++++|.++|+.+.+.+ +.+..+|+.++.+|.+.|++++|.++|+
T Consensus       388 ~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  465 (597)
T 2xpi_A          388 KISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQ  465 (597)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999998742 2357799999999999999999999999988764 3478899999999999999999999999


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHh----CCCCcc--cceeeccc
Q 042756          284 KMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELED----SSVLDE--AMKWDSGE  357 (425)
Q Consensus       284 ~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~--~~~~~~li  357 (425)
                      +|.+.. ..+..+|+.+...|.+.|+++++..                     .+.++++    .+..|+  ..+|+.+.
T Consensus       466 ~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~---------------------~~~~~~~~~~~~~~~p~~~~~~~~~l~  523 (597)
T 2xpi_A          466 SSYALF-QYDPLLLNELGVVAFNKSDMQTAIN---------------------HFQNALLLVKKTQSNEKPWAATWANLG  523 (597)
T ss_dssp             HHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHH---------------------HHHHHHHHHHHSCCCSGGGHHHHHHHH
T ss_pred             HHHHhC-CCChHHHHHHHHHHHHhCCHHHHHH---------------------HHHHHHHhhhccccchhhHHHHHHHHH
Confidence            998753 3467889999999988888766532                     1122221    244565  56777777


Q ss_pred             cchhcccCcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeeeeccccccccccchHHHHHHHHH
Q 042756          358 TKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKAMVKKM  421 (425)
Q Consensus       358 ~~~~~~~~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~  421 (425)
                      .+|.+.|++++|     .++|+++.+     .+ ..+..+|..+...+...+..+......+++
T Consensus       524 ~~~~~~g~~~~A-----~~~~~~~~~-----~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  576 (597)
T 2xpi_A          524 HAYRKLKMYDAA-----IDALNQGLL-----LS-TNDANVHTAIALVYLHKKIPGLAITHLHES  576 (597)
T ss_dssp             HHHHHTTCHHHH-----HHHHHHHHH-----HS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHH-----HHHHHHHHH-----hC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            777777777777     777777766     22 224556666666666655555555555544

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.88  E-value=1e-22  Score=206.62  Aligned_cols=121  Identities=15%  Similarity=0.173  Sum_probs=113.5

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHH---cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRV---KGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                      ..|||+||++||+.|++++|.++|++|.+   .|+.||.+|||+||++||+.|++++|.++|++|.+.|+.||.+|||+|
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            35999999999999999999999998874   589999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCH-HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Q 042756          266 LSSYGDHNEL-SRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       266 i~~~~~~g~~-~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~  309 (425)
                      |.++|+.|+. ++|.++|++|.+.|+.||..||+++++++.+.+-
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~v  251 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATV  251 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHH
Confidence            9999999984 7899999999999999999999999998776433

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.84  E-value=2.1e-21  Score=197.14  Aligned_cols=152  Identities=13%  Similarity=0.156  Sum_probs=122.3

Q ss_pred             hHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHH
Q 042756          147 ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFE  226 (425)
Q Consensus       147 ~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  226 (425)
                      ....||++||++||+.|+.+++.+++..+.++...+  +.||++|||+||++||+.|++++|.++|++|.+.|+.||.+|
T Consensus       125 ~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG--~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvT  202 (1134)
T 3spa_A          125 GQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKR--KLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS  202 (1134)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHH--TTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             hHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcC--CCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence            335689999999999999554444444445444444  789999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCC-HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC------HHHHHH
Q 042756          227 YKCIIYGYGRLGL-LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS------VRTYNS  299 (425)
Q Consensus       227 y~~ll~~~~~~g~-~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd------~~t~~~  299 (425)
                      ||++|+++|+.|+ .++|.++|++|.+.|+.||.++||+++.++.+.    .+++..+++ ..++.|+      ..|...
T Consensus       203 YntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv-~P~f~p~~~~~~~~~t~~L  277 (1134)
T 3spa_A          203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKV-KPTFSLPPQLPPPVNTSKL  277 (1134)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGG-CCCCCCCCCCCCCCCCCTT
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH----HHHHHHHHh-CcccCCCCCCcccccchHH
Confidence            9999999999998 578999999999999999999999999877655    344444555 4556665      444444


Q ss_pred             HHHHHH
Q 042756          300 VLNSCS  305 (425)
Q Consensus       300 ll~~~~  305 (425)
                      |.+-|.
T Consensus       278 L~dl~s  283 (1134)
T 3spa_A          278 LRDVYA  283 (1134)
T ss_dssp             THHHHC
T ss_pred             HHHHHc
Confidence            444444

>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=99.81  E-value=4.5e-17  Score=155.40  Aligned_cols=334  Identities=11%  Similarity=-0.056  Sum_probs=196.3

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHHH
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAFP   96 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~~   96 (425)
                      ....|++++|.+.++.+....+.+...+..+...+...|+.+.+...+...+.......             +.+++|.+
T Consensus         9 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~~~A~~   88 (388)
T 1w3b_A            9 EYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIE   88 (388)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHH
Confidence            34566666777666666554444455555555666666666666666665544332211             23566666


Q ss_pred             HHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756           97 LYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus        97 lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      .|+++.+.+  +-+...|..+..++.+.|++++|.+.|+++.+..    |+....+..+-..+...|+++   ++...+.
T Consensus        89 ~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~---~A~~~~~  159 (388)
T 1w3b_A           89 HYRHALRLK--PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN----PDLYCVRSDLGNLLKALGRLE---EAKACYL  159 (388)
T ss_dssp             HHHHHHHHC--TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC----TTCTHHHHHHHHHHHTTSCHH---HHHHHHH
T ss_pred             HHHHHHHcC--cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCcHHHHHHHHHHHHHccCHH---HHHHHHH
Confidence            666665543  1244556667777777777777777777766541    111224555666666667633   3333333


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      +.....+   -+..+|+.+...+.+.|++++|...|+++.+.+ +-+...|..+-..+...|++++|...|+...+.. +
T Consensus       160 ~al~~~p---~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p  234 (388)
T 1w3b_A          160 KAIETQP---NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-P  234 (388)
T ss_dssp             HHHHHCT---TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-T
T ss_pred             HHHHhCC---CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-c
Confidence            3332211   123467777777777777777777777776642 1234566666667777777777777776665542 1


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cCCc---hhhHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SNDF---PLSIL  324 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~~~---~~~~~  324 (425)
                      -+..+|+.+...|.+.|++++|.+.|+++.+.+ ..+..+|..+...+.+.|+++++..         +...   ..+..
T Consensus       235 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~  313 (388)
T 1w3b_A          235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLAN  313 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHH
Confidence            245666777777777777777777777766542 1234566666666666666555532         1111   11112


Q ss_pred             HHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          325 ELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .+...+..+++....+-.-.....+..+|..+...|.+.|++++|     .+.|+++.+
T Consensus       314 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~a~~  367 (388)
T 1w3b_A          314 IKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEA-----LMHYKEAIR  367 (388)
T ss_dssp             HHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHH-----HHHHHHHHT
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHh
Confidence            334444445554443333333334567899999999999999999     999999987

>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=99.73  E-value=3.2e-15  Score=142.50  Aligned_cols=266  Identities=12%  Similarity=-0.007  Sum_probs=144.8

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhhHHHHH
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSLAFPLY   98 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~a~~lf   98 (425)
                      ..+..++|..+++......+.+..+|..+...+.+.|+++.|...+.+++.......             +.+++|.+.|
T Consensus        45 ~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  124 (388)
T 1w3b_A           45 QCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAY  124 (388)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            345666666666665554445666666666666666666666666666654322211             2345566666


Q ss_pred             HHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756           99 MRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus        99 ~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      +++.+.+.  -+...+..+-..+...|++++|.++|+++.+.    .|....+|..+...+.+.|+++.   +...+.+.
T Consensus       125 ~~al~~~p--~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~l~~~~~~~g~~~~---A~~~~~~a  195 (388)
T 1w3b_A          125 VSALQYNP--DLYCVRSDLGNLLKALGRLEEAKACYLKAIET----QPNFAVAWSNLGCVFNAQGEIWL---AIHHFEKA  195 (388)
T ss_dssp             HHHHHHCT--TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHTTTCHHH---HHHHHHHH
T ss_pred             HHHHHhCC--CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHH---HHHHHHHH
Confidence            66554431  12334445555556666666666666666553    11122355666666666666333   33333333


Q ss_pred             hhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          179 VNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       179 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      ....+   -+...|..+...+...|++++|...|++....  .| +..++..+..+|.+.|++++|.+.|+.+.+..- .
T Consensus       196 l~~~p---~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~  269 (388)
T 1w3b_A          196 VTLDP---NFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQP-H  269 (388)
T ss_dssp             HHHCT---TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCS-S
T ss_pred             HhcCC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-C
Confidence            22221   12235666666666666666666666665553  23 345666666666666666666666666655421 1


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      +..+|+.+...|.+.|++++|.++|+++.+.. ..+..++..+...+...|+++++
T Consensus       270 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  324 (388)
T 1w3b_A          270 FPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEA  324 (388)
T ss_dssp             CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHH
Confidence            34556666666666666666666666665442 33455666666666555555544

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.73  E-value=4.4e-15  Score=144.14  Aligned_cols=294  Identities=14%  Similarity=0.031  Sum_probs=217.3

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .....|.+++|.++|+.+....+.+..+|..+...+...|+++.|...+.+++                     +.+  +
T Consensus        35 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al---------------------~~~--p   91 (450)
T 2y4t_A           35 KLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVI---------------------QLK--M   91 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--T
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------hcC--C
Confidence            34566799999999999987766689999999999999997777766666654                     222  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHH------------HHHHhcCCcccHHHHHHHHH
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLI------------DSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li------------~~~~~~g~~~~~~~~~~~~~  176 (425)
                      .+..++..+...|.+.|++++|.+.|+++.+... ........+..+.            ..+.+.|++   +++...+.
T Consensus        92 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~A~~~~~  167 (450)
T 2y4t_A           92 DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNP-SENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDY---TAAIAFLD  167 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCH---HHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCH---HHHHHHHH
Confidence            3577888999999999999999999999986422 1110003445553            348888995   45555555


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ++....   ..+..++..+..+|.+.|++++|.++|+++.+.. +.+..++..+..+|.+.|++++|.+.|+.+.+..- 
T Consensus       168 ~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p-  242 (450)
T 2y4t_A          168 KILEVC---VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQ-  242 (450)
T ss_dssp             HHHHHC---TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHhC---CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-
Confidence            544322   1245689999999999999999999999998752 34678999999999999999999999999986531 


Q ss_pred             cCHHhHHHH------------HHHHHhcCCHHHHHHHHHHHHhCCCCCC-----HHHHHHHHHHHHHHHHHHHhhccCCc
Q 042756          257 VDTVCSNMV------------LSSYGDHNELSRMVLWLQKMKDSGIPFS-----VRTYNSVLNSCSTIMSMLQDLNSNDF  319 (425)
Q Consensus       257 ~~~~~yn~l------------i~~~~~~g~~~~A~~l~~~M~~~g~~pd-----~~t~~~ll~~~~~~~~~~~~~~~~~~  319 (425)
                      .+...+..+            ...|...|++++|..+|+++.+.  .|+     ...|..+...+.+.|++++++     
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~-----  315 (450)
T 2y4t_A          243 DHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAI-----  315 (450)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHH-----
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHH-----
Confidence            244555555            78999999999999999999874  455     335555656665555554432     


Q ss_pred             hhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          320 PLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                                      ..+.+.++. ...+..+|..+..+|...|++++|     .+.|++..+
T Consensus       316 ----------------~~~~~a~~~-~p~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~al~  357 (450)
T 2y4t_A          316 ----------------RVCSEVLQM-EPDNVNALKDRAEAYLIEEMYDEA-----IQDYETAQE  357 (450)
T ss_dssp             ----------------HHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHT
T ss_pred             ----------------HHHHHHHHh-CcccHHHHHHHHHHHHHhcCHHHH-----HHHHHHHHH
Confidence                            222233322 223567899999999999999999     999999986

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.63  E-value=1.3e-13  Score=135.87  Aligned_cols=244  Identities=7%  Similarity=-0.097  Sum_probs=144.1

Q ss_pred             cCChhHHHHHHHHHHH-----hc-CCCc----hhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHH
Q 042756          124 QGQREEAETLILETLS-----KL-GSRE----RELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALK  193 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~-----~~-~~~~----~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~  193 (425)
                      .|++++|.++|+++.+     .. .+..    +....++..+...+...|++   +++...+.+.....    |+...|.
T Consensus       202 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~A~~~~~~~l~~~----~~~~~~~  274 (514)
T 2gw1_A          202 PESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDP---LGAHEDIKKAIELF----PRVNSYI  274 (514)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCH---HHHHHHHHHHHHHC----CCHHHHH
T ss_pred             hccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCH---HHHHHHHHHHHhhC----ccHHHHH
Confidence            5677777777777665     21 1111    23344566666667777773   33444444433322    2244667


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHN  273 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g  273 (425)
                      .+...|...|++++|.+.|++..... +.+..++..+...|.+.|++++|...|+...+..- .+...|..+...|...|
T Consensus       275 ~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~  352 (514)
T 2gw1_A          275 YMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDP-ENIFPYIQLACLAYREN  352 (514)
T ss_dssp             HHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCS-SCSHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCh-hhHHHHHHHHHHHHHcC
Confidence            77777777777777777777766542 22455666677777777777777777777665432 24566667777777777


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cC---------CchhhHHHHHh---hcch
Q 042756          274 ELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SN---------DFPLSILELTE---VLNE  332 (425)
Q Consensus       274 ~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~---------~~~~~~~~~~~---~~~~  332 (425)
                      ++++|..+|+++.+.. ..+..++..+...+...|+.+.+..         +.         .+..+...+..   .+..
T Consensus       353 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  431 (514)
T 2gw1_A          353 KFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENF  431 (514)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHH
T ss_pred             CHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCH
Confidence            7777777777765531 2234566666666666665555422         11         11111223444   4444


Q ss_pred             hhHHHHH-HHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          333 EEVSVVK-ELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       333 ~~~~~~~-~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      +++.... +.++. ...+..+|..+...|...|++++|     .+.|++..+
T Consensus       432 ~~A~~~~~~a~~~-~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~a~~  477 (514)
T 2gw1_A          432 IEATNLLEKASKL-DPRSEQAKIGLAQMKLQQEDIDEA-----ITLFEESAD  477 (514)
T ss_dssp             HHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHHHh-CcccHHHHHHHHHHHHHhcCHHHH-----HHHHHHHHH
Confidence            4444333 33332 223456788889999999999999     999999887

>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=99.61  E-value=1.1e-12  Score=127.04  Aligned_cols=253  Identities=9%  Similarity=0.034  Sum_probs=194.4

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC----------------------
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP----------------------   88 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~----------------------   88 (425)
                      ...|+.++|.+.|+.+.+..+.+..++..+...|.+.|+++.|...+.+++......+                      
T Consensus        71 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  150 (450)
T 2y4t_A           71 LAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQA  150 (450)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999887666789999999999999999999999999987654322                      


Q ss_pred             ------chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc
Q 042756           89 ------RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH  162 (425)
Q Consensus        89 ------~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~  162 (425)
                            +.+++|...|+.+.+.+  +.+..++..+...|.+.|++++|.++|+++.+....    ...+|..+...|.+.
T Consensus       151 ~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~~~~~~l~~~~~~~  224 (450)
T 2y4t_A          151 LNAFGSGDYTAAIAFLDKILEVC--VWDAELRELRAECFIKEGEPRKAISDLKAASKLKND----NTEAFYKISTLYYQL  224 (450)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCS----CHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CHHHHHHHHHHHHHc
Confidence                  24677888888887654  247788888999999999999999999998775221    234678899999999


Q ss_pred             CCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHH------------HHHHHhcCChhHHHHHHHHHHHcCCCCC-----H
Q 042756          163 DSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSM------------ISGLCEMGQPHEAENLIEEMRVKGLEPS-----G  224 (425)
Q Consensus       163 g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~l------------i~~~~~~g~~~~a~~~~~~m~~~g~~p~-----~  224 (425)
                      |+++   ++...+.++....    |+ ...+..+            ...|.+.|++++|.+.|+++...  .|+     .
T Consensus       225 g~~~---~A~~~~~~~~~~~----p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~  295 (450)
T 2y4t_A          225 GDHE---LSLSEVRECLKLD----QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTV  295 (450)
T ss_dssp             TCHH---HHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHH
T ss_pred             CCHH---HHHHHHHHHHHhC----CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHH
Confidence            9954   4444444444322    22 2244444            78889999999999999999874  454     4


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHH
Q 042756          225 FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVL  301 (425)
Q Consensus       225 ~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll  301 (425)
                      ..|..+..++.+.|++++|...++.+.+.. +.+...|..+..+|...|++++|...|++..+.  .|+. ..+..+-
T Consensus       296 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~  370 (450)
T 2y4t_A          296 RSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYETAQEH--NENDQQIREGLE  370 (450)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--SSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CcchHHHHHHHH
Confidence            578888899999999999999999887653 236789999999999999999999999998863  5654 3444443

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.55  E-value=6.3e-12  Score=117.37  Aligned_cols=294  Identities=13%  Similarity=0.016  Sum_probs=211.0

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      ..+..|++++|.+.|+......+.+..++..+...+...|+++.|...+.+++.                     .+  +
T Consensus        12 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---------------------~~--~   68 (359)
T 3ieg_A           12 KLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIA---------------------LK--M   68 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---------------------HC--T
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHH---------------------hC--C
Confidence            345678999999999999887666788999999999999977777766666542                     22  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHH------------HHHHHhcCCcccHHHHHHHHH
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNL------------IDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~l------------i~~~~~~g~~~~~~~~~~~~~  176 (425)
                      -+...+..+...+.+.|++++|.+.|++..+.... .......+..+            ...+...|+++   ++...+.
T Consensus        69 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~A~~~~~  144 (359)
T 3ieg_A           69 DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPS-EQEEKEAESQLVKADEMQRLRSQALDAFDGADYT---AAITFLD  144 (359)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHH---HHHHHHH
T ss_pred             CcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCc-ccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHH---HHHHHHH
Confidence            25678888999999999999999999998764110 00223344444            57788899955   4555554


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      +.....+   .+...+..+...+...|++++|...|++..... +.+..++..+...+...|++++|.+.|+...+..- 
T Consensus       145 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~-  219 (359)
T 3ieg_A          145 KILEVCV---WDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQ-  219 (359)
T ss_dssp             HHHHHCT---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHhCC---CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-
Confidence            4443321   234589999999999999999999999998753 34678999999999999999999999999887532 


Q ss_pred             cCHHhHH------------HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH-----HHHHHHHHHHHHHHHHhhccCCc
Q 042756          257 VDTVCSN------------MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT-----YNSVLNSCSTIMSMLQDLNSNDF  319 (425)
Q Consensus       257 ~~~~~yn------------~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t-----~~~ll~~~~~~~~~~~~~~~~~~  319 (425)
                      .+...+.            .+...+.+.|++++|...|++..+.  .|+...     +..+-..+...|+++++      
T Consensus       220 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~la~~~~~~~~~~~A------  291 (359)
T 3ieg_A          220 DHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSVAEYTVRSKERICHCFSKDEKPVEA------  291 (359)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHHTTCHHHH------
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHHHHHccCHHHH------
Confidence            2333333            2366689999999999999998875  344322     22233444444444332      


Q ss_pred             hhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          320 PLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       320 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                                     ...+.+.++. ...+..+|..+...|...|++++|     .+.|++..+
T Consensus       292 ---------------~~~~~~~~~~-~~~~~~~~~~~~~~~~~~g~~~~A-----~~~~~~a~~  334 (359)
T 3ieg_A          292 ---------------IRICSEVLQM-EPDNVNALKDRAEAYLIEEMYDEA-----IQDYEAAQE  334 (359)
T ss_dssp             ---------------HHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHT
T ss_pred             ---------------HHHHHHHHHh-CcccHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHh
Confidence                           1222333332 223566888899999999999999     999999987

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.55  E-value=1.4e-12  Score=128.49  Aligned_cols=322  Identities=9%  Similarity=-0.090  Sum_probs=233.6

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      ..+..|++++|.+.|+.+... .||..+|..+..++.+.|+++.|...+.+++.                     .+  +
T Consensus        15 ~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~---------------------~~--p   70 (514)
T 2gw1_A           15 QFFRNKKYDDAIKYYNWALEL-KEDPVFYSNLSACYVSVGDLKKVVEMSTKALE---------------------LK--P   70 (514)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---------------------HC--S
T ss_pred             HHHHhccHHHHHHHHHHHHhc-CccHHHHHhHHHHHHHHhhHHHHHHHHHHHhc---------------------cC--h
Confidence            345678999999999999886 47999999999999999987777777766542                     22  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCc-------------------------------------------
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRE-------------------------------------------  145 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~-------------------------------------------  145 (425)
                      -+...+..+..+|.+.|++++|.+.|+++.+......                                           
T Consensus        71 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  150 (514)
T 2gw1_A           71 DYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKE  150 (514)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhH
Confidence            3566788888888888999998888888765432100                                           


Q ss_pred             --------------------------------hhHHHHHHHHHHHHH---hcCCcccHHHHHHHHHH-----HhhcCCCC
Q 042756          146 --------------------------------RELVLFYCNLIDSFC---KHDSKRGFDDTYARLNQ-----LVNSSSSV  185 (425)
Q Consensus       146 --------------------------------~~~~~~y~~li~~~~---~~g~~~~~~~~~~~~~~-----~~~~~~~~  185 (425)
                                                      ++....+......+.   +.|+++.+.+.++...+     ........
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~  230 (514)
T 2gw1_A          151 RKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDE  230 (514)
T ss_dssp             ------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCH
T ss_pred             HHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCcccc
Confidence                                            111223333444344   38999999998888877     31111111


Q ss_pred             ---ccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhH
Q 042756          186 ---YVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCS  262 (425)
Q Consensus       186 ---~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~y  262 (425)
                         ..+..+|..+...+...|++++|...|++.....  |+..++..+..++...|++++|.+.++...+.. +.+...|
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  307 (514)
T 2gw1_A          231 KLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVY  307 (514)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHH
T ss_pred             ccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHH
Confidence               1234699999999999999999999999998864  447899999999999999999999999998764 2367889


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc---------cCCchhh---HHHHHhhc
Q 042756          263 NMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN---------SNDFPLS---ILELTEVL  330 (425)
Q Consensus       263 n~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~---------~~~~~~~---~~~~~~~~  330 (425)
                      ..+...|...|++++|...|++..+.. ..+...+..+...+...|+++.+..         +......   ...+...+
T Consensus       308 ~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~  386 (514)
T 2gw1_A          308 YHRGQMNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKN  386 (514)
T ss_dssp             HHHHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCC
Confidence            999999999999999999999998753 2356788888888888777766632         1112211   22455556


Q ss_pred             chhhHHHHH-HHHhCCC-Ccc----cceeeccccchhc---ccCcchhHHHHHHHHHHHHHh
Q 042756          331 NEEEVSVVK-ELEDSSV-LDE----AMKWDSGETKLDL---HGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       331 ~~~~~~~~~-~~~~~~~-~~~----~~~~~~li~~~~~---~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ..+++.... +.++... .++    ..+|..+...|..   .|++++|     .+.|++..+
T Consensus       387 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A-----~~~~~~a~~  443 (514)
T 2gw1_A          387 DFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEA-----TNLLEKASK  443 (514)
T ss_dssp             CHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHH-----HHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHH-----HHHHHHHHH
Confidence            555554333 3332111 122    3378888899999   9999999     999999987

>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=99.54  E-value=1.3e-11  Score=122.20  Aligned_cols=241  Identities=7%  Similarity=-0.118  Sum_probs=127.9

Q ss_pred             ChhHHHHHHHHHHHhcCCCchh----HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh
Q 042756          126 QREEAETLILETLSKLGSRERE----LVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE  201 (425)
Q Consensus       126 ~~~~A~~l~~~m~~~~~~~~~~----~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~  201 (425)
                      ++++|.++|+++.+.... .+.    ...+|..+-..+...|+++   ++...+.+....    .|+...|..+...|..
T Consensus       217 ~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~---~A~~~~~~~~~~----~~~~~~~~~l~~~~~~  288 (537)
T 3fp2_A          217 LLTKSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNNLL---DAQVLLQESINL----HPTPNSYIFLALTLAD  288 (537)
T ss_dssp             HHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTCHH---HHHHHHHHHHHH----CCCHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhcccHH---HHHHHHHHHHhc----CCCchHHHHHHHHHHH
Confidence            566666666665543221 111    0113444445555556633   333333333322    1333456666666666


Q ss_pred             cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHH
Q 042756          202 MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      .|++++|...|++..... +.+..+|..+...+...|++++|.+.|+...+..- .+...|..+...|...|++++|..+
T Consensus       289 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~  366 (537)
T 3fp2_A          289 KENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNP-ENVYPYIQLACLLYKQGKFTESEAF  366 (537)
T ss_dssp             SSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCSHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            666666666666665532 22355666666666666666666666666655421 1345566666666666666666666


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc------------cCCchhh------HHHHHhh----------cchh
Q 042756          282 LQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN------------SNDFPLS------ILELTEV----------LNEE  333 (425)
Q Consensus       282 ~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~------------~~~~~~~------~~~~~~~----------~~~~  333 (425)
                      |++..+.. ..+...+..+...+...|++..+..            ...+..+      ...+...          +..+
T Consensus       367 ~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  445 (537)
T 3fp2_A          367 FNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFN  445 (537)
T ss_dssp             HHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHH
T ss_pred             HHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHH
Confidence            66665432 2233455555555555555544422            1111111      0122222          3333


Q ss_pred             hHHHH-HHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          334 EVSVV-KELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       334 ~~~~~-~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ++... .+.++. ...+..+|..+...|...|++++|     .+.|++..+
T Consensus       446 ~A~~~~~~a~~~-~p~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~al~  490 (537)
T 3fp2_A          446 AAIKLLTKACEL-DPRSEQAKIGLAQLKLQMEKIDEA-----IELFEDSAI  490 (537)
T ss_dssp             HHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhccHHHH-----HHHHHHHHH
Confidence            33333 333332 223456788899999999999999     999999887

>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=99.51  E-value=7.7e-12  Score=115.51  Aligned_cols=251  Identities=10%  Similarity=-0.053  Sum_probs=177.2

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ......|++++|.++|+.+....+.+...+..+...+...|+.+.|...+.+++.                     .+  
T Consensus        30 ~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~---------------------~~--   86 (330)
T 3hym_B           30 ERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVD---------------------LY--   86 (330)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHH---------------------HC--
T ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHH---------------------hC--
Confidence            4445678999999999999877555666777788888888877766666666543                     22  


Q ss_pred             ccCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          108 QWNPKLVAEIIAFLDKQG-QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g-~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      +-+...+..+...+...| ++++|.+.|++..+...    .....|..+...+...|+++.+.+.++...+..+.     
T Consensus        87 ~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~----~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-----  157 (330)
T 3hym_B           87 PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEK----TYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG-----  157 (330)
T ss_dssp             TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCT----TCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT-----
T ss_pred             cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCC----ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc-----
Confidence            124566777888888888 88888888888776422    11235777888888888855444444444443222     


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--------CCcC
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG--------TRVD  258 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g--------~~~~  258 (425)
                       +...+..+...|...|++++|.+.|++..+.. +.+..++..+...+.+.|++++|.+.|+...+..        ...+
T Consensus       158 -~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  235 (330)
T 3hym_B          158 -CHLPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKW  235 (330)
T ss_dssp             -CSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTC
T ss_pred             -cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHH
Confidence             23467778888888888888888888887753 3356788888888888888888888888776531        1234


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          259 TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       259 ~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      ..+|..+...|...|++++|...|++..+.. ..+...+..+-..+...|+..++
T Consensus       236 ~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A  289 (330)
T 3hym_B          236 EPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENA  289 (330)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHH
Confidence            5788888888888888888888888887642 22456677777777666665444

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.51  E-value=6.1e-12  Score=118.53  Aligned_cols=251  Identities=9%  Similarity=-0.080  Sum_probs=184.8

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ......|++++|.+.|+.+....+.+..+|..+...+...|+++.|...+.+++                     ..+  
T Consensus        73 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al---------------------~~~--  129 (365)
T 4eqf_A           73 LKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCL---------------------ELQ--  129 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------hcC--
Confidence            445667899999999999988766689999999999999997777776666654                     222  


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHH----------HHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELV----------LFYCNLIDSFCKHDSKRGFDDTYARLNQ  177 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~----------~~y~~li~~~~~~g~~~~~~~~~~~~~~  177 (425)
                      +.+..++..+...|.+.|++++|.+.|+++.+.    .+...          ..+..+...+.+.|+++   ++...+.+
T Consensus       130 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~---~A~~~~~~  202 (365)
T 4eqf_A          130 PNNLKALMALAVSYTNTSHQQDACEALKNWIKQ----NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLE---GVKELYLE  202 (365)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CHHHHCC-------------------CCHHHH---HHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHh----CccchHHHhhhccchHHHHHHHHHHhhhhhHH---HHHHHHHH
Confidence            135778999999999999999999999998764    11111          12334577888888854   45555555


Q ss_pred             HhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          178 LVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       178 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      .....+. .++..+|..+...|.+.|++++|.+.|++..+.. +.+..+|..+..+|.+.|++++|.+.|+...+.. +.
T Consensus       203 al~~~p~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~  279 (365)
T 4eqf_A          203 AAHQNGD-MIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PG  279 (365)
T ss_dssp             HHHHSCS-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHhCcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CC
Confidence            5443321 1246699999999999999999999999998853 3357899999999999999999999999988763 23


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC---CCC--------CHHHHHHHHHHHHHHHHHH
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG---IPF--------SVRTYNSVLNSCSTIMSML  311 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g---~~p--------d~~t~~~ll~~~~~~~~~~  311 (425)
                      +..+|..+...|.+.|++++|...|++..+..   ..|        +...|..+-.++...|+.+
T Consensus       280 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  344 (365)
T 4eqf_A          280 FIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPE  344 (365)
T ss_dssp             CHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHH
Confidence            58899999999999999999999999987521   111        2456677766666655543

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.49  E-value=1.6e-12  Score=122.47  Aligned_cols=270  Identities=9%  Similarity=-0.053  Sum_probs=185.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +...+..+...+.+.|+++.|...+.+++                     ..+  +.+..++..+...|.+.|++++|.+
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al---------------------~~~--p~~~~~~~~lg~~~~~~g~~~~A~~  120 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAI---------------------LQD--PGDAEAWQFLGITQAENENEQAAIV  120 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHH---------------------HHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------HhC--cCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            34457777777777776666555555543                     332  2367889999999999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc----cChhHHHHHHHHHHhcCChhHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY----VKRQALKSMISGLCEMGQPHEA  208 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~----p~~~~~~~li~~~~~~g~~~~a  208 (425)
                      .|++..+..    |....+|..+...|.+.|+++++.+.++...+..+......    .....++.+...+.+.|++++|
T Consensus       121 ~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  196 (365)
T 4eqf_A          121 ALQRCLELQ----PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGV  196 (365)
T ss_dssp             HHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHH
T ss_pred             HHHHHHhcC----CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHH
Confidence            999988752    22234788999999999996655555555544432211110    0112445568899999999999


Q ss_pred             HHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          209 ENLIEEMRVKGLE-PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       209 ~~~~~~m~~~g~~-p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .++|+++....-. ++..++..+...|.+.|++++|.+.|+...+.. +.+..+|+.+...|...|++++|...|++..+
T Consensus       197 ~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  275 (365)
T 4eqf_A          197 KELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALE  275 (365)
T ss_dssp             HHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            9999999986321 258899999999999999999999999988764 23688999999999999999999999999987


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCC--------cccceeeccccc
Q 042756          288 SGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVL--------DEAMKWDSGETK  359 (425)
Q Consensus       288 ~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~li~~  359 (425)
                      .. ..+..++..+...|...|+..++..                  ....+.++......        .+..+|..+-.+
T Consensus       276 ~~-p~~~~~~~~l~~~~~~~g~~~~A~~------------------~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~  336 (365)
T 4eqf_A          276 IQ-PGFIRSRYNLGISCINLGAYREAVS------------------NFLTALSLQRKSRNQQQVPHPAISGNIWAALRIA  336 (365)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCCHHHHH------------------HHHHHHHHHHCC------------CHHHHHHHHH
T ss_pred             cC-CCchHHHHHHHHHHHHCCCHHHHHH------------------HHHHHHHhCcccCCCcccchhhhHHHHHHHHHHH
Confidence            52 2246788888888888877766532                  11111111111111        135678888888


Q ss_pred             hhcccCcchh
Q 042756          360 LDLHGMHLGS  369 (425)
Q Consensus       360 ~~~~~~~~~a  369 (425)
                      +...|+.+.+
T Consensus       337 ~~~~g~~~~a  346 (365)
T 4eqf_A          337 LSLMDQPELF  346 (365)
T ss_dssp             HHHHTCHHHH
T ss_pred             HHHcCcHHHH
Confidence            9989987776

>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=99.48  E-value=2.4e-12  Score=121.10  Aligned_cols=289  Identities=9%  Similarity=-0.051  Sum_probs=195.2

Q ss_pred             hhHHHHHH-HHHHhHHh--cCC--CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           34 RLTKQGQR-FLSSLALA--VTR--DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        34 ~~~~~a~~-~~~~m~~~--~~~--d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      +.++.|.+ .|+.....  -.|  +...+..+...+.+.|+++.|...+.+++                     +.+  +
T Consensus        39 ~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al---------------------~~~--p   95 (368)
T 1fch_A           39 SDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAV---------------------QQD--P   95 (368)
T ss_dssp             -------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HSC--T
T ss_pred             HHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHH---------------------HhC--C
Confidence            45555665 55543333  111  34556667777777776555555555543                     332  2


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .+..++..+...+.+.|++++|.+.|++..+...    ....++..+...|...|+++   ++...+.+.....+.. + 
T Consensus        96 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~----~~~~~~~~l~~~~~~~g~~~---~A~~~~~~~~~~~~~~-~-  166 (368)
T 1fch_A           96 KHMEAWQYLGTTQAENEQELLAISALRRCLELKP----DNQTALMALAVSFTNESLQR---QACEILRDWLRYTPAY-A-  166 (368)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHH---HHHHHHHHHHHTSTTT-G-
T ss_pred             CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHHHHcCCHH---HHHHHHHHHHHhCcCc-H-
Confidence            3677888899999999999999999999887532    22346888999999999955   4555554444332111 1 


Q ss_pred             hhHHHH---------------HHHHHHhcCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          189 RQALKS---------------MISGLCEMGQPHEAENLIEEMRVKGLE-PSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       189 ~~~~~~---------------li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                       ..+..               .+..+...|++++|...|+++....-. ++..++..+...|.+.|++++|...|+...+
T Consensus       167 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  245 (368)
T 1fch_A          167 -HLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALS  245 (368)
T ss_dssp             -GGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             12211               244444899999999999999885321 1588999999999999999999999999887


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcch
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNE  332 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  332 (425)
                      .. +.+..+|+.+...|...|++++|...|+++.+.. ..+...+..+...|.+.|+...+..                 
T Consensus       246 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~-----------------  306 (368)
T 1fch_A          246 VR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVE-----------------  306 (368)
T ss_dssp             HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH-----------------
T ss_pred             hC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHH-----------------
Confidence            53 2357899999999999999999999999988752 3356788888888888888766532                 


Q ss_pred             hhHHHHHHHHhCCC-------CcccceeeccccchhcccCcchhHHHHHHHHHHH
Q 042756          333 EEVSVVKELEDSSV-------LDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDE  380 (425)
Q Consensus       333 ~~~~~~~~~~~~~~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  380 (425)
                       ....+.++.....       .....+|..+..+|...|+.++|     ..++.+
T Consensus       307 -~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~  355 (368)
T 1fch_A          307 -HFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY-----GAADAR  355 (368)
T ss_dssp             -HHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH-----HHHHTT
T ss_pred             -HHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhH-----HHhHHH
Confidence             1111111111110       11246799999999999999999     766653

>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=99.48  E-value=3.3e-12  Score=117.99  Aligned_cols=271  Identities=10%  Similarity=0.010  Sum_probs=197.4

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHH
Q 042756           51 TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEA  130 (425)
Q Consensus        51 ~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A  130 (425)
                      +.+...+..+...+...|+++.|..++.+++                     ..+.  .+...+..+...+.+.|++++|
T Consensus        19 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l---------------------~~~p--~~~~~~~~~~~~~~~~~~~~~A   75 (330)
T 3hym_B           19 QENLDVVVSLAERHYYNCDFKMCYKLTSVVM---------------------EKDP--FHASCLPVHIGTLVELNKANEL   75 (330)
T ss_dssp             -CCCTTHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHCT--TCTTTHHHHHHHHHHHTCHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------------HcCC--CChhhHHHHHHHHHHhhhHHHH
Confidence            4455566667777777776555555555543                     3332  2344566677888999999999


Q ss_pred             HHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcC-CcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHH
Q 042756          131 ETLILETLSKLGSRERELVLFYCNLIDSFCKHD-SKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAE  209 (425)
Q Consensus       131 ~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g-~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~  209 (425)
                      .++++++.+.... .   ...|..+...+...| +   .+++...+.+.....+   .+...|..+...+...|++++|.
T Consensus        76 ~~~~~~~~~~~~~-~---~~~~~~l~~~~~~~~~~---~~~A~~~~~~a~~~~~---~~~~~~~~l~~~~~~~~~~~~A~  145 (330)
T 3hym_B           76 FYLSHKLVDLYPS-N---PVSWFAVGCYYLMVGHK---NEHARRYLSKATTLEK---TYGPAWIAYGHSFAVESEHDQAM  145 (330)
T ss_dssp             HHHHHHHHHHCTT-S---THHHHHHHHHHHHSCSC---HHHHHHHHHHHHTTCT---TCTHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHhCcC-C---HHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhCC---ccHHHHHHHHHHHHHccCHHHHH
Confidence            9999999875222 2   236778889999999 7   4555555555543321   13458999999999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          210 NLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       210 ~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      +.|++..+.. +.+...+..+...|...|++++|.+.++...+.. +.+...|+.+...|...|++++|...|++..+..
T Consensus       146 ~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~  223 (330)
T 3hym_B          146 AAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKI  223 (330)
T ss_dssp             HHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHh
Confidence            9999998863 2245677779999999999999999999998764 3467899999999999999999999999987531


Q ss_pred             --------CCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchh
Q 042756          290 --------IPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLD  361 (425)
Q Consensus       290 --------~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~  361 (425)
                              ...+..++..+...+...|+++.+..                     .+.+.++. ...+...|..+...|.
T Consensus       224 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~---------------------~~~~a~~~-~~~~~~~~~~la~~~~  281 (330)
T 3hym_B          224 KAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALD---------------------YHRQALVL-IPQNASTYSAIGYIHS  281 (330)
T ss_dssp             TTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHH---------------------HHHHHHHH-STTCSHHHHHHHHHHH
T ss_pred             hhccccccccHHHHHHHHHHHHHHHhcCHHHHHH---------------------HHHHHHhh-CccchHHHHHHHHHHH
Confidence                    12335677888888777777655422                     22222222 1235667888899999


Q ss_pred             cccCcchhHHHHHHHHHHHHHh
Q 042756          362 LHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       362 ~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ..|++++|     .+.|++..+
T Consensus       282 ~~g~~~~A-----~~~~~~al~  298 (330)
T 3hym_B          282 LMGNFENA-----VDYFHTALG  298 (330)
T ss_dssp             HHTCHHHH-----HHHHHTTTT
T ss_pred             HhccHHHH-----HHHHHHHHc
Confidence            99999999     999998765

>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=99.44  E-value=2.2e-11  Score=112.22  Aligned_cols=251  Identities=9%  Similarity=-0.075  Sum_probs=189.4

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ......|++++|.++|+.+.+..+.+..++..+...+...|+++.|...+.+++                     +.+  
T Consensus        29 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~---------------------~~~--   85 (327)
T 3cv0_A           29 LSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHAR---------------------MLD--   85 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------------hcC--
Confidence            445667899999999999988766688999999999999997777776666653                     222  


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHH--------------HH-HHHhcCCcccHHHHH
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNL--------------ID-SFCKHDSKRGFDDTY  172 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~l--------------i~-~~~~~g~~~~~~~~~  172 (425)
                      +.+..++..+...+...|++++|.+.|++..+...... .   .+..+              .. .+...|+   .+++.
T Consensus        86 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~-~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~A~  158 (327)
T 3cv0_A           86 PKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYE-Q---LGSVNLQADVDIDDLNVQSEDFFFAAPNE---YRECR  158 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTT-T---C--------------------CCTTSHHH---HHHHH
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccH-H---HHHHHhHHHHHHHHHHHHHHhHHHHHccc---HHHHH
Confidence            23677888899999999999999999999887532211 1   22222              11 2555666   45555


Q ss_pred             HHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          173 ARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ..+.+.....+   .+...+..+...|.+.|++++|.+.|++..+.. +.+..++..+...+.+.|++++|.+.|+...+
T Consensus       159 ~~~~~~~~~~~---~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  234 (327)
T 3cv0_A          159 TLLHAALEMNP---NDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALD  234 (327)
T ss_dssp             HHHHHHHHHST---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCC---CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55555544321   245699999999999999999999999998763 33578999999999999999999999999887


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-----------CHHHHHHHHHHHHHHHHHHHh
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-----------SVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-----------d~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .. +.+..+|..+...|...|++++|.+.|++..+..-..           +..++..+..++.+.|+.+.+
T Consensus       235 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  305 (327)
T 3cv0_A          235 IN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLV  305 (327)
T ss_dssp             HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHH
Confidence            54 2367899999999999999999999999987642111           356777888888877777665

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.44  E-value=3e-10  Score=105.85  Aligned_cols=262  Identities=10%  Similarity=0.008  Sum_probs=193.7

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCC---C------------------
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDT---T------------------   86 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~---~------------------   86 (425)
                      ......|++++|.+.|+......+-+...|..+...+...|+++.|...+.+.+....   .                  
T Consensus        45 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  124 (359)
T 3ieg_A           45 TVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLR  124 (359)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHH
Confidence            3445677999999999998877555789999999999999999999999999987654   1                  


Q ss_pred             -------CCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH
Q 042756           87 -------HPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSF  159 (425)
Q Consensus        87 -------~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~  159 (425)
                             ..+.+++|.+.|++..+...  .+...+..+...+.+.|++++|.+.|++..+..    +.....+..+...+
T Consensus       125 ~~a~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~~~~la~~~  198 (359)
T 3ieg_A          125 SQALDAFDGADYTAAITFLDKILEVCV--WDAELRELRAECFIKEGEPRKAISDLKAASKLK----SDNTEAFYKISTLY  198 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----SCCHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHhCC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHH
Confidence                   12346778888888776542  467788889999999999999999999987642    22234678888889


Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccChhHHH------------HHHHHHHhcCChhHHHHHHHHHHHcCCCCC-H--
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALK------------SMISGLCEMGQPHEAENLIEEMRVKGLEPS-G--  224 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~------------~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~--  224 (425)
                      ...|+++.+.+.++...+..+..      ...+.            .+...+.+.|++++|...|++.....  |+ .  
T Consensus       199 ~~~~~~~~A~~~~~~a~~~~~~~------~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~  270 (359)
T 3ieg_A          199 YQLGDHELSLSEVRECLKLDQDH------KRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVAEY  270 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTTC------HHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSHHH
T ss_pred             HHcCCHHHHHHHHHHHHhhCccc------hHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHH
Confidence            99999554444444444332111      11232            23666888999999999999988753  33 2  


Q ss_pred             --HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH
Q 042756          225 --FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVL  301 (425)
Q Consensus       225 --~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll  301 (425)
                        ..+..+..++.+.|++++|.+.++...+.. +.+..+|..+...|...|++++|...|++..+.  .|+ ...+..+.
T Consensus       271 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~  347 (359)
T 3ieg_A          271 TVRSKERICHCFSKDEKPVEAIRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH--NENDQQIREGLE  347 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChHHHHHHH
Confidence              235557788999999999999999888753 236788999999999999999999999998865  455 44555555


Q ss_pred             HHHHH
Q 042756          302 NSCST  306 (425)
Q Consensus       302 ~~~~~  306 (425)
                      .+...
T Consensus       348 ~~~~~  352 (359)
T 3ieg_A          348 KAQRL  352 (359)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>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=99.43  E-value=3.9e-11  Score=112.76  Aligned_cols=253  Identities=8%  Similarity=-0.062  Sum_probs=192.1

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ......|++++|.+.|+.+.+..+.+..+|..+...+...|+++.|...+.+++.                     .+  
T Consensus        72 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---------------------~~--  128 (368)
T 1fch_A           72 LRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLE---------------------LK--  128 (368)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------------HC--
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHh---------------------cC--
Confidence            4446678999999999999887666889999999999999977777776666542                     22  


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHH---------------HHHHHHhcCCcccHHHHH
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCN---------------LIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~---------------li~~~~~~g~~~~~~~~~  172 (425)
                      +.+..++..+...|...|++++|.+.|+++.+...... .   .+..               .+..+...|++   +++.
T Consensus       129 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~-~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~A~  201 (368)
T 1fch_A          129 PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYA-H---LVTPAEEGAGGAGLGPSKRILGSLLSDSLF---LEVK  201 (368)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTG-G---GCC---------------CTTHHHHHHHHH---HHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcH-H---HHHHHHHHhhhhcccHHHHHHHHHhhcccH---HHHH
Confidence            23677899999999999999999999999887532211 1   1111               23334477774   4555


Q ss_pred             HHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          173 ARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       173 ~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ..+.+.....+. .++..+|..+...|.+.|++++|...|++..... +.+..+|..+...+.+.|++++|.+.|+...+
T Consensus       202 ~~~~~a~~~~p~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  279 (368)
T 1fch_A          202 ELFLAAVRLDPT-SIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALE  279 (368)
T ss_dssp             HHHHHHHHHSTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            555555443321 1246799999999999999999999999998852 33578999999999999999999999999887


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC---CCC-------CHHHHHHHHHHHHHHHHHHHh
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG---IPF-------SVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g---~~p-------d~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .. +.+..+|..+...|.+.|++++|...|++..+..   ..|       ...+|..+..+|...|+.+.+
T Consensus       280 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  349 (368)
T 1fch_A          280 LQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  349 (368)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             hC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhH
Confidence            53 2367899999999999999999999999987531   111       157888888888888776654

>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=99.40  E-value=9.3e-14  Score=131.47  Aligned_cols=179  Identities=13%  Similarity=0.068  Sum_probs=65.8

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+++|.+.++++..+       .+|..+..++.+.|++++|.+.|.+.      +.   ...|..++.++...|+++++.
T Consensus        18 ~ld~A~~fae~~~~~-------~vWs~La~A~l~~g~~~eAIdsfika------~D---~~~y~~V~~~ae~~g~~EeAi   81 (449)
T 1b89_A           18 NLDRAYEFAERCNEP-------AVWSQLAKAQLQKGMVKEAIDSYIKA------DD---PSSYMEVVQAANTSGNWEELV   81 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHhCCCh-------HHHHHHHHHHHHcCCHHHHHHHHHcC------CC---HHHHHHHHHHHHhCCCHHHHH
Confidence            578888888887432       36777999999999999999999653      12   236889999999999965544


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      ..++..++.       .++..+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|++++|..+|..
T Consensus        82 ~yl~~ark~-------~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~  147 (449)
T 1b89_A           82 KYLQMARKK-------ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNN  147 (449)
T ss_dssp             ----------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHH
T ss_pred             HHHHHHHHh-------CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            433333331       2345589999999999999999999885       48888999999999999999999999997


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      +         ..|+.|+.++.+.|++++|++.+.++      -+..||..++.+|...|+++.+
T Consensus       148 a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA  196 (449)
T 1b89_A          148 V---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLA  196 (449)
T ss_dssp             T---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             h---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHH
Confidence            6         36999999999999999999999998      2789999999999999998887

>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=99.40  E-value=3.6e-13  Score=127.47  Aligned_cols=269  Identities=11%  Similarity=0.041  Sum_probs=84.4

Q ss_pred             hhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCC--------CCCchhhhHHHHHHHhhhcC
Q 042756           34 RLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDT--------THPRLSSLAFPLYMRITEES  105 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~--------~~~~~~~~a~~lf~~m~~~~  105 (425)
                      |++++|.++++++     ++..+|..|..++.+.|+...|.+.|++.-...+        ...+.+++|++.++...+ .
T Consensus        17 ~~ld~A~~fae~~-----~~~~vWs~La~A~l~~g~~~eAIdsfika~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark-~   90 (449)
T 1b89_A           17 GNLDRAYEFAERC-----NEPAVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARK-K   90 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCHHHHHHHHHhC-----CChHHHHHHHHHHHHcCCHHHHHHHHHcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-h
Confidence            5688899999987     3345999999999999988888877766411110        012345555553333322 1


Q ss_pred             CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCC
Q 042756          106 WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSV  185 (425)
Q Consensus       106 ~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  185 (425)
                        .+++.+.+.++.+|.+.|+++++.++++.       |.   ..+|..+.+.|...|.++.+...+...          
T Consensus        91 --~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~-------pn---~~a~~~IGd~~~~~g~yeeA~~~Y~~a----------  148 (449)
T 1b89_A           91 --ARESYVETELIFALAKTNRLAELEEFING-------PN---NAHIQQVGDRCYDEKMYDAAKLLYNNV----------  148 (449)
T ss_dssp             --------------------CHHHHTTTTTC-------C-------------------CTTTHHHHHHHT----------
T ss_pred             --CccchhHHHHHHHHHHhCCHHHHHHHHcC-------Cc---HHHHHHHHHHHHHcCCHHHHHHHHHHh----------
Confidence              13345555566666666666665555531       11   124556666666666644444333321          


Q ss_pred             ccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHH
Q 042756          186 YVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMV  265 (425)
Q Consensus       186 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~l  265 (425)
                          ..|..+..++.+.|++++|.+.+.++      -++.+|..++.+|+..|+++.|......+.   +.|+  -...+
T Consensus       149 ----~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~---~~ad--~l~~l  213 (449)
T 1b89_A          149 ----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV---VHAD--ELEEL  213 (449)
T ss_dssp             ----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT---TCHH--HHHHH
T ss_pred             ----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH---hCHh--hHHHH
Confidence                15666666666666666666666655      145566666666666666666644333211   1222  23345


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHH-hC
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELE-DS  344 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  344 (425)
                      +..|.+.|++++|..+|+...... .--...|.-|--.|++                       ...+....-.+.+ .+
T Consensus       214 v~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~k-----------------------y~p~k~~ehl~~~~~~  269 (449)
T 1b89_A          214 INYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSK-----------------------FKPQKMREHLELFWSR  269 (449)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHT-----------------------TCHHHHHHHHHHHSTT
T ss_pred             HHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHh-----------------------cCHHHHHHHHHHHHHH
Confidence            556666666666666666544221 1122233333222222                       1122222222222 22


Q ss_pred             CCCc-------ccceeeccccchhcccCcchh
Q 042756          345 SVLD-------EAMKWDSGETKLDLHGMHLGS  369 (425)
Q Consensus       345 ~~~~-------~~~~~~~li~~~~~~~~~~~a  369 (425)
                      ...|       +...|.-+.--|...++++.|
T Consensus       270 ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A  301 (449)
T 1b89_A          270 VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNA  301 (449)
T ss_dssp             SCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHH
T ss_pred             hcCcHHHHHHHHHHHHHHHHHHHHhhchHHHH
Confidence            2222       467888888889999999888

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.39  E-value=6.2e-11  Score=108.36  Aligned_cols=238  Identities=10%  Similarity=0.015  Sum_probs=171.3

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHhcCCC--HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           27 LVQCLTARLTKQGQRFLSSLALAVTRD--SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~~~~d--~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      +.+.+..|....|++.++..... .|+  ....-.+.++|...|+++.+...+..                        .
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~-~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~------------------------~   60 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPS-SPERDVERDVFLYRAYLAQRKYGVVLDEIKP------------------------S   60 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCC-SHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT------------------------T
T ss_pred             HHHHHHHHHHHHHHHHHHhcccC-CchhhHHHHHHHHHHHHHCCCHHHHHHHhcc------------------------c
Confidence            56677888999999988775432 333  34556678889998877766653322                        1


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS  184 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~  184 (425)
                        -.|+..++..+...+...|+.++|.+.++++......|..  ...+..+-..+.+.|+   .+++...+.+       
T Consensus        61 --~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~--~~~~~~la~~~~~~g~---~~~Al~~l~~-------  126 (291)
T 3mkr_A           61 --SAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTN--TTFLLMAASIYFYDQN---PDAALRTLHQ-------  126 (291)
T ss_dssp             --SCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSC--HHHHHHHHHHHHHTTC---HHHHHHHHTT-------
T ss_pred             --CChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCC--HHHHHHHHHHHHHCCC---HHHHHHHHhC-------
Confidence              2356778888888899999999999999998765422222  2245667788889999   5556665554       


Q ss_pred             CccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHh
Q 042756          185 VYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEY---KCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVC  261 (425)
Q Consensus       185 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty---~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~  261 (425)
                       ..+...+..+...|.+.|++++|.+.|+++.+..  |+..-+   ...+..+...|++++|..+|+++.+. .+.+...
T Consensus       127 -~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~  202 (291)
T 3mkr_A          127 -GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLL  202 (291)
T ss_dssp             -CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHH
T ss_pred             -CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHH
Confidence             1344588889999999999999999999998863  653211   22334455668999999999999876 3457888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHH
Q 042756          262 SNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       262 yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~  309 (425)
                      |+.+..+|.+.|++++|+..|++..+.  .| +..++..+...+...|+
T Consensus       203 ~~~la~~~~~~g~~~eA~~~l~~al~~--~p~~~~~l~~l~~~~~~~g~  249 (291)
T 3mkr_A          203 LNGQAACHMAQGRWEAAEGVLQEALDK--DSGHPETLINLVVLSQHLGK  249 (291)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            999999999999999999999998764  34 55677777766665444

>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=99.37  E-value=3.1e-11  Score=111.23  Aligned_cols=253  Identities=8%  Similarity=-0.114  Sum_probs=178.6

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+++|..+|+++.+.+  +-+...+..+...+.+.|++++|.+.|++..+...    ....++..+...|...|+++.+.
T Consensus        36 ~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~----~~~~~~~~la~~~~~~~~~~~A~  109 (327)
T 3cv0_A           36 NLAEAALAFEAVCQAA--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP----KDIAVHAALAVSHTNEHNANAAL  109 (327)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc----CCHHHHHHHHHHHHHcCCHHHHH
Confidence            3444444444444433  13677888899999999999999999999887622    22346788999999999955544


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHH--------------HH-HHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSM--------------IS-GLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGY  234 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~l--------------i~-~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~  234 (425)
                      +.++...+..+..      ...+..+              .. .+...|++++|.+.|++..+.. +.+..++..+...|
T Consensus       110 ~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~  182 (327)
T 3cv0_A          110 ASLRAWLLSQPQY------EQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLY  182 (327)
T ss_dssp             HHHHHHHHTSTTT------TTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcc------HHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            4444444332221      1133333              22 3778899999999999998863 33678999999999


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhh
Q 042756          235 GRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       235 ~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      .+.|++++|.++++...+.. +.+..+|..+...|...|++++|...|++..+.. ..+..++..+...+...|+.+.+.
T Consensus       183 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~  260 (327)
T 3cv0_A          183 NLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAA  260 (327)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHH
Confidence            99999999999999988764 2367899999999999999999999999988753 235677777777777777765542


Q ss_pred             ccCCchhhHHHHHhhcchhhHHHHHHHHhCCCC-----------cccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          315 NSNDFPLSILELTEVLNEEEVSVVKELEDSSVL-----------DEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .                     .+.+.++....           .+..+|..+...|...|+.++|     ..++++..+
T Consensus       261 ~---------------------~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A-----~~~~~~~l~  314 (327)
T 3cv0_A          261 K---------------------QLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLV-----ELTYAQNVE  314 (327)
T ss_dssp             H---------------------HHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHH-----HHHTTCCSH
T ss_pred             H---------------------HHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHH-----HHHHHHHHH
Confidence            2                     12222221111           1466888899999999999999     777765443

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.37  E-value=4.9e-11  Score=109.03  Aligned_cols=244  Identities=12%  Similarity=-0.010  Sum_probs=174.7

Q ss_pred             hhhhHHHHHHHhhhcCCCccCH--HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCccc
Q 042756           90 LSSLAFPLYMRITEESWFQWNP--KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRG  167 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~--~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~  167 (425)
                      .+..|+..++....   ..|+.  .....+..+|...|+++.|..-++..       .++...++..+...+...++   
T Consensus        14 ~y~~ai~~~~~~~~---~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~-------~~~~~~a~~~la~~~~~~~~---   80 (291)
T 3mkr_A           14 SYQQCINEAQRVKP---SSPERDVERDVFLYRAYLAQRKYGVVLDEIKPS-------SAPELQAVRMFAEYLASHSR---   80 (291)
T ss_dssp             CHHHHHHHHHHSCC---CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTT-------SCHHHHHHHHHHHHHHCSTT---
T ss_pred             HHHHHHHHHHhccc---CCchhhHHHHHHHHHHHHHCCCHHHHHHHhccc-------CChhHHHHHHHHHHHcCCCc---
Confidence            44455555444322   22333  24455788999999999998766441       22235577888899999988   


Q ss_pred             HHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERI  246 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~  246 (425)
                      .+++.+.+.++....  ..|+ ...+..+-..+...|++++|++.|++      ..+...+..+...+.+.|++++|.+.
T Consensus        81 ~~~A~~~l~~ll~~~--~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~  152 (291)
T 3mkr_A           81 RDAIVAELDREMSRS--VDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKE  152 (291)
T ss_dssp             HHHHHHHHHHHHHSC--CCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhcc--cCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            667777777766543  2343 34666777999999999999999998      46788999999999999999999999


Q ss_pred             HHHHHHCCCCcCHHhH---HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhH
Q 042756          247 VNQMESDGTRVDTVCS---NMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSI  323 (425)
Q Consensus       247 ~~~m~~~g~~~~~~~y---n~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~  323 (425)
                      |+.+.+..  |+....   ..++..+...|++++|..+|+++.+. ...+...++.+-.++.+.|+++.+.         
T Consensus       153 l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~---------  220 (291)
T 3mkr_A          153 LKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAE---------  220 (291)
T ss_dssp             HHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHH---------
T ss_pred             HHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHH---------
Confidence            99998763  554322   22334445569999999999999876 3557788888888888888875542         


Q ss_pred             HHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          324 LELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                                  ..+.+.++.. .-+..+|+.++..+...|+.++++    .++++++.+
T Consensus       221 ------------~~l~~al~~~-p~~~~~l~~l~~~~~~~g~~~eaa----~~~~~~~~~  263 (291)
T 3mkr_A          221 ------------GVLQEALDKD-SGHPETLINLVVLSQHLGKPPEVT----NRYLSQLKD  263 (291)
T ss_dssp             ------------HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHH----HHHHHHHHH
T ss_pred             ------------HHHHHHHHhC-CCCHHHHHHHHHHHHHcCCCHHHH----HHHHHHHHH
Confidence                        2233333322 235567888888899999997752    688888876

>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=99.34  E-value=3.2e-10  Score=112.25  Aligned_cols=300  Identities=9%  Similarity=-0.061  Sum_probs=203.2

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .....|++++|.+.|+......+.+..+|..+...+.+.|+++.|...+.+++..+                       +
T Consensus        34 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-----------------------p   90 (537)
T 3fp2_A           34 HFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-----------------------P   90 (537)
T ss_dssp             HHHHTTCCC-CHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-----------------------T
T ss_pred             HHHHhccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-----------------------C
Confidence            34556788889999999988766689999999999999998877777777765322                       1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcC------------------------------------CCchhHHH--
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLG------------------------------------SRERELVL--  150 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~------------------------------------~~~~~~~~--  150 (425)
                      .+...+..+...+.+.|++++|.+.|+.+.....                                    .+......  
T Consensus        91 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~  170 (537)
T 3fp2_A           91 DHSKALLRRASANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASF  170 (537)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHH
Confidence            2455666666667777777777776643311100                                    00000000  


Q ss_pred             -------------------------HHHHHHHHHHhc-CCc----ccHHHHHHHHHHHhhcCCCCccC-----hhHHHHH
Q 042756          151 -------------------------FYCNLIDSFCKH-DSK----RGFDDTYARLNQLVNSSSSVYVK-----RQALKSM  195 (425)
Q Consensus       151 -------------------------~y~~li~~~~~~-g~~----~~~~~~~~~~~~~~~~~~~~~p~-----~~~~~~l  195 (425)
                                               ....+...+... +++    ....++...+.+.....+.. ++     ..+|..+
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~-~~~~~~~~~~~~~~  249 (537)
T 3fp2_A          171 FGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVD-DPLRENAALALCYT  249 (537)
T ss_dssp             HHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCC-HHHHHHHHHHHHHH
T ss_pred             HHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCc-chhhHHHHHHHHHH
Confidence                                     111111111111 000    02455666666665433211 11     2367777


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCH
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~  275 (425)
                      -..+...|++++|.+.|++....  .|+..++..+...+...|++++|.+.|+...+..- .+..+|..+...|...|++
T Consensus       250 g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~  326 (537)
T 3fp2_A          250 GIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNP-EYPPTYYHRGQMYFILQDY  326 (537)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCC-CCHHHHHHHHHHHHhcCCH
Confidence            88899999999999999999985  56788999999999999999999999999887542 3678899999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeec
Q 042756          276 SRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDS  355 (425)
Q Consensus       276 ~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  355 (425)
                      ++|...|++..+.. .-+...+..+...+...|+++.+.                     ..+.+.++. ...+...|..
T Consensus       327 ~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~---------------------~~~~~~~~~-~~~~~~~~~~  383 (537)
T 3fp2_A          327 KNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESE---------------------AFFNETKLK-FPTLPEVPTF  383 (537)
T ss_dssp             HHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHH---------------------HHHHHHHHH-CTTCTHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHH---------------------HHHHHHHHh-CCCChHHHHH
Confidence            99999999998753 224567777777777766665542                     122233322 2234567888


Q ss_pred             cccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          356 GETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       356 li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      +...|...|++++|     .+.|+++.+
T Consensus       384 l~~~~~~~g~~~~A-----~~~~~~a~~  406 (537)
T 3fp2_A          384 FAEILTDRGDFDTA-----IKQYDIAKR  406 (537)
T ss_dssp             HHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHhCCHHHH-----HHHHHHHHH
Confidence            88999999999999     999999887

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.32  E-value=9.7e-10  Score=95.23  Aligned_cols=215  Identities=11%  Similarity=-0.020  Sum_probs=161.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +...+..+...+...|+++.|...+.+++                     +..  +.+...+..+...|...|++++|.+
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~---------------------~~~--~~~~~~~~~l~~~~~~~~~~~~A~~   63 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDAL---------------------KSD--PKNELAWLVRAEIYQYLKVNDKAQE   63 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHH---------------------HhC--ccchHHHHHHHHHHHHcCChHHHHH
Confidence            45677777888888886666666665543                     322  1356788889999999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhc-CCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKH-DSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENL  211 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~-g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  211 (425)
                      .|++..+...    ....++..+...+... |+   .+++...+.+... .+....+...|..+..++.+.|++++|.+.
T Consensus        64 ~~~~a~~~~~----~~~~~~~~l~~~~~~~~~~---~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  135 (225)
T 2vq2_A           64 SFRQALSIKP----DSAEINNNYGWFLCGRLNR---PAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAY  135 (225)
T ss_dssp             HHHHHHHHCT----TCHHHHHHHHHHHHTTTCC---HHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHhCC----CChHHHHHHHHHHHHhcCc---HHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999887522    1234678889999999 99   4555555555554 111112356889999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 042756          212 IEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIP  291 (425)
Q Consensus       212 ~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~  291 (425)
                      |++..+.. +.+...+..+...+.+.|++++|.++++...+..-..+...+..+...+...|+.++|..+++.+.+.  .
T Consensus       136 ~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~  212 (225)
T 2vq2_A          136 LKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--F  212 (225)
T ss_dssp             HHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C
T ss_pred             HHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--C
Confidence            99998753 23478899999999999999999999999887542246778888888899999999999999998754  4


Q ss_pred             CCHHHHHHHH
Q 042756          292 FSVRTYNSVL  301 (425)
Q Consensus       292 pd~~t~~~ll  301 (425)
                      |+...+..++
T Consensus       213 p~~~~~~~~l  222 (225)
T 2vq2_A          213 PYSEELQTVL  222 (225)
T ss_dssp             TTCHHHHHHH
T ss_pred             CCCHHHHHHh
Confidence            6655554443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.31  E-value=1.8e-10  Score=100.36  Aligned_cols=200  Identities=11%  Similarity=-0.038  Sum_probs=138.0

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHH
Q 042756           51 TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEA  130 (425)
Q Consensus        51 ~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A  130 (425)
                      +++...+..+-..+.+.|+++.|...+.+.+..                     +  +-++..+..+-..+.+.|++++|
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---------------------~--p~~~~a~~~lg~~~~~~g~~~~A   58 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKE---------------------N--PQDPEALYWLARTQLKLGLVNPA   58 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTT---------------------S--SSCHHHHHHHHHHHHHTTCHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------------------C--CCCHHHHHHHHHHHHHcCCHHHH
Confidence            456677778888888888766666666665433                     2  13677888889999999999999


Q ss_pred             HHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc-----------CCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHH
Q 042756          131 ETLILETLSKLGSRERELVLFYCNLIDSFCKH-----------DSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGL  199 (425)
Q Consensus       131 ~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~-----------g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~  199 (425)
                      .+.|++..+..    |+....+..+-..+.+.           |+++   ++...+.+.....+.   +...|..+-..|
T Consensus        59 ~~~~~~al~~~----P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~---~A~~~~~~al~~~P~---~~~~~~~lg~~~  128 (217)
T 2pl2_A           59 LENGKTLVART----PRYLGGYMVLSEAYVALYRQAEDRERGKGYLE---QALSVLKDAERVNPR---YAPLHLQRGLVY  128 (217)
T ss_dssp             HHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHH---HHHHHHHHHHHHCTT---CHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC----CCcHHHHHHHHHHHHHhhhhhhhhcccccCHH---HHHHHHHHHHHhCcc---cHHHHHHHHHHH
Confidence            99999987752    22234677788888888           8844   444444444332211   235888888899


Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHH
Q 042756          200 CEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMV  279 (425)
Q Consensus       200 ~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~  279 (425)
                      ...|++++|+..|++..+..  .+...+..+-.+|...|++++|...|+...+.. +-+...+..+...+...|++++|.
T Consensus       129 ~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~  205 (217)
T 2pl2_A          129 ALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAA  205 (217)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC--------
T ss_pred             HHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHH
Confidence            99999999999999998877  678888999999999999999999999887753 235778888889999999999999


Q ss_pred             HHHHHHH
Q 042756          280 LWLQKMK  286 (425)
Q Consensus       280 ~l~~~M~  286 (425)
                      ..|++..
T Consensus       206 ~~~~~~~  212 (217)
T 2pl2_A          206 RAAALEH  212 (217)
T ss_dssp             -------
T ss_pred             HHHHHHh
Confidence            8887754

>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=99.30  E-value=2.9e-09  Score=94.29  Aligned_cols=211  Identities=10%  Similarity=0.029  Sum_probs=162.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHH
Q 042756           54 SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETL  133 (425)
Q Consensus        54 ~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l  133 (425)
                      ...|..+...+...|+++.|...+.+++                     ..+  +.+...+..+...|.+.|++++|.+.
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al---------------------~~~--~~~~~~~~~la~~~~~~~~~~~A~~~   93 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKAL---------------------EID--PSSADAHAALAVVFQTEMEPKLADEE   93 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHH---------------------HHC--TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHH---------------------hcC--CChHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4566777777888886666666655543                     222  23677888899999999999999999


Q ss_pred             HHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc-ChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          134 ILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV-KRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       134 ~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      |++..+....    ....+..+...|...|+   .+++...+.+.....  ..| +...|..+...+.+.|++++|.+.|
T Consensus        94 ~~~a~~~~~~----~~~~~~~la~~~~~~g~---~~~A~~~~~~~~~~~--~~~~~~~~~~~la~~~~~~g~~~~A~~~~  164 (252)
T 2ho1_A           94 YRKALASDSR----NARVLNNYGGFLYEQKR---YEEAYQRLLEASQDT--LYPERSRVFENLGLVSLQMKKPAQAKEYF  164 (252)
T ss_dssp             HHHHHHHCTT----CHHHHHHHHHHHHHTTC---HHHHHHHHHHHTTCT--TCTTHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHCcC----cHHHHHHHHHHHHHHhH---HHHHHHHHHHHHhCc--cCcccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            9998875321    23467888999999999   556666666665411  223 4568899999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF  292 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p  292 (425)
                      ++..+.. +.+...+..+...+.+.|++++|..+++...+.. ..+...+..+...|...|+.++|.++++++.+.  .|
T Consensus       165 ~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p  240 (252)
T 2ho1_A          165 EKSLRLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL--YP  240 (252)
T ss_dssp             HHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT
T ss_pred             HHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CC
Confidence            9998863 2357889999999999999999999999988753 346788999999999999999999999999875  46


Q ss_pred             CHHHHHHH
Q 042756          293 SVRTYNSV  300 (425)
Q Consensus       293 d~~t~~~l  300 (425)
                      +...+..+
T Consensus       241 ~~~~~~~~  248 (252)
T 2ho1_A          241 GSLEYQEF  248 (252)
T ss_dssp             TSHHHHHH
T ss_pred             CCHHHHHH
Confidence            55544433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.27  E-value=6.3e-10  Score=99.82  Aligned_cols=243  Identities=9%  Similarity=-0.039  Sum_probs=176.4

Q ss_pred             HhhHHHHHHHHHHhHHh-c---CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           33 ARLTKQGQRFLSSLALA-V---TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~-~---~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .+++++|.+.|+.+.+. .   +.+..+|..+...+...|+++.|...+.+++                     ..+  +
T Consensus        18 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al---------------------~~~--~   74 (275)
T 1xnf_A           18 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQAL---------------------AIR--P   74 (275)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--C
T ss_pred             cchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHH---------------------HcC--C
Confidence            47899999999999876 1   1256788888999999887777766666654                     222  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .+..++..+...|...|++++|.+.|++..+.... .   ..++..+...|.+.|++++   +...+.+....    .|+
T Consensus        75 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~-~---~~~~~~la~~~~~~g~~~~---A~~~~~~a~~~----~~~  143 (275)
T 1xnf_A           75 DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-Y---NYAHLNRGIALYYGGRDKL---AQDDLLAFYQD----DPN  143 (275)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-C---THHHHHHHHHHHHTTCHHH---HHHHHHHHHHH----CTT
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCcc-c---cHHHHHHHHHHHHhccHHH---HHHHHHHHHHh----CCC
Confidence            36788999999999999999999999999875322 2   2367889999999999554   44444444432    233


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc---CHHhHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV---DTVCSNMV  265 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~---~~~~yn~l  265 (425)
                      ...+...+..+...|++++|...|++..... .++...+. +...+...++.++|.+.+....+.....   +..+|..+
T Consensus       144 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l  221 (275)
T 1xnf_A          144 DPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYL  221 (275)
T ss_dssp             CHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHH
Confidence            3355556666677899999999998887752 33444444 7777888899999999999887642211   26889999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN  315 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~  315 (425)
                      ...|...|++++|...|++..+.  .|+.  +.....++...|++.+++.
T Consensus       222 a~~~~~~g~~~~A~~~~~~al~~--~p~~--~~~~~~~~~~l~~~~~a~~  267 (275)
T 1xnf_A          222 GKYYLSLGDLDSATALFKLAVAN--NVHN--FVEHRYALLELSLLGQDQD  267 (275)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTT--CCTT--CHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhC--Cchh--HHHHHHHHHHHHHHHhhHH
Confidence            99999999999999999999875  4533  2223446667777766643

>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=99.24  E-value=1.3e-09  Score=96.62  Aligned_cols=191  Identities=11%  Similarity=-0.016  Sum_probs=150.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      +..+..+...+...|++++|.+.|++..+...    .....+..+...|.+.|+++++.+.++...+.   .+   .+..
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~----~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~---~~---~~~~  106 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDP----SSADAHAALAVVFQTEMEPKLADEEYRKALAS---DS---RNAR  106 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CT---TCHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCC----ChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---Cc---CcHH
Confidence            56788888999999999999999999887522    22346788999999999955555444444443   21   2345


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .|..+...|...|++++|.++|++....+..| +...+..+...+.+.|++++|.+.|+...+.. +.+...|..+...|
T Consensus       107 ~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~  185 (252)
T 2ho1_A          107 VLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLL  185 (252)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHH
Confidence            89999999999999999999999998854556 46688889999999999999999999988764 23688899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      ...|++++|..+|++..+.. ..+...+..+...+...|+.+.+
T Consensus       186 ~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A  228 (252)
T 2ho1_A          186 YKEREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTA  228 (252)
T ss_dssp             HHTTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHH
Confidence            99999999999999988653 34566677777777766666554

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.22  E-value=1.8e-09  Score=93.49  Aligned_cols=190  Identities=7%  Similarity=-0.021  Sum_probs=146.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++..+..+...+...|++++|.+.|++..+.... .   ...+..+...|...|+++.+.+.++...+.   .+   .+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~---~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~---~~---~~~   76 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSDPK-N---ELAWLVRAEIYQYLKVNDKAQESFRQALSI---KP---DSA   76 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-C---HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CT---TCH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCcc-c---hHHHHHHHHHHHHcCChHHHHHHHHHHHHh---CC---CCh
Confidence            5667888899999999999999999998875321 2   336788999999999955544444444433   21   234


Q ss_pred             hHHHHHHHHHHhc-CChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          190 QALKSMISGLCEM-GQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       190 ~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      .+|..+...|... |++++|.+.|+++.+.+..|+ ...+..+..++.+.|++++|.+.|+...+..- .+...|..+..
T Consensus        77 ~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~  155 (225)
T 2vq2_A           77 EINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQP-QFPPAFKELAR  155 (225)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCchHHHHHHH
Confidence            5899999999999 999999999999998444454 66889999999999999999999999887542 35888999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSM  310 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~  310 (425)
                      .|...|++++|..+|++..+..-..+...+..+...+...|+.
T Consensus       156 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (225)
T 2vq2_A          156 TKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNA  198 (225)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcH
Confidence            9999999999999999987653113555665555555444443

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.22  E-value=8.2e-10  Score=97.89  Aligned_cols=230  Identities=10%  Similarity=-0.005  Sum_probs=164.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-h
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-R  189 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~  189 (425)
                      +..+..+-..+...|++++|.+.|++..+..  ..+   ..|..+...|...|+++.+.+.++...+..+......|. .
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~---~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~   79 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDI---TYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVIS   79 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCT---HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccH---HHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHH
Confidence            4567778888889999999999999988765  232   267788888999999666555555555543332111111 4


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .+|..+...|.+.|++++|...|++....  .|+.       ..+.+.|++++|.+.++...... +.+...|..+...|
T Consensus        80 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~  149 (258)
T 3uq3_A           80 KSFARIGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEY  149 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHH
Confidence            68889999999999999999999999884  4553       34666788999999999888753 23567888888899


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcc
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDE  349 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (425)
                      ...|++++|...|++..+.. ..+..++..+...+...|+++.++.                     .+.+.++. ...+
T Consensus       150 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~---------------------~~~~al~~-~~~~  206 (258)
T 3uq3_A          150 FTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIA---------------------DCNKAIEK-DPNF  206 (258)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH---------------------HHHHHHHH-CTTC
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHH---------------------HHHHHHHh-CHHH
Confidence            99999999999999987653 2356677777777776666654421                     22222222 1234


Q ss_pred             cceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          350 AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       350 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ..+|..+...|...|++++|     .+.|++..+
T Consensus       207 ~~~~~~l~~~~~~~g~~~~A-----~~~~~~a~~  235 (258)
T 3uq3_A          207 VRAYIRKATAQIAVKEYASA-----LETLDAART  235 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHH-----HHHHHHHHH
Confidence            56677888889999999999     888888876

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.21  E-value=7.8e-10  Score=96.30  Aligned_cols=190  Identities=11%  Similarity=-0.059  Sum_probs=147.6

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      +++..+..+-..+.+.|++++|...|++..+.    .|.....+..+-..+.+.|+++++.+.++...+..+.      +
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~----~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~------~   72 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKE----NPQDPEALYWLARTQLKLGLVNPALENGKTLVARTPR------Y   72 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTT----SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------C
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC------c
Confidence            46667788888999999999999999998764    2333446788999999999955544444444443221      3


Q ss_pred             hhHHHHHHHHHHhc-----------CChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          189 RQALKSMISGLCEM-----------GQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       189 ~~~~~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ...|..+-.++.+.           |++++|...|++..+.  .| +...+..+-.++...|++++|...|+...+..  
T Consensus        73 ~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--  148 (217)
T 2pl2_A           73 LGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--  148 (217)
T ss_dssp             HHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--
Confidence            45899999999999           9999999999999885  45 46788999999999999999999999998877  


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHhh
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      .+...|..+-..|...|++++|...|++..+.  .| +...+..+...+...|+.+++.
T Consensus       149 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~  205 (217)
T 2pl2_A          149 DTPEIRSALAELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYASALLLKGKAEEAA  205 (217)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTC--------
T ss_pred             cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHH
Confidence            68899999999999999999999999998875  34 5567777777777777776653

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.21  E-value=6.6e-09  Score=91.92  Aligned_cols=207  Identities=10%  Similarity=-0.022  Sum_probs=107.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHH
Q 042756           54 SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETL  133 (425)
Q Consensus        54 ~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l  133 (425)
                      ...|..+-..+...|+++.|...+.+.+                     +.+   .+...+..+...+...|++++|.+.
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~---------------------~~~---~~~~~~~~~~~~~~~~~~~~~A~~~   60 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAW---------------------ELH---KDITYLNNRAAAEYEKGEYETAIST   60 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHS---CCTHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHH---------------------Hhh---ccHHHHHHHHHHHHHcccHHHHHHH
Confidence            3456667777777776666665555543                     333   3556677777777777777777777


Q ss_pred             HHHHHHhcCC---CchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCC-------------------CCcc-Chh
Q 042756          134 ILETLSKLGS---RERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSS-------------------SVYV-KRQ  190 (425)
Q Consensus       134 ~~~m~~~~~~---~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~-------------------~~~p-~~~  190 (425)
                      |++..+....   ..+....+|..+...|.+.|+++.+.+.++...+..+...                   ...| +..
T Consensus        61 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  140 (258)
T 3uq3_A           61 LNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAE  140 (258)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_pred             HHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHH
Confidence            7776653111   1111134566777777777774443333333333210000                   0001 123


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .|..+...+...|++++|...|++..... +.+..+|..+..+|.+.|++++|.+.|+...+.. +.+...|..+...|.
T Consensus       141 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~  218 (258)
T 3uq3_A          141 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQI  218 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHH
Confidence            45555555555555555555555554432 1234455555555555555555555555554432 123445555555555


Q ss_pred             hcCCHHHHHHHHHHHH
Q 042756          271 DHNELSRMVLWLQKMK  286 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~  286 (425)
                      ..|++++|...|++..
T Consensus       219 ~~g~~~~A~~~~~~a~  234 (258)
T 3uq3_A          219 AVKEYASALETLDAAR  234 (258)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHH
Confidence            5555555555555543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.21  E-value=1.2e-09  Score=99.71  Aligned_cols=220  Identities=10%  Similarity=0.071  Sum_probs=159.3

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +..++..+...+...|+++.|...+.+++              +++......+ ......++..+...|...|++++|.+
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~--------------~~~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~   90 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQAL--------------EDLEKTSGHD-HPDVATMLNILALVYRDQNKYKDAAN   90 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHHHCSS-SHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHH--------------HHHHHHcCCC-CHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            45677888888899998888888777743              3333333222 22356678889999999999999999


Q ss_pred             HHHHHHHhc----CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC--CCCccChhHHHHHHHHHHhcCChh
Q 042756          133 LILETLSKL----GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS--SSVYVKRQALKSMISGLCEMGQPH  206 (425)
Q Consensus       133 l~~~m~~~~----~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~--~~~~p~~~~~~~li~~~~~~g~~~  206 (425)
                      .|++..+..    +...+....++..+...|...|+++++.+.+....+.....  .........|..+...|...|+++
T Consensus        91 ~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~  170 (311)
T 3nf1_A           91 LLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYE  170 (311)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHH
Confidence            999987642    12234445678889999999999666555555554443111  111223458899999999999999


Q ss_pred             HHHHHHHHHHHc------CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--------------------------
Q 042756          207 EAENLIEEMRVK------GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESD--------------------------  253 (425)
Q Consensus       207 ~a~~~~~~m~~~------g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~--------------------------  253 (425)
                      +|.++|++....      +-.|+ ..++..+...|.+.|++++|.++|+...+.                          
T Consensus       171 ~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (311)
T 3nf1_A          171 EVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREEC  250 (311)
T ss_dssp             HHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHh
Confidence            999999999875      22443 457888999999999999999999988752                          


Q ss_pred             ----------------------CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          254 ----------------------GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       254 ----------------------g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                                            .-..+..+|..+...|.+.|++++|.++|++..+
T Consensus       251 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          251 KGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             -------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                                  1122456777888888888888888888887654

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.21  E-value=8.6e-10  Score=96.96  Aligned_cols=201  Identities=11%  Similarity=0.030  Sum_probs=138.2

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +..+|..+...+...|+++.|...+.+++                     +.+  +.+...+..+...+.+.|++++|.+
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l---------------------~~~--~~~~~~~~~la~~~~~~~~~~~A~~   78 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAI---------------------EEN--KEDAIPYINFANLLSSVNELERALA   78 (243)
T ss_dssp             --------------------CCTTHHHHH---------------------TTC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHH---------------------HhC--cccHHHHHHHHHHHHHcCCHHHHHH
Confidence            34455555555666665555554444443                     322  2357788888889999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      .|++..+...    .....+..+...+...|+++.+.+.++...+..+      .+...|..+...+.+.|++++|...|
T Consensus        79 ~~~~~~~~~~----~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~------~~~~~~~~~a~~~~~~~~~~~A~~~~  148 (243)
T 2q7f_A           79 FYDKALELDS----SAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGM------ENGDLFYMLGTVLVKLEQPKLALPYL  148 (243)
T ss_dssp             HHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTC------CSHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCC----cchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC------CCHHHHHHHHHHHHHhccHHHHHHHH
Confidence            9999877522    1234677888889999995555554444444321      23458889999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ++..+.. +.+...+..+...+.+.|++++|.+.|+...+.. ..+..+|..+...|...|++++|.+.|++..+.
T Consensus       149 ~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          149 QRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc
Confidence            9988753 3357788899999999999999999999888753 235788999999999999999999999998764

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.19  E-value=5.5e-10  Score=101.96  Aligned_cols=255  Identities=9%  Similarity=0.000  Sum_probs=168.8

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHh----cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC--
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSK----LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS--  182 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~----~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~--  182 (425)
                      .+..++..+...+...|++++|.++|++..+.    .+...+....++..+...|...|+++.+.+.++...+.....  
T Consensus        25 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  104 (311)
T 3nf1_A           25 ARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLG  104 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhC
Confidence            35677888999999999999999999998762    111244445678889999999999666555555544443211  


Q ss_pred             CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--
Q 042756          183 SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK------GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD--  253 (425)
Q Consensus       183 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~--  253 (425)
                      ........+|..+...|...|++++|.+.|++..+.      +-.| ...++..+...+...|++++|.++|+...+.  
T Consensus       105 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~  184 (311)
T 3nf1_A          105 KDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQ  184 (311)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            111223568999999999999999999999999875      3333 3557888999999999999999999988764  


Q ss_pred             ----CCCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC-------CCCCCHHHHHHHHHHHHHHHHHHHhhccCCchh
Q 042756          254 ----GTRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDS-------GIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPL  321 (425)
Q Consensus       254 ----g~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~-------g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~  321 (425)
                          +-.| ...++..+...|...|++++|..+|+++.+.       ...|...........+...+.....        
T Consensus       185 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  256 (311)
T 3nf1_A          185 TKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKD--------  256 (311)
T ss_dssp             HTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC--------------
T ss_pred             HHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhh--------
Confidence                2122 4568999999999999999999999998752       2233333322223332222221111        


Q ss_pred             hHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          322 SILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                             ......+....+........+..+|..+...|.+.|++++|     .++|++..+
T Consensus       257 -------~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~al~  306 (311)
T 3nf1_A          257 -------GTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAA-----ETLEEAAMR  306 (311)
T ss_dssp             --------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHH
T ss_pred             -------HHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH
Confidence                   01111111111111111123345788889999999999999     999988775

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.18  E-value=3.5e-10  Score=101.52  Aligned_cols=210  Identities=10%  Similarity=-0.023  Sum_probs=150.9

Q ss_pred             CCchhhhHHHHHHHhhhcCCCc--cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCC
Q 042756           87 HPRLSSLAFPLYMRITEESWFQ--WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDS  164 (425)
Q Consensus        87 ~~~~~~~a~~lf~~m~~~~~~~--~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~  164 (425)
                      ..+.+++|++.|+.+.+.....  .+..++..+...+...|++++|.+.|++..+....    ...+|..+...|...|+
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~----~~~~~~~la~~~~~~~~   92 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD----MPEVFNYLGIYLTQAGN   92 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC----CHHHHHHHHHHHHHTTC
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCC----cHHHHHHHHHHHHHccC
Confidence            3457889999999887653221  25678888999999999999999999998875322    23468889999999999


Q ss_pred             cccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHH
Q 042756          165 KRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~  244 (425)
                      ++++.+.++...+..+.      +..+|..+...|.+.|++++|.+.|+++.+.  .|+.......+..+...|++++|.
T Consensus        93 ~~~A~~~~~~al~~~~~------~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~  164 (275)
T 1xnf_A           93 FDAAYEAFDSVLELDPT------YNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAK  164 (275)
T ss_dssp             HHHHHHHHHHHHHHCTT------CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHH
T ss_pred             HHHHHHHHHHHHhcCcc------ccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHH
Confidence            65555555544443221      3459999999999999999999999999884  465555555666667889999999


Q ss_pred             HHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--C-CHHHHHHHHHHHHHHHHH
Q 042756          245 RIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIP--F-SVRTYNSVLNSCSTIMSM  310 (425)
Q Consensus       245 ~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~--p-d~~t~~~ll~~~~~~~~~  310 (425)
                      ..++...... .++...|+ ++..+...++.++|...+.+..+..-.  | +..++..+...|...|+.
T Consensus       165 ~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  231 (275)
T 1xnf_A          165 EVLKQHFEKS-DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDL  231 (275)
T ss_dssp             HHHHHHHHHS-CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhcC-CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCH
Confidence            9998777643 23444444 778888888999999999988654211  0 134445555555444444

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.17  E-value=4.3e-09  Score=100.46  Aligned_cols=241  Identities=14%  Similarity=0.016  Sum_probs=173.9

Q ss_pred             HHHHhhHHHHHHHHHHhHHhcCCCH----HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcC
Q 042756           30 CLTARLTKQGQRFLSSLALAVTRDS----KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEES  105 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~~~~d~----~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~  105 (425)
                      ....|++++|.+.|+......+.+.    .+|..+-..+...|+++.|...+.+.+              +++.....  
T Consensus        58 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al--------------~~~~~~~~--  121 (411)
T 4a1s_A           58 LCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDL--------------TLAKSMND--  121 (411)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH--------------HHHHHTTC--
T ss_pred             HHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--------------HHHHHccC--
Confidence            3566799999999999988733343    578888899999999888888777743              33333221  


Q ss_pred             CCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCC-----------------cc
Q 042756          106 WFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDS-----------------KR  166 (425)
Q Consensus       106 ~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~-----------------~~  166 (425)
                       ......++..+-..|...|++++|.+.|++..+..  ....+....++..+-..|...|+                 ++
T Consensus       122 -~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~  200 (411)
T 4a1s_A          122 -RLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALT  200 (411)
T ss_dssp             -HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHH
T ss_pred             -chHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHH
Confidence             22355678889999999999999999999876521  11233445577888888888888                 66


Q ss_pred             cHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHcCCCHH
Q 042756          167 GFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGL-EPS----GFEYKCIIYGYGRLGLLE  241 (425)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~----~~ty~~ll~~~~~~g~~~  241 (425)
                      .+.+.+....+.............+|..+...|...|++++|.+.|++..+..- .++    ..++..+...|...|+++
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            666555554444332211112235888899999999999999999999876411 011    237888899999999999


Q ss_pred             HHHHHHHHHHHCC----CC-cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          242 DMERIVNQMESDG----TR-VDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       242 ~a~~~~~~m~~~g----~~-~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +|.+.++...+..    -. ....++..+...|...|++++|..+|++..+
T Consensus       281 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  331 (411)
T 4a1s_A          281 DAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLA  331 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999776531    11 1257888899999999999999999998764

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.15  E-value=4.4e-09  Score=96.67  Aligned_cols=268  Identities=16%  Similarity=0.050  Sum_probs=186.3

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCC----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRD----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      .....|++++|.+.|+...+..+.+    ...+..+...+...|+++.|...+.+.+              ++...... 
T Consensus        14 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al--------------~~~~~~~~-   78 (338)
T 3ro2_A           14 RLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDL--------------TLARTIGD-   78 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHHTC-
T ss_pred             HHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH--------------HHhhcccc-
Confidence            3456789999999999998873334    4778889999999999998888777743              23333211 


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCC------------------
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDS------------------  164 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~------------------  164 (425)
                        ......++..+...+...|++++|.+.+++..+..  ....+....++..+...|...|+                  
T Consensus        79 --~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~  156 (338)
T 3ro2_A           79 --QLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVR  156 (338)
T ss_dssp             --HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHH
T ss_pred             --cHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHH
Confidence              22345678889999999999999999999876521  11222334467778888888888                  


Q ss_pred             --cccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcC
Q 042756          165 --KRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEP-SGFEYKCIIYGYGRL  237 (425)
Q Consensus       165 --~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~  237 (425)
                        ++.+.+.++...+.............++..+...+...|++++|.+.|++..+.    +..+ ...++..+...+...
T Consensus       157 ~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~  236 (338)
T 3ro2_A          157 NALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFL  236 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHc
Confidence              665555555444433222111122358888999999999999999999998753    1111 133888889999999


Q ss_pred             CCHHHHHHHHHHHHHC----CCCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHHH
Q 042756          238 GLLEDMERIVNQMESD----GTRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDS----GIPF-SVRTYNSVLNSCSTI  307 (425)
Q Consensus       238 g~~~~a~~~~~~m~~~----g~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~----g~~p-d~~t~~~ll~~~~~~  307 (425)
                      |++++|.+.++...+.    +-.+ ...++..+...|...|++++|...|++..+.    +-.+ ...++..+-..+...
T Consensus       237 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~  316 (338)
T 3ro2_A          237 GEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTAL  316 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHc
Confidence            9999999999987642    1111 1678888999999999999999999987642    1111 123555566666666


Q ss_pred             HHHHHh
Q 042756          308 MSMLQD  313 (425)
Q Consensus       308 ~~~~~~  313 (425)
                      |+++++
T Consensus       317 g~~~~A  322 (338)
T 3ro2_A          317 GNHDQA  322 (338)
T ss_dssp             TCHHHH
T ss_pred             CChHHH
Confidence            665554

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.13  E-value=7.4e-09  Score=98.22  Aligned_cols=270  Identities=15%  Similarity=0.033  Sum_probs=190.5

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCC----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhh
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRD----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITE  103 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~  103 (425)
                      ......|++++|.+.|+......+.+    ..+|..+-..+...|+++.|...+.+.+              .+......
T Consensus        17 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al--------------~~~~~~~~   82 (406)
T 3sf4_A           17 ERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDL--------------TLARTIGD   82 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHTTC
T ss_pred             HHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH--------------HHHHhccc
Confidence            34466789999999999998873334    4678888899999999888888777743              33333211


Q ss_pred             cCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCC-----------------
Q 042756          104 ESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDS-----------------  164 (425)
Q Consensus       104 ~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~-----------------  164 (425)
                         ......++..+...|...|++++|.+.+++..+..  .........++..+-..|...|+                 
T Consensus        83 ---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a  159 (406)
T 3sf4_A           83 ---QLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEV  159 (406)
T ss_dssp             ---HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHH
T ss_pred             ---cHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhH
Confidence               11245678888999999999999999999876521  11222334467788888888888                 


Q ss_pred             ---cccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCC----HHHHHHHHHHHHc
Q 042756          165 ---KRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKG-LEPS----GFEYKCIIYGYGR  236 (425)
Q Consensus       165 ---~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~----~~ty~~ll~~~~~  236 (425)
                         ++.+.+.+....+.............+|+.+...|...|++++|...|++..+.. -.++    ..++..+...|..
T Consensus       160 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~  239 (406)
T 3sf4_A          160 RDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIF  239 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHH
Confidence               6666666555555433332222224588999999999999999999999987541 1122    3488889999999


Q ss_pred             CCCHHHHHHHHHHHHHC----CCCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHHH
Q 042756          237 LGLLEDMERIVNQMESD----GTRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGI-PFS----VRTYNSVLNSCST  306 (425)
Q Consensus       237 ~g~~~~a~~~~~~m~~~----g~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~-~pd----~~t~~~ll~~~~~  306 (425)
                      .|++++|...++...+.    +-.+ ...++..+...|...|++++|...|++..+..- .++    ..++..+-..|..
T Consensus       240 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~  319 (406)
T 3sf4_A          240 LGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTA  319 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             cCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHH
Confidence            99999999999987642    2111 167888999999999999999999999764210 112    3456666666777


Q ss_pred             HHHHHHhh
Q 042756          307 IMSMLQDL  314 (425)
Q Consensus       307 ~~~~~~~~  314 (425)
                      .|+..++.
T Consensus       320 ~g~~~~A~  327 (406)
T 3sf4_A          320 LGNHDQAM  327 (406)
T ss_dssp             HTCHHHHH
T ss_pred             cCCHHHHH
Confidence            77766653

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.13  E-value=8.9e-09  Score=86.61  Aligned_cols=172  Identities=10%  Similarity=-0.001  Sum_probs=138.0

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++.+|..+-..|.+.|++++|.+.|++..+.    .|.....|..+...|.+.|+++.+.+.+.......+.      +.
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~------~~   73 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKA----DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT------SA   73 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC------CH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch------hH
Confidence            6778999999999999999999999998875    2233447888999999999955544444444333221      23


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..+..+...+...++++.|...+.+..... +-+...+..+-.+|.+.|++++|.+.|+...+.. +.+..+|..+-..|
T Consensus        74 ~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~  151 (184)
T 3vtx_A           74 EAYYILGSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAY  151 (184)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHH
Confidence            478888889999999999999999988752 2357788999999999999999999999988764 23678999999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      .+.|++++|.+.|++..+.  .|+..
T Consensus       152 ~~~g~~~~A~~~~~~al~~--~p~~a  175 (184)
T 3vtx_A          152 EGKGLRDEAVKYFKKALEK--EEKKA  175 (184)
T ss_dssp             HHTTCHHHHHHHHHHHHHT--THHHH
T ss_pred             HHCCCHHHHHHHHHHHHhC--CccCH
Confidence            9999999999999998864  45543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.13  E-value=3.6e-09  Score=94.78  Aligned_cols=241  Identities=10%  Similarity=-0.072  Sum_probs=161.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..+-.....+.+.|++++|.+.|++..+.... ..   ..+..+...|.+.|++   +++...+.+..............
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~-~~---~~~~~l~~~~~~~~~~---~~A~~~~~~a~~~~~~~~~~~~~   76 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKKYN-SP---YIYNRRAVCYYELAKY---DLAQKDIETYFSKVNATKAKSAD   76 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCC-CS---TTHHHHHHHHHHTTCH---HHHHHHHHHHHTTSCTTTCCHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-cH---HHHHHHHHHHHHHhhH---HHHHHHHHHHHhccCchhHHHHH
Confidence            34445677888999999999999998875322 22   2567788899999995   45555555554422111122346


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      |..+...|...|++++|.+.|++..+.. +.+..++..+-..|.+.|++++|.+.|+...+.. +.+...|..+...+..
T Consensus        77 ~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~  154 (272)
T 3u4t_A           77 FEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYY  154 (272)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHH
Confidence            8999999999999999999999998853 2245789999999999999999999999887762 2356677777624445


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCc--
Q 042756          272 HNELSRMVLWLQKMKDSGIPFS-VRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLD--  348 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  348 (425)
                      .+++++|.+.|++..+.  .|+ ...+..+...+...++.      ..+...+..+         ..+.++......+  
T Consensus       155 ~~~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~------~~~~~A~~~~---------~~a~~~~~~~~~~~~  217 (272)
T 3u4t_A          155 NKEYVKADSSFVKVLEL--KPNIYIGYLWRARANAAQDPD------TKQGLAKPYY---------EKLIEVCAPGGAKYK  217 (272)
T ss_dssp             TTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHSTT------CSSCTTHHHH---------HHHHHHHGGGGGGGH
T ss_pred             HHHHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHcCcc------hhhHHHHHHH---------HHHHHHHhcccccch
Confidence            56999999999999875  344 44454444444443320      0011111111         1111122111111  


Q ss_pred             --ccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          349 --EAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       349 --~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                        -..+|..+-..|...|++++|     .+.|++..+
T Consensus       218 ~~~~~~~~~l~~~~~~~~~~~~A-----~~~~~~al~  249 (272)
T 3u4t_A          218 DELIEANEYIAYYYTINRDKVKA-----DAAWKNILA  249 (272)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHh
Confidence              124677788888999999999     999999987

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.11  E-value=8e-08  Score=95.27  Aligned_cols=341  Identities=6%  Similarity=-0.088  Sum_probs=214.9

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-------------chhhh----
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-------------RLSSL----   93 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-------------~~~~~----   93 (425)
                      ...|..++|..+|+.+....+-+...|..++..+.+.|+.+.|..+|.+++.......             +..+.    
T Consensus        23 ~~~~~~~~a~~~~e~al~~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~~~~~~~~~~~~a~~~  102 (530)
T 2ooe_A           23 AQNQPIDKARKTYERLVAQFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEK  102 (530)
T ss_dssp             HHSSCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHTTTSTTHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHccchhhHHHH
Confidence            3467899999999999887777899999999999999999999999999987653110             11222    


Q ss_pred             HHHHHHHhhhcCCCc-cCHHHHHHHHHHHHh---------cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHH---HH
Q 042756           94 AFPLYMRITEESWFQ-WNPKLVAEIIAFLDK---------QGQREEAETLILETLSKLGSRERELVLFYCNLIDS---FC  160 (425)
Q Consensus        94 a~~lf~~m~~~~~~~-~~~~~~~~ll~~~~~---------~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~---~~  160 (425)
                      +.++|+.....-+.. .+...|...+....+         .|+++.|..+|++..+.   |.......|......   +.
T Consensus       103 ~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~---P~~~~~~~~~~~~~~e~~~~  179 (530)
T 2ooe_A          103 MAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVN---PMINIEQLWRDYNKYEEGIN  179 (530)
T ss_dssp             HHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTS---CCTTHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhc---hhhhHHHHHHHHHHHHHhhc
Confidence            233666654331222 355677766666554         68899999999998762   222212233322221   10


Q ss_pred             ----------hcCCcccHHHHHHHHHH---HhhcC-CCCccC--------hhHHHHHHHHHHhc----CCh----hHHHH
Q 042756          161 ----------KHDSKRGFDDTYARLNQ---LVNSS-SSVYVK--------RQALKSMISGLCEM----GQP----HEAEN  210 (425)
Q Consensus       161 ----------~~g~~~~~~~~~~~~~~---~~~~~-~~~~p~--------~~~~~~li~~~~~~----g~~----~~a~~  210 (425)
                                +.+++..+..++..+..   ..... ..+.|+        ...|...+..-...    ++.    +.|..
T Consensus       180 ~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~  259 (530)
T 2ooe_A          180 IHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMF  259 (530)
T ss_dssp             HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHH
T ss_pred             hhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHH
Confidence                      11222222222222111   11111 012333        24666666443332    222    37778


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHc-------CCCHH-------HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHH
Q 042756          211 LIEEMRVKGLEPSGFEYKCIIYGYGR-------LGLLE-------DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELS  276 (425)
Q Consensus       211 ~~~~m~~~g~~p~~~ty~~ll~~~~~-------~g~~~-------~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~  276 (425)
                      +|++.... .+-+...|......+.+       .|+++       +|..+|+...+.-.+-+...|..+...+.+.|+++
T Consensus       260 ~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~  338 (530)
T 2ooe_A          260 AYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYE  338 (530)
T ss_dssp             HHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHH
Confidence            88888875 22356777777777765       78887       88999998876222335888999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCH--HHHHHHHHHHHHHHHHHHhhc---------cCCchhhHH-HH---HhhcchhhHHHHHH-
Q 042756          277 RMVLWLQKMKDSGIPFSV--RTYNSVLNSCSTIMSMLQDLN---------SNDFPLSIL-EL---TEVLNEEEVSVVKE-  340 (425)
Q Consensus       277 ~A~~l~~~M~~~g~~pd~--~t~~~ll~~~~~~~~~~~~~~---------~~~~~~~~~-~~---~~~~~~~~~~~~~~-  340 (425)
                      +|..+|++..+.  .|+.  ..|......+.+.|+++.+..         +..+...+. .+   ...+..+.+..+.+ 
T Consensus       339 ~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~  416 (530)
T 2ooe_A          339 KVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFEL  416 (530)
T ss_dssp             HHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHH
Confidence            999999998874  5643  467777777777777766632         112222222 11   23444455544433 


Q ss_pred             HHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          341 LEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       341 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .++. ...+...|..++..+.+.|+.++|     ..+|++...
T Consensus       417 al~~-~p~~~~~~~~~~~~~~~~g~~~~A-----r~~~~~al~  453 (530)
T 2ooe_A          417 GLKK-YGDIPEYVLAYIDYLSHLNEDNNT-----RVLFERVLT  453 (530)
T ss_dssp             HHHH-HTTCHHHHHHHHHHHTTTTCHHHH-----HHHHHHHHH
T ss_pred             HHHH-CCCCHHHHHHHHHHHHhCCCHhhH-----HHHHHHHHh
Confidence            3332 223467889999999999999999     999999987

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.08  E-value=9.8e-09  Score=90.09  Aligned_cols=192  Identities=9%  Similarity=-0.069  Sum_probs=143.3

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .....|++++|.+.|+......+.+..++..+...+...|+++.|...+.+.+.                     .+  +
T Consensus        32 ~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~---------------------~~--~   88 (243)
T 2q7f_A           32 RGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALE---------------------LD--S   88 (243)
T ss_dssp             ----------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------------HC--T
T ss_pred             HHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---------------------cC--C
Confidence            345678999999999998876566789999999999999877777766666532                     22  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .+..++..+...+...|++++|.+.|++..+.... .   ...+..+...+.+.|+++.+.+.++...+..+      .+
T Consensus        89 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~---~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~------~~  158 (243)
T 2q7f_A           89 SAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGME-N---GDLFYMLGTVLVKLEQPKLALPYLQRAVELNE------ND  158 (243)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCC-S---HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT------TC
T ss_pred             cchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-C---HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC------cc
Confidence            36778888999999999999999999998875322 2   23677888999999995554444444443321      23


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      ...|..+...+.+.|++++|.+.|++..... +.+..++..+..+|.+.|++++|.+.++...+..
T Consensus       159 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          159 TEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            4589999999999999999999999998763 3357799999999999999999999999998753

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.07  E-value=5.7e-08  Score=89.20  Aligned_cols=226  Identities=10%  Similarity=-0.037  Sum_probs=164.3

Q ss_pred             HHHHHHHHHhHHhcCCCHHHHHHHHHHHHhc-------CChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc-CCCc
Q 042756           37 KQGQRFLSSLALAVTRDSKAASRLISKFVAS-------SPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE-SWFQ  108 (425)
Q Consensus        37 ~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~-------~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~-~~~~  108 (425)
                      ++|..+|++.....+.+...|..+...+...       |+....              .+..++|..+|++.... +  +
T Consensus        33 ~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~--------------~~~~~~A~~~~~rAl~~~~--p   96 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNA--------------KLFSDEAANIYERAISTLL--K   96 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHH--------------HHHHHHHHHHHHHHHTTTT--T
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhc--------------ccchHHHHHHHHHHHHHhC--c
Confidence            6788889888877677888898888887643       432100              01235666666665542 2  1


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      -+...|..+...+.+.|++++|.++|++..+..  |... ...|..+...+.+.|+.   +++...+.+.....+   ++
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~-~~~~~~~~~~~~~~~~~---~~A~~~~~~a~~~~p---~~  167 (308)
T 2ond_A           97 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIE--DIDP-TLVYIQYMKFARRAEGI---KSGRMIFKKAREDAR---TR  167 (308)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSS--SSCT-HHHHHHHHHHHHHHHCH---HHHHHHHHHHHTSTT---CC
T ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcc--ccCc-cHHHHHHHHHHHHhcCH---HHHHHHHHHHHhcCC---CC
Confidence            256688889999999999999999999998741  1111 12678888889999984   555555555544321   22


Q ss_pred             hhHHHHHHHHHH-hcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCc--CHHhHHH
Q 042756          189 RQALKSMISGLC-EMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG-TRV--DTVCSNM  264 (425)
Q Consensus       189 ~~~~~~li~~~~-~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g-~~~--~~~~yn~  264 (425)
                      ...|........ ..|++++|..+|++..+.. +-+...|..++..+.+.|++++|..+|+...+.. +.|  ....|..
T Consensus       168 ~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~  246 (308)
T 2ond_A          168 HHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWAR  246 (308)
T ss_dssp             THHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHH
Confidence            335544333322 3699999999999998752 2257789999999999999999999999999863 455  4678999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          265 VLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       265 li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ++..+.+.|+.++|..+++++.+.
T Consensus       247 ~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          247 FLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999998764

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.07  E-value=5.2e-08  Score=87.10  Aligned_cols=234  Identities=7%  Similarity=-0.032  Sum_probs=175.1

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ......|.+++|.+.|+...+..+.+...+..+...+...|+++.|...+.+.+...                    +..
T Consensus        11 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--------------------~~~   70 (272)
T 3u4t_A           11 DFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV--------------------NAT   70 (272)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS--------------------CTT
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc--------------------Cch
Confidence            344567899999999999987644566688889999999998888888888776521                    112


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      ......|..+...+.+.|++++|.+.|++..+.... .   ..+|..+...|...|+   .+++...+.+.....+   -
T Consensus        71 ~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~-~---~~~~~~l~~~~~~~~~---~~~A~~~~~~al~~~~---~  140 (272)
T 3u4t_A           71 KAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTT-R---LDMYGQIGSYFYNKGN---FPLAIQYMEKQIRPTT---T  140 (272)
T ss_dssp             TCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-C---THHHHHHHHHHHHTTC---HHHHHHHHGGGCCSSC---C
T ss_pred             hHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcc-c---HHHHHHHHHHHHHccC---HHHHHHHHHHHhhcCC---C
Confidence            234566888999999999999999999998875322 2   2368899999999999   6667777766654321   2


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCC-CCcC----
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGL---LEDMERIVNQMESDG-TRVD----  258 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~---~~~a~~~~~~m~~~g-~~~~----  258 (425)
                      +...|..+...+...+++++|.+.|++..+.  .|+ ...+..+..++...|+   .++|...++...+.. -.|+    
T Consensus       141 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~  218 (272)
T 3u4t_A          141 DPKVFYELGQAYYYNKEYVKADSSFVKVLEL--KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKD  218 (272)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchH
Confidence            3457777772444456999999999999885  343 6777788888888888   888888888776531 1233    


Q ss_pred             --HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          259 --TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       259 --~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                        ..+|..+-..|...|++++|.+.|++..+.  .|+..
T Consensus       219 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~  255 (272)
T 3u4t_A          219 ELIEANEYIAYYYTINRDKVKADAAWKNILAL--DPTNK  255 (272)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CccHH
Confidence              368888999999999999999999998865  45543

>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=99.06  E-value=1.4e-08  Score=90.89  Aligned_cols=196  Identities=11%  Similarity=0.055  Sum_probs=143.4

Q ss_pred             hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc----CCCchhHHHHHHHHHHHHHhcCCcc
Q 042756           91 SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL----GSRERELVLFYCNLIDSFCKHDSKR  166 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~----~~~~~~~~~~y~~li~~~~~~g~~~  166 (425)
                      +++|++++......+ .+....++..+-..|...|++++|.+.|++..+..    +...+....++..+...|...|+++
T Consensus        24 ~~~al~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  102 (283)
T 3edt_B           24 CKQALEDLEKTSGHD-HPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYK  102 (283)
T ss_dssp             HHHHHHHHHHHHCSS-SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHH
Confidence            344556666654433 23456788899999999999999999999987642    1224455667889999999999976


Q ss_pred             cHHHHHHHHHHHhhcC--CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHcC
Q 042756          167 GFDDTYARLNQLVNSS--SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK------GLEP-SGFEYKCIIYGYGRL  237 (425)
Q Consensus       167 ~~~~~~~~~~~~~~~~--~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~ty~~ll~~~~~~  237 (425)
                      .+.+.+....+.....  ........+|..+...|...|++++|.++|++....      +-.| ...++..+...|.+.
T Consensus       103 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~  182 (283)
T 3edt_B          103 EAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQ  182 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHc
Confidence            6655555554443211  101123468999999999999999999999999875      2234 356888999999999


Q ss_pred             CCHHHHHHHHHHHHHC------------------------------------------------CCCcCHHhHHHHHHHH
Q 042756          238 GLLEDMERIVNQMESD------------------------------------------------GTRVDTVCSNMVLSSY  269 (425)
Q Consensus       238 g~~~~a~~~~~~m~~~------------------------------------------------g~~~~~~~yn~li~~~  269 (425)
                      |++++|.++++...+.                                                .......+|..+...|
T Consensus       183 g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~  262 (283)
T 3edt_B          183 GKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALY  262 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence            9999999999988753                                                1122345777888888


Q ss_pred             HhcCCHHHHHHHHHHHHh
Q 042756          270 GDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~  287 (425)
                      ...|++++|..+|++..+
T Consensus       263 ~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          263 RRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHTTCHHHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            888888888888887664

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.06  E-value=3.3e-08  Score=96.13  Aligned_cols=341  Identities=9%  Similarity=-0.029  Sum_probs=190.9

Q ss_pred             HHhhHHHHHHHHHHhHHh--------cCC-CHHHHHHHHHHHHhcCChHHHHHHHHhhhCC-----CCCC----------
Q 042756           32 TARLTKQGQRFLSSLALA--------VTR-DSKAASRLISKFVASSPQFIALNALSHLLSP-----DTTH----------   87 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~--------~~~-d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~-----~~~~----------   87 (425)
                      ..|..++|++.|+...+.        ..| ...+|+.+-..|...|+++.|...+.+.+.-     +...          
T Consensus        63 ~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~  142 (472)
T 4g1t_A           63 LKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEE  142 (472)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHH
Confidence            467888898888765442        123 4688999999999999999999988876421     1000          


Q ss_pred             --------CchhhhHHHHHHHhhhcCCCccCHHHHHHHHHH---HHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHH
Q 042756           88 --------PRLSSLAFPLYMRITEESWFQWNPKLVAEIIAF---LDKQGQREEAETLILETLSKLGSRERELVLFYCNLI  156 (425)
Q Consensus        88 --------~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~---~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li  156 (425)
                              .+.+++|++.|++..+.+.  -++..+..+...   +...++.++|++.|++..+...    .....+..+.
T Consensus       143 g~~~~~~~~~~y~~A~~~~~kal~~~p--~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p----~~~~~~~~l~  216 (472)
T 4g1t_A          143 GWTRLKCGGNQNERAKVCFEKALEKKP--KNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNP----DNQYLKVLLA  216 (472)
T ss_dssp             HHHHHHHCTTHHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCS----SCHHHHHHHH
T ss_pred             HHHHHHHccccHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCC----cchHHHHHHH
Confidence                    1247889999999776552  244444444333   4566888889998888766422    1123455555


Q ss_pred             HHHHhcCCcc-cHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHH
Q 042756          157 DSFCKHDSKR-GFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGY  234 (425)
Q Consensus       157 ~~~~~~g~~~-~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~  234 (425)
                      ..+...+... ..+++...+.+.....+   .+..+++.+...|.+.|++++|...|++..+.  .|+ ..++..+-.+|
T Consensus       217 ~~~~~~~~~~~~~~~a~~~~~~al~~~~---~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~y  291 (472)
T 4g1t_A          217 LKLHKMREEGEEEGEGEKLVEEALEKAP---GVTDVLRSAAKFYRRKDEPDKAIELLKKALEY--IPNNAYLHCQIGCCY  291 (472)
T ss_dssp             HHHHHCC------CHHHHHHHHHHHHCS---SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHhCc---cHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCChHHHHHHHHHHH
Confidence            5555543321 13344444444433221   23458999999999999999999999999875  453 55666665554


Q ss_pred             HcC-------------------CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          235 GRL-------------------GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       235 ~~~-------------------g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      ...                   +..+.|...|+...+.. +.+..+|..+-..|...|++++|+..|++..+...  +..
T Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~--~~~  368 (472)
T 4g1t_A          292 RAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKEL--TPV  368 (472)
T ss_dssp             HHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCC--CHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCC--CCh
Confidence            322                   23566777777766543 23567888999999999999999999999887643  332


Q ss_pred             HHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcc--------hhhHHHHHHHHh---CCCCcccceeeccccchhccc
Q 042756          296 TYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLN--------EEEVSVVKELED---SSVLDEAMKWDSGETKLDLHG  364 (425)
Q Consensus       296 t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~---~~~~~~~~~~~~li~~~~~~~  364 (425)
                      .-..+...+.......    ...+...+..|.+...        ......+..+.+   .....+..+|+.+-..|...|
T Consensus       369 ~~~~~~~~~~~~~~~~----~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g  444 (472)
T 4g1t_A          369 AKQLLHLRYGNFQLYQ----MKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNE  444 (472)
T ss_dssp             HHHHHHHHHHHHHHHT----SSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH----CCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            2222211121111100    0011122222222211        001111112211   112345678999999999999


Q ss_pred             CcchhHHHHHHHHHHHHHhhccCCCCCCCCeeeee
Q 042756          365 MHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVV  399 (425)
Q Consensus       365 ~~~~a~~~~~~~~~~~m~~~~~~~~g~~p~~~t~~  399 (425)
                      ++++|     ++.|++..+    .....|+..+|.
T Consensus       445 ~~~~A-----~~~y~kALe----~~~~~p~a~~~~  470 (472)
T 4g1t_A          445 KMQQA-----DEDSERGLE----SGSLIPSASSWN  470 (472)
T ss_dssp             HCC--------------------------------
T ss_pred             CHHHH-----HHHHHHHHh----cCCCCCcHhhcC
Confidence            99999     999999987    245567776664

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.06  E-value=3.5e-08  Score=93.43  Aligned_cols=324  Identities=9%  Similarity=-0.044  Sum_probs=195.0

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHh---cCCCH--HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHh
Q 042756           27 LVQCLTARLTKQGQRFLSSLALA---VTRDS--KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRI  101 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~---~~~d~--~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m  101 (425)
                      -|..+.++++++|.++++.+.+.   ...|.  ..|-.++..-.     ....+-+..........+   ....++++.+
T Consensus        19 w~~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~-----~~~~~~~~~~~~~~~e~~---~~~~~~~~~i   90 (383)
T 3ulq_A           19 WYMYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRH-----NLMLEYLEPLEKMRIEEQ---PRLSDLLLEI   90 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHH-----HHHHHHHGGGGGSCGGGS---CCHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHH-----HHHHhhcCcccccccccc---cchhhHHHHH
Confidence            48889999999999999999887   33443  33333332111     111111111100000000   0111444544


Q ss_pred             hhcCCCccC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 042756          102 TEESWFQWN----PKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARL  175 (425)
Q Consensus       102 ~~~~~~~~~----~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~  175 (425)
                      .... ...+    ...+-..-..+...|++++|.+.|++..+.  .....+....+|..+-..|...|+++.+.+.+...
T Consensus        91 ~~~~-~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~a  169 (383)
T 3ulq_A           91 DKKQ-ARLTGLLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQA  169 (383)
T ss_dssp             HHHT-HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HhcC-CCchhHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3321 1001    111222445567889999999999998763  12223334567888999999999977666666655


Q ss_pred             HHHhhcCCCCcc-ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          176 NQLVNSSSSVYV-KRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       176 ~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                      .+.........| ...+++.+-..|...|++++|.+.|++..+.    +-.+ ...++..+-..|...|++++|.+.|+.
T Consensus       170 l~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~  249 (383)
T 3ulq_A          170 YEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKR  249 (383)
T ss_dssp             HHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            555444322112 2458999999999999999999999998754    2111 124888899999999999999999998


Q ss_pred             HHHC----CC-CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCCHHHHHHHHHHHHHHHHHHHhhccCCchhhH
Q 042756          250 MESD----GT-RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGI-PFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSI  323 (425)
Q Consensus       250 m~~~----g~-~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~-~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~  323 (425)
                      ..+.    +. .....++..+-..|.+.|++++|...|++..+..- .+|......    +...+.+-..          
T Consensus       250 al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~----~~~l~~~~~~----------  315 (383)
T 3ulq_A          250 AIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSE----FEFLKSLYLS----------  315 (383)
T ss_dssp             HHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH----HHHHHHHHTS----------
T ss_pred             HHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH----HHHHHHHHhC----------
Confidence            8762    33 33577899999999999999999999999764211 112211111    1112222111          


Q ss_pred             HHHHhhcchhhHHHHHHHHhC-CCCcc-cceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          324 LELTEVLNEEEVSVVKELEDS-SVLDE-AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                           .+..+....+...++. +..|+ ...+..+-..|...|++++|     .+.|++..+
T Consensus       316 -----~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A-----~~~~~~al~  367 (383)
T 3ulq_A          316 -----GPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKA-----SAYFLKVEQ  367 (383)
T ss_dssp             -----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             -----CCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH
Confidence                 1111112222222222 22222 23566777889999999999     999988765

>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=99.04  E-value=2.3e-07  Score=83.28  Aligned_cols=222  Identities=8%  Similarity=-0.075  Sum_probs=149.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----cCCcccHHHHHHHHHHHhhcCCCC
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----HDSKRGFDDTYARLNQLVNSSSSV  185 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~g~~~~~~~~~~~~~~~~~~~~~~  185 (425)
                      ++..+..+-..+.+.|++++|.+.|++..+.   ..+   ..+..+-..|..    .++   .+++...+.+....+   
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~---~a~~~lg~~~~~g~~~~~~---~~~A~~~~~~a~~~~---   72 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KEN---SGCFNLGVLYYQGQGVEKN---LKKAASFYAKACDLN---   72 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCH---HHHHHHHHHHHHTSSSCCC---HHHHHHHHHHHHHTT---
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCH---HHHHHHHHHHHcCCCcCCC---HHHHHHHHHHHHHCC---
Confidence            4556666777788888888888888887762   122   245667777777    777   455555555554443   


Q ss_pred             ccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCc
Q 042756          186 YVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       186 ~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a~~~~~~m~~~g~~~  257 (425)
                        +...+..+-..|..    .+++++|+..|++..+.+   +...+..+-..|..    .+++++|.+.|+...+.+   
T Consensus        73 --~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---  144 (273)
T 1ouv_A           73 --YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---  144 (273)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---
T ss_pred             --CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---
Confidence              33478888888888    888888888888888765   66778888888888    888888888888888765   


Q ss_pred             CHHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH----HHHHHHhhccCCchhhHHHHHhh
Q 042756          258 DTVCSNMVLSSYGD----HNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST----IMSMLQDLNSNDFPLSILELTEV  329 (425)
Q Consensus       258 ~~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~----~~~~~~~~~~~~~~~~~~~~~~~  329 (425)
                      +...+..+-..|..    .+++++|...|++..+.+   +...+..+-..|..    .++..++                
T Consensus       145 ~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A----------------  205 (273)
T 1ouv_A          145 DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEA----------------  205 (273)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHH----------------
T ss_pred             cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHH----------------
Confidence            56677777777777    888888888888887764   33444444444433    2222222                


Q ss_pred             cchhhHHHHHHHHhCCCCcccceeeccccchhc----ccCcchhHHHHHHHHHHHHHh
Q 042756          330 LNEEEVSVVKELEDSSVLDEAMKWDSGETKLDL----HGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~m~~  383 (425)
                           ...+.+.++.+.   ...+..+-..|..    .++.++|     .++|++..+
T Consensus       206 -----~~~~~~a~~~~~---~~a~~~l~~~~~~g~~~~~~~~~A-----~~~~~~a~~  250 (273)
T 1ouv_A          206 -----LARYSKACELEN---GGGCFNLGAMQYNGEGVTRNEKQA-----IENFKKGCK  250 (273)
T ss_dssp             -----HHHHHHHHHTTC---HHHHHHHHHHHHTTSSSSCCSTTH-----HHHHHHHHH
T ss_pred             -----HHHHHHHHhCCC---HHHHHHHHHHHHcCCCcccCHHHH-----HHHHHHHHH
Confidence                 111222223321   3344444555555    8899999     999988877

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.03  E-value=3.6e-09  Score=97.25  Aligned_cols=250  Identities=11%  Similarity=-0.048  Sum_probs=169.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      ...+..+...+...|++++|.+.+++..+.  .....+....++..+...|...|+++.+.+.+....+..+........
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            467888999999999999999999986542  111233335577888899999999776666666655554443222222


Q ss_pred             hhHHHHHHHHHHhcCC--------------------hhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHH
Q 042756          189 RQALKSMISGLCEMGQ--------------------PHEAENLIEEMRVK----GLEP-SGFEYKCIIYGYGRLGLLEDM  243 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~--------------------~~~a~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~g~~~~a  243 (425)
                      ..++..+...|...|+                    +++|.+.|++....    +-.| ...++..+...+...|++++|
T Consensus       123 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  202 (338)
T 3ro2_A          123 ARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDA  202 (338)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHH
Confidence            4588899999999999                    99999999887543    2222 244788888999999999999


Q ss_pred             HHHHHHHHHC----CC-CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHHHHHHHHHh
Q 042756          244 ERIVNQMESD----GT-RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGI-PFS----VRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       244 ~~~~~~m~~~----g~-~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~-~pd----~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .+.++...+.    +- .....++..+...|...|++++|...|++..+..- .++    ..++..+-..+...|+.+++
T Consensus       203 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  282 (338)
T 3ro2_A          203 VIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKA  282 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHH
Confidence            9999987643    11 11244889999999999999999999998764210 112    33455555555555555444


Q ss_pred             hccCCchhhHHHHHhhcchhhHHHHHHHHh-CCCC-cccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          314 LNSNDFPLSILELTEVLNEEEVSVVKELED-SSVL-DEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ..         .+         ..+.++.. .+.. ....+|..+...|...|++++|     .++|++..+
T Consensus       283 ~~---------~~---------~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~a~~  331 (338)
T 3ro2_A          283 ID---------YH---------LKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQA-----MHFAEKHLE  331 (338)
T ss_dssp             HH---------HH---------HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHH
T ss_pred             HH---------HH---------HHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH-----HHHHHHHHH
Confidence            22         00         01111111 1111 1234677788899999999999     999999876

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.03  E-value=5.7e-09  Score=99.00  Aligned_cols=288  Identities=10%  Similarity=-0.060  Sum_probs=188.0

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccC--HHHHHHHHHHHHhcCChhH
Q 042756           52 RDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWN--PKLVAEIIAFLDKQGQREE  129 (425)
Q Consensus        52 ~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~--~~~~~~ll~~~~~~g~~~~  129 (425)
                      .....+...-..+...|+++.|...+.+.+                     ..+.-.+.  ..++..+...+...|++++
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al---------------------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~   65 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAV---------------------QVGTEDLKTLSAIYSQLGNAYFYLHDYAK   65 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHCCSCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHH---------------------hcCcccHHHHHHHHHHHHHHHHHhcCHHH
Confidence            445555666666777776666666665553                     22211111  3578888899999999999


Q ss_pred             HHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCC---
Q 042756          130 AETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQ---  204 (425)
Q Consensus       130 A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~---  204 (425)
                      |.+.|++..+.  .....+....++..+...|...|+++.+.+.+....+..+..........++..+-..|...|+   
T Consensus        66 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  145 (406)
T 3sf4_A           66 ALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFG  145 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCccc
Confidence            99999987542  1222344455778888899999997666665555555443322111224588999999999999   


Q ss_pred             -----------------hhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCC-c
Q 042756          205 -----------------PHEAENLIEEMRVK----GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTR-V  257 (425)
Q Consensus       205 -----------------~~~a~~~~~~m~~~----g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~-~  257 (425)
                                       +++|.+.|++....    +-.|. ..++..+-..|...|++++|.+.++...+.    +-. .
T Consensus       146 ~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  225 (406)
T 3sf4_A          146 CPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAA  225 (406)
T ss_dssp             -------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             ccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHH
Confidence                             99999999887643    22222 347888899999999999999999987643    111 1


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcch
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGI-PFS----VRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNE  332 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~-~pd----~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  332 (425)
                      ...+|..+...|...|++++|...|++..+..- .++    ..++..+-..|...|+++++..         .+      
T Consensus       226 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~---------~~------  290 (406)
T 3sf4_A          226 ERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAID---------YH------  290 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH---------HH------
T ss_pred             HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHH---------HH------
Confidence            235889999999999999999999998764210 112    3455556666666666555432         00      


Q ss_pred             hhHHHHHHHHh-CCCCc-ccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          333 EEVSVVKELED-SSVLD-EAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       333 ~~~~~~~~~~~-~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                         ..+.++.. .+..+ ...+|..+-..|...|++++|     .++|++..+
T Consensus       291 ---~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~~~~al~  335 (406)
T 3sf4_A          291 ---LKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQA-----MHFAEKHLE  335 (406)
T ss_dssp             ---HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHH
T ss_pred             ---HHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHH
Confidence               11111111 11111 134667777888888999998     777777654

>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=99.01  E-value=1.6e-07  Score=88.82  Aligned_cols=234  Identities=8%  Similarity=-0.023  Sum_probs=175.7

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCC-hHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCH
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSP-QFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNP  111 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~-~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~  111 (425)
                      .|++++|++.|+.....-+-+..+|+.+-..+...|+ ++.|+..+.++                     ...+  +-+.
T Consensus       110 ~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~a---------------------l~l~--P~~~  166 (382)
T 2h6f_A          110 DERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAI---------------------IEEQ--PKNY  166 (382)
T ss_dssp             TCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHH---------------------HHHC--TTCH
T ss_pred             CCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHH---------------------HHHC--CCCH
Confidence            4578899999999887655578889999999988885 55555555554                     3333  1277


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..|..+-..+.+.|++++|+..|++..+.    .+.....|..+-.++.+.|+++++.+.++...+.-+.      +...
T Consensus       167 ~a~~~~g~~~~~~g~~~eAl~~~~kal~l----dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~------~~~a  236 (382)
T 2h6f_A          167 QVWHHRRVLVEWLRDPSQELEFIADILNQ----DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR------NNSV  236 (382)
T ss_dssp             HHHHHHHHHHHHHTCCTTHHHHHHHHHHH----CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT------CHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh----CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC------CHHH
Confidence            78999999999999999999999999875    3333457888999999999987766666666554322      3459


Q ss_pred             HHHHHHHHHh-cCChhHH-----HHHHHHHHHcCCCC-CHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHCCCCcCHHhH
Q 042756          192 LKSMISGLCE-MGQPHEA-----ENLIEEMRVKGLEP-SGFEYKCIIYGYGRLG--LLEDMERIVNQMESDGTRVDTVCS  262 (425)
Q Consensus       192 ~~~li~~~~~-~g~~~~a-----~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g--~~~~a~~~~~~m~~~g~~~~~~~y  262 (425)
                      |+.+-.++.+ .|..++|     ++.|++....  .| +...|..+-..+.+.|  ++++|.+.+..+ +. -..+...+
T Consensus       237 ~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al  312 (382)
T 2h6f_A          237 WNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLI  312 (382)
T ss_dssp             HHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHH
T ss_pred             HHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHH
Confidence            9999999999 6666888     4888888774  45 4678888888899988  689999999887 32 23467888


Q ss_pred             HHHHHHHHhcC---------CHHHHHHHHHHH-HhCCCCCCH-HHHHHHHHHHH
Q 042756          263 NMVLSSYGDHN---------ELSRMVLWLQKM-KDSGIPFSV-RTYNSVLNSCS  305 (425)
Q Consensus       263 n~li~~~~~~g---------~~~~A~~l~~~M-~~~g~~pd~-~t~~~ll~~~~  305 (425)
                      ..+...|.+.|         ..++|+++|++. .+.  .|+. ..|..+...+.
T Consensus       313 ~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~--DP~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          313 AFLVDIYEDMLENQCDNKEDILNKALELCEILAKEK--DTIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTT--CGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHh--CchhHHHHHHHHHHHH
Confidence            99999998874         358999999998 543  5544 45665555543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.01  E-value=1e-06  Score=85.52  Aligned_cols=233  Identities=9%  Similarity=-0.041  Sum_probs=152.9

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHH
Q 042756           51 TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEA  130 (425)
Q Consensus        51 ~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A  130 (425)
                      ......||.|-..+...|++++|+..+.+              |++++........-.-...+|+.+-..|...|++++|
T Consensus        48 ~~~a~~yn~Lg~~~~~~G~~~eAl~~~~k--------------Al~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A  113 (472)
T 4g1t_A           48 EFKATMCNLLAYLKHLKGQNEAALECLRK--------------AEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDV  113 (472)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHH--------------HHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHH--------------HHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHH
Confidence            34467899999999999999999887776              4555555433222223567899999999999999999


Q ss_pred             HHHHHHHHHh----cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHH---HHhc
Q 042756          131 ETLILETLSK----LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISG---LCEM  202 (425)
Q Consensus       131 ~~l~~~m~~~----~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~---~~~~  202 (425)
                      ...|++..+.    ..........+|..+-.++.+.|..+ .++|...+.+.....    |+ ...+..+..+   +...
T Consensus       114 ~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-y~~A~~~~~kal~~~----p~~~~~~~~~~~~~~~l~~~  188 (472)
T 4g1t_A          114 QIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQ-NERAKVCFEKALEKK----PKNPEFTSGLAIASYRLDNW  188 (472)
T ss_dssp             HHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTH-HHHHHHHHHHHHHHS----TTCHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHcccc-HHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHhcCc
Confidence            9999887642    11111122235655555565544311 444555555544322    22 2244444433   4556


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC----CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL----GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRM  278 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~----g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A  278 (425)
                      ++.++|++.|++..+.. +.+..++..+...+.+.    |++++|.++++...... +.+...++.+...|...|++++|
T Consensus       189 ~~~~~al~~~~~al~l~-p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A  266 (472)
T 4g1t_A          189 PPSQNAIDPLRQAIRLN-PDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKA  266 (472)
T ss_dssp             CCCCCTHHHHHHHHHHC-SSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hHHHHHHHHHHHHhhcC-CcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHH
Confidence            88899999999887742 22456666665555544    57889999999887654 23678899999999999999999


Q ss_pred             HHHHHHHHhCCCCCC-HHHHHHHHHHHHH
Q 042756          279 VLWLQKMKDSGIPFS-VRTYNSVLNSCST  306 (425)
Q Consensus       279 ~~l~~~M~~~g~~pd-~~t~~~ll~~~~~  306 (425)
                      ...|++..+.  .|+ ..++..+-.+|..
T Consensus       267 ~~~~~~al~~--~p~~~~~~~~lg~~y~~  293 (472)
T 4g1t_A          267 IELLKKALEY--IPNNAYLHCQIGCCYRA  293 (472)
T ss_dssp             HHHHHHHHHH--STTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCChHHHHHHHHHHHHH
Confidence            9999998865  454 4566666555544

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.99  E-value=2.4e-08  Score=95.21  Aligned_cols=241  Identities=9%  Similarity=-0.035  Sum_probs=174.2

Q ss_pred             HHHhhHHHHHHHHHHhHHh---c---CCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           31 LTARLTKQGQRFLSSLALA---V---TRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~---~---~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      ...|++++|.+.|+.....   .   .....++..+-..|...|+++.|...+.+.              ++++..... 
T Consensus        97 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a--------------l~~~~~~~~-  161 (411)
T 4a1s_A           97 FYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERH--------------LTLARQLGD-  161 (411)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH--------------HHHHHHHTC-
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHH--------------HHHHHHhhc-
Confidence            4467888899988887765   1   224567888888888899988888877774              334333321 


Q ss_pred             CCCccCHHHHHHHHHHHHhcCC-----------------hhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCc
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQ-----------------REEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSK  165 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~-----------------~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~  165 (425)
                        ......++..+-..|...|+                 +++|.+.+++..+.  .....+....++..+-..|...|++
T Consensus       162 --~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~  239 (411)
T 4a1s_A          162 --RLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDF  239 (411)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             --hHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCh
Confidence              12345678888999999999                 99999998886542  1112233445778888999999997


Q ss_pred             ccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC--C--C-CCHHHHHHHHHHHHcCCCH
Q 042756          166 RGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKG--L--E-PSGFEYKCIIYGYGRLGLL  240 (425)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~--~-p~~~ty~~ll~~~~~~g~~  240 (425)
                      +.+.+.++...+.............+|..+...|...|++++|.+.|++.....  .  . ....++..+...|.+.|++
T Consensus       240 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~  319 (411)
T 4a1s_A          240 QAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEF  319 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCH
Confidence            766666665555543322111123488999999999999999999999887641  1  1 1256888899999999999


Q ss_pred             HHHHHHHHHHHHC----CC-CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          241 EDMERIVNQMESD----GT-RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       241 ~~a~~~~~~m~~~----g~-~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ++|.+.++...+.    +- .....+|..+...|...|++++|...|++..+.
T Consensus       320 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          320 NTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            9999999987653    11 112458888999999999999999999998754

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.99  E-value=7.3e-07  Score=79.90  Aligned_cols=212  Identities=6%  Similarity=-0.087  Sum_probs=159.6

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHh----cCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCC
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVA----SSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~----~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~  106 (425)
                      ...++.++|.+.|+...+  .-+..++..+-..|..    .++.                     ++|.+.|++..+.+ 
T Consensus        17 ~~~~~~~~A~~~~~~a~~--~~~~~a~~~lg~~~~~g~~~~~~~---------------------~~A~~~~~~a~~~~-   72 (273)
T 1ouv_A           17 YKEKDFTQAKKYFEKACD--LKENSGCFNLGVLYYQGQGVEKNL---------------------KKAASFYAKACDLN-   72 (273)
T ss_dssp             HHTTCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCH---------------------HHHHHHHHHHHHTT-
T ss_pred             HhCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHcCCCcCCCH---------------------HHHHHHHHHHHHCC-
Confidence            345688888888888776  3455667767666666    5544                     44555555544443 


Q ss_pred             CccCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----cCCcccHHHHHHHHHHH
Q 042756          107 FQWNPKLVAEIIAFLDK----QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----HDSKRGFDDTYARLNQL  178 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~----~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~g~~~~~~~~~~~~~~~  178 (425)
                         ++..+..+-..|..    .+++++|.+.|++..+.+   .   ...+..+-..|..    .++   .+++...+.+.
T Consensus        73 ---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~---~~a~~~lg~~~~~~~~~~~~---~~~A~~~~~~a  140 (273)
T 1ouv_A           73 ---YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---Y---AEGCASLGGIYHDGKVVTRD---FKKAVEYFTKA  140 (273)
T ss_dssp             ---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---C---HHHHHHHHHHHHHCSSSCCC---HHHHHHHHHHH
T ss_pred             ---CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---C---ccHHHHHHHHHHcCCCcccC---HHHHHHHHHHH
Confidence               66777788888888    999999999999987752   2   2256777778887    777   55666666666


Q ss_pred             hhcCCCCccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHH
Q 042756          179 VNSSSSVYVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDMERIVNQM  250 (425)
Q Consensus       179 ~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a~~~~~~m  250 (425)
                      ...+     +...+..+-..|..    .+++++|...|++..+.+   +...+..+-..|.+    .+++++|.+.|+..
T Consensus       141 ~~~~-----~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a  212 (273)
T 1ouv_A          141 CDLN-----DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKA  212 (273)
T ss_dssp             HHTT-----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHH
T ss_pred             HhcC-----cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHH
Confidence            5443     23478888888888    899999999999998875   56778888888888    99999999999998


Q ss_pred             HHCCCCcCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCC
Q 042756          251 ESDGTRVDTVCSNMVLSSYGD----HNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       251 ~~~g~~~~~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g  289 (425)
                      .+.+   +...+..+-..|..    .++.++|.+.|++..+.|
T Consensus       213 ~~~~---~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          213 CELE---NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHTT---CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HhCC---CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            8875   36778888888888    899999999999988765

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.98  E-value=4.6e-08  Score=81.56  Aligned_cols=166  Identities=9%  Similarity=-0.071  Sum_probs=131.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ...|..+...+...|++++|.+.|++..+...    .....+..+...+...|+++.+.+.++...+.   .   ..+..
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~---~~~~~   77 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADA----FDVDVALHLGIAYVKTGAVDRGTELLERSLAD---A---PDNVK   77 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTS----CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---C---TTCHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc----cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---C---CCCHH
Confidence            45667788888999999999999998765321    12346788889999999955544444444333   2   12345


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .|..+...+...|++++|.+.|++..... +.+...+..+...+.+.|++++|.++++...+.. ..+...|..+...|.
T Consensus        78 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~  155 (186)
T 3as5_A           78 VATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYE  155 (186)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHH
Confidence            88999999999999999999999998763 3467888999999999999999999999988764 336789999999999


Q ss_pred             hcCCHHHHHHHHHHHHhC
Q 042756          271 DHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~~  288 (425)
                      ..|++++|...|++..+.
T Consensus       156 ~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          156 QMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHc
Confidence            999999999999998653

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.97  E-value=6.4e-08  Score=94.63  Aligned_cols=211  Identities=9%  Similarity=-0.003  Sum_probs=168.1

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCCh-hHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQR-EEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~-~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      .+++++..+++.....  ..+...+..+-..+...|++ ++|.+.|++..+..    |.....|..+-..|.+.|++   
T Consensus        83 ~~~~al~~l~~~~~~~--~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~----p~~~~a~~~lg~~~~~~g~~---  153 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSA--QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE----PELVEAWNQLGEVYWKKGDV---  153 (474)
T ss_dssp             HHHHHHHHHHHHHTTC--CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCH---
T ss_pred             HHHHHHHHHHHHhccC--chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC----CCCHHHHHHHHHHHHHcCCH---
Confidence            4567777787765543  24788888899999999999 99999999988752    22234788999999999994   


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc---------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC--
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM---------GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL--  237 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~---------g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~--  237 (425)
                      +++...+.+....    .|+...|..+-..|...         |++++|.+.|++..+.. +-+...|..+-.+|...  
T Consensus       154 ~~A~~~~~~al~~----~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~  228 (474)
T 4abn_A          154 TSAHTCFSGALTH----CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYF  228 (474)
T ss_dssp             HHHHHHHHHHHTT----CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh----CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHH
Confidence            5555555555543    35667999999999999         99999999999998853 22577899999999998  


Q ss_pred             ------CCHHHHHHHHHHHHHCCCC--cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Q 042756          238 ------GLLEDMERIVNQMESDGTR--VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       238 ------g~~~~a~~~~~~m~~~g~~--~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~  309 (425)
                            |++++|.+.|+...+..-.  -+...|..+-..|...|++++|.+.|++..+.. .-+...+..+-..+...|+
T Consensus       229 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~  307 (474)
T 4abn_A          229 NTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSR  307 (474)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             hhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHH
Confidence                  9999999999998875310  378999999999999999999999999987652 2245578888888888888


Q ss_pred             HHHhhc
Q 042756          310 MLQDLN  315 (425)
Q Consensus       310 ~~~~~~  315 (425)
                      .+.++.
T Consensus       308 ~~eAi~  313 (474)
T 4abn_A          308 LTSLLE  313 (474)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877743

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.97  E-value=2.1e-07  Score=87.98  Aligned_cols=238  Identities=9%  Similarity=-0.007  Sum_probs=171.1

Q ss_pred             HHHhhHHHHHHHHHHhHHh--cCCC----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           31 LTARLTKQGQRFLSSLALA--VTRD----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~--~~~d----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      ...|++++|.+.|+.....  -.+|    ..+|..+-..+...|+++.|...+.+.              ++++......
T Consensus       114 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~a--------------l~~~~~~~~~  179 (383)
T 3ulq_A          114 LDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQA--------------YEIYKEHEAY  179 (383)
T ss_dssp             HHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH--------------HHHHHTCSTT
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH--------------HHHHHhCccc
Confidence            4457889999999998776  2343    467888888999999999888877664              4454443210


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS  182 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~  182 (425)
                        ......+++.+-..|...|++++|.+.|++..+.  .....+....++..+-..|...|+++.+.+.++...+.....
T Consensus       180 --~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~  257 (383)
T 3ulq_A          180 --NIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEES  257 (383)
T ss_dssp             --HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             --hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence              1123567888999999999999999999987652  112233334578889999999999766666555555543332


Q ss_pred             CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCC
Q 042756          183 SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKG----LEPSGFEYKCIIYGYGRLGL---LEDMERIVNQMESDGT  255 (425)
Q Consensus       183 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~ty~~ll~~~~~~g~---~~~a~~~~~~m~~~g~  255 (425)
                      ....-...++..+-..|.+.|++++|...|++.....    -......+..+-..|...|+   +++|..+++..   +.
T Consensus       258 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~  334 (383)
T 3ulq_A          258 NILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---ML  334 (383)
T ss_dssp             TCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TC
T ss_pred             ccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cC
Confidence            2111224689999999999999999999999987641    12223346778888999999   77777777665   33


Q ss_pred             Cc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          256 RV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       256 ~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .| ....+..+-..|...|++++|...|++..+
T Consensus       335 ~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          335 YADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33 355778889999999999999999998754

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.97  E-value=1.7e-07  Score=88.57  Aligned_cols=324  Identities=8%  Similarity=-0.026  Sum_probs=192.4

Q ss_pred             HHHHHHHhhHHHHHHHHHHhHHh---cCCCHH--HHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHh
Q 042756           27 LVQCLTARLTKQGQRFLSSLALA---VTRDSK--AASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRI  101 (425)
Q Consensus        27 ~~~~l~~~~~~~a~~~~~~m~~~---~~~d~~--~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m  101 (425)
                      -|..+.++++++|.++++++...   ...|..  .|-.++..         -..++..-+.... ..+......+.++.+
T Consensus        19 wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~---------r~~~~~~~~~~~~-~~~~~~~~~~~l~~i   88 (378)
T 3q15_A           19 WYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCF---------RHQLMLDYLEPGK-TYGNRPTVTELLETI   88 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHH---------HHHHHHHTCCC---------CHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHH---------HHHHHHhhcCccc-ccccccchHHHHHHH
Confidence            38889999999999999998776   434433  22333321         1112222211110 000112222444444


Q ss_pred             hhcCC-CccCH--HHHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756          102 TEESW-FQWNP--KLVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus       102 ~~~~~-~~~~~--~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      ..... ..+..  ..|-..-..+...|++++|.+.|++..+..  ....+....++..+-..|...|+++.+.+.+....
T Consensus        89 ~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al  168 (378)
T 3q15_A           89 ETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQAL  168 (378)
T ss_dssp             HGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            32210 00011  112223344568899999999999987632  22234445578889999999999766665555555


Q ss_pred             HHhhcCCCCcc-ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          177 QLVNSSSSVYV-KRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       177 ~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                      +.........+ ...+++.+-..|...|++++|.+.|++..+.    +-.+ ...++..+-..|...|++++|.+.|+..
T Consensus       169 ~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~a  248 (378)
T 3q15_A          169 DIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKA  248 (378)
T ss_dssp             HHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            55444322222 2458899999999999999999999988763    2111 2357888899999999999999999988


Q ss_pred             HHC----CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHH
Q 042756          251 ESD----GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILEL  326 (425)
Q Consensus       251 ~~~----g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~  326 (425)
                      .+.    +.+....++..+...|.+.|++++|...|++..+..-..+...+...+..+   +.+-..             
T Consensus       249 l~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l---~~ly~~-------------  312 (378)
T 3q15_A          249 AKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFL---QAVYKE-------------  312 (378)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHH---HHHHSS-------------
T ss_pred             HHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH---HHHHhC-------------
Confidence            761    223347889999999999999999999999987532211111222222111   111110             


Q ss_pred             HhhcchhhHHHHHHHHh-CCCCcc-cceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          327 TEVLNEEEVSVVKELED-SSVLDE-AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       327 ~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                        .+..+....+...++ .+..|+ ...+..+-..|...|++++|     .+.|++..+
T Consensus       313 --~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A-----~~~~~~al~  364 (378)
T 3q15_A          313 --TVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQA-----AAFYRKVLK  364 (378)
T ss_dssp             --SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH-----HHHHHHHHH
T ss_pred             --CCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH
Confidence              001001111112221 111122 23456677889999999999     888887754

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.95  E-value=8.5e-08  Score=85.76  Aligned_cols=204  Identities=16%  Similarity=0.126  Sum_probs=147.3

Q ss_pred             hhHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHH
Q 042756           34 RLTKQGQRFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPK  112 (425)
Q Consensus        34 ~~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~  112 (425)
                      ..+++|+++++..... .+....++..+-..+...|+++.|...+.+.+              ++++.....+ ......
T Consensus        22 ~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al--------------~~~~~~~~~~-~~~~~~   86 (283)
T 3edt_B           22 PLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDAL--------------AIREKTLGKD-HPAVAA   86 (283)
T ss_dssp             HHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHHTCTT-CHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHH--------------HHHHHHcCCc-chHHHH
Confidence            3556677777766543 23357888999999999999999888877753              3444432222 234567


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHh----cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC--CCCc
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSK----LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS--SSVY  186 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~----~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~--~~~~  186 (425)
                      ++..+...|...|++++|.+.|++..+.    .+...+....+|..+...|...|+++.+.+.++...+.....  ....
T Consensus        87 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  166 (283)
T 3edt_B           87 TLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDP  166 (283)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            8889999999999999999999997653    233345556678899999999999666655555555442211  1111


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-----------------------------------------------
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKG-----------------------------------------------  219 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-----------------------------------------------  219 (425)
                      ....++..+...|.+.|++++|.++|++.....                                               
T Consensus       167 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (283)
T 3edt_B          167 NVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV  246 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC
Confidence            234689999999999999999999999987630                                               


Q ss_pred             CCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          220 LEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       220 ~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ..| ...++..+...|.+.|++++|.++|+...+
T Consensus       247 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          247 DSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            112 345788899999999999999999998765

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.95  E-value=2.5e-07  Score=97.95  Aligned_cols=301  Identities=11%  Similarity=0.120  Sum_probs=171.5

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHh---cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCC-------CCCCchhhhHHHH
Q 042756           28 VQCLTARLTKQGQRFLSSLALA---VTRDSKAASRLISKFVASSPQFIALNALSHLLSPD-------TTHPRLSSLAFPL   97 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~---~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~-------~~~~~~~~~a~~l   97 (425)
                      -.....|...+|+++++.....   +.-+....|.++.+..+.+ .....+...+.-.-.       ....+.+++|..+
T Consensus       993 Kaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIkaD-~~Rv~eyI~kLd~~d~~eIA~Iai~lglyEEAf~I 1071 (1630)
T 1xi4_A          993 KAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKAD-RTRVMEYINRLDNYDAPDIANIAISNELFEEAFAI 1071 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHhC-hhhHHHHHHHhhhccHHHHHHHHHhCCCHHHHHHH
Confidence            3445667888888888888744   2234566666777777663 233333333321000       0112367888888


Q ss_pred             HHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 042756           98 YMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQ  177 (425)
Q Consensus        98 f~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~  177 (425)
                      |++...      .....+.++.   ..|++++|.++.++..      .+.   +|..+-.++.+.|+   ..+|.+.+.+
T Consensus      1072 YkKa~~------~~~A~~VLie---~i~nldrAiE~Aervn------~p~---vWsqLAKAql~~G~---~kEAIdsYiK 1130 (1630)
T 1xi4_A         1072 FRKFDV------NTSAVQVLIE---HIGNLDRAYEFAERCN------EPA---VWSQLAKAQLQKGM---VKEAIDSYIK 1130 (1630)
T ss_pred             HHHcCC------HHHHHHHHHH---HHhhHHHHHHHHHhcC------CHH---HHHHHHHHHHhCCC---HHHHHHHHHh
Confidence            887531      1112222222   6677888888777541      222   57788888888888   4444444433


Q ss_pred             HhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          178 LVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       178 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      .        -|...|.-++.+|.+.|++++|.+++...++..  ++....+.+..+|++.+++++...+.    +   .+
T Consensus      1131 A--------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~---~~ 1193 (1630)
T 1xi4_A         1131 A--------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N---GP 1193 (1630)
T ss_pred             c--------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h---CC
Confidence            2        122377778888888888888888888766543  34344445777888887777544432    2   24


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc----cCCchhhHHHHHhhcchh
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN----SNDFPLSILELTEVLNEE  333 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~  333 (425)
                      +...|..+-..|...|++++|..+|...         ..|..+..++++.|+++.+.+    .....++.+.-..+...+
T Consensus      1194 n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~ 1264 (1630)
T 1xi4_A         1194 NNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGK 1264 (1630)
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhh
Confidence            5556666777777777888887777773         377777777777777666533    111111111000010000


Q ss_pred             hHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHH
Q 042756          334 EVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMR  382 (425)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~  382 (425)
                      +-..+... .-.+..+...+..++.-|.+.|.+++|     +.+++.-.
T Consensus      1265 Ef~LA~~c-gl~Iiv~~deLeeli~yYe~~G~feEA-----I~LlE~aL 1307 (1630)
T 1xi4_A         1265 EFRLAQMC-GLHIVVHADELEELINYYQDRGYFEEL-----ITMLEAAL 1307 (1630)
T ss_pred             HHHHHHHH-HHhhhcCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHh
Confidence            10111111 111223444556777778888888888     77776554

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.93  E-value=2.9e-06  Score=83.09  Aligned_cols=314  Identities=7%  Similarity=-0.018  Sum_probs=222.9

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHh----cCChHHHHHHHHhhhCCCC---------------CCCchhhh
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVA----SSPQFIALNALSHLLSPDT---------------THPRLSSL   93 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~----~~~~~~a~~~~~~~l~~~~---------------~~~~~~~~   93 (425)
                      .++.++|.+.|+...+.  -+..++..|-..|..    .++.+.|...+.+....+.               ..+...++
T Consensus        56 ~~~~~~A~~~~~~a~~~--~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~  133 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQ--GYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAE  133 (490)
T ss_dssp             CCCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             CcCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHH
Confidence            58999999999988764  677888889899988    8899999999988765432               12456889


Q ss_pred             HHHHHHHhhhcCCCccCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----cCCc
Q 042756           94 AFPLYMRITEESWFQWNPKLVAEIIAFLDK----QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----HDSK  165 (425)
Q Consensus        94 a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~----~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~g~~  165 (425)
                      |.+.|+...+.+    ++..+..+-..|..    .++.++|.+.|++..+.+   .+   ..+..+-..|..    .++ 
T Consensus       134 A~~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~---~a~~~Lg~~y~~g~g~~~~-  202 (490)
T 2xm6_A          134 SVKWFRLAAEQG----RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NV---WSCNQLGYMYSRGLGVERN-  202 (490)
T ss_dssp             HHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH---HHHHHHHHHHHHTSSSCCC-
T ss_pred             HHHHHHHHHHCC----CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH---HHHHHHHHHHhcCCCCCcC-
Confidence            999999987776    56677777777877    789999999999987752   22   245667777776    566 


Q ss_pred             ccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----C
Q 042756          166 RGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----L  237 (425)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~  237 (425)
                        .+++...+.+....++     ...+..+-..|..    .+++++|.++|++..+.|   +...+..+-..|..    .
T Consensus       203 --~~~A~~~~~~a~~~~~-----~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~  272 (490)
T 2xm6_A          203 --DAISAQWYRKSATSGD-----ELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGA  272 (490)
T ss_dssp             --HHHHHHHHHHHHHTTC-----HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSS
T ss_pred             --HHHHHHHHHHHHHCCC-----HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCC
Confidence              6677777777666543     2378888888887    889999999999998865   45666667677777    8


Q ss_pred             CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH---HH
Q 042756          238 GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH-----NELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI---MS  309 (425)
Q Consensus       238 g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~-----g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~---~~  309 (425)
                      ++.++|.+.|+...+.|   +...+..|-..|...     ++.++|..+|++..+.|   +...+..+-..|...   .+
T Consensus       273 ~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~  346 (490)
T 2xm6_A          273 KEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEE  346 (490)
T ss_dssp             CCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHH
T ss_pred             CCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCccc
Confidence            99999999999988765   566777888888877     89999999999998876   345555555555442   24


Q ss_pred             HHHhhc-------cCCchhhHH---HHHh----hcchhhHHH-HHHHHhCCCCcccceeeccccchhc----ccCcchhH
Q 042756          310 MLQDLN-------SNDFPLSIL---ELTE----VLNEEEVSV-VKELEDSSVLDEAMKWDSGETKLDL----HGMHLGSA  370 (425)
Q Consensus       310 ~~~~~~-------~~~~~~~~~---~~~~----~~~~~~~~~-~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~  370 (425)
                      ..+++.       .........   .|..    ..+.+.+.. +....+.+   +...+..|-..|..    .++.++| 
T Consensus       347 ~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A-  422 (490)
T 2xm6_A          347 HKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDYVQA-  422 (490)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH-
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHHHH-
Confidence            444322       111111111   2333    122333332 23333443   34456666666666    8999999 


Q ss_pred             HHHHHHHHHHHHh
Q 042756          371 YFIILQWMDEMRN  383 (425)
Q Consensus       371 ~~~~~~~~~~m~~  383 (425)
                          .++|++..+
T Consensus       423 ----~~~~~~A~~  431 (490)
T 2xm6_A          423 ----WAWFDTAST  431 (490)
T ss_dssp             ----HHHHHHHHH
T ss_pred             ----HHHHHHHHH
Confidence                999999987

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.93  E-value=5.1e-07  Score=85.41  Aligned_cols=218  Identities=7%  Similarity=-0.059  Sum_probs=164.2

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCC-hhHHHH
Q 042756           54 SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQ-REEAET  132 (425)
Q Consensus        54 ~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~-~~~A~~  132 (425)
                      ..+|+.+-..+.+.|+++.|+                     +.|+.....+  +-+...|+.+-..+.+.|+ +++|++
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al---------------------~~~~~al~l~--P~~~~a~~~~g~~l~~~g~d~~eAl~  153 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAF---------------------KLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMN  153 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHH---------------------HHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHH---------------------HHHHHHHHhC--ccCHHHHHHHHHHHHHcccCHHHHHH
Confidence            456666666666666555544                     4444444433  1267788999999999997 999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      .|++..+.    .|.....|..+-.++.+.|+++++.+.++...+.-+.      +...|+.+-.++.+.|++++|+..|
T Consensus       154 ~~~~al~l----~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~------~~~a~~~lg~~~~~~g~~~eAl~~~  223 (382)
T 2h6f_A          154 YITAIIEE----QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAK------NYHAWQHRQWVIQEFKLWDNELQYV  223 (382)
T ss_dssp             HHHHHHHH----CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT------CHHHHHHHHHHHHHHTCCTTHHHHH
T ss_pred             HHHHHHHH----CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcc------CHHHHHHHHHHHHHcCChHHHHHHH
Confidence            99998875    2333457888999999999988777777766665332      3459999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHc-CCCHHHH-----HHHHHHHHHCCCCcCHHhHHHHHHHHHhcC--CHHHHHHHHHH
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGR-LGLLEDM-----ERIVNQMESDGTRVDTVCSNMVLSSYGDHN--ELSRMVLWLQK  284 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~-~g~~~~a-----~~~~~~m~~~g~~~~~~~yn~li~~~~~~g--~~~~A~~l~~~  284 (425)
                      +++.+.. .-+...|+.+-.++.+ .|..++|     ...|+...+..- -+...|+.+...|...|  +.++|++.+.+
T Consensus       224 ~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P-~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~  301 (382)
T 2h6f_A          224 DQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQDRGLSKYPNLLNQLLD  301 (382)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTTTCGGGCHHHHHHHHH
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHccCccchHHHHHHHHH
Confidence            9999853 2257899999999999 6665777     477887776532 25789999999999988  68999999988


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHHHH
Q 042756          285 MKDSGIPFSVRTYNSVLNSCSTIM  308 (425)
Q Consensus       285 M~~~g~~pd~~t~~~ll~~~~~~~  308 (425)
                      + +. -..+...+..+...|.+.+
T Consensus       302 ~-~~-~p~~~~al~~La~~~~~~~  323 (382)
T 2h6f_A          302 L-QP-SHSSPYLIAFLVDIYEDML  323 (382)
T ss_dssp             H-TT-TCCCHHHHHHHHHHHHHHH
T ss_pred             h-cc-CCCCHHHHHHHHHHHHHHh
Confidence            8 32 2345577888888887765

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.92  E-value=8.6e-06  Score=79.72  Aligned_cols=298  Identities=8%  Similarity=0.009  Sum_probs=204.1

Q ss_pred             CCCHHHHHHHHHHHHh----cCChHHHHHHHHhhhCC---------------CCCCCchhhhHHHHHHHhhhcCCCccCH
Q 042756           51 TRDSKAASRLISKFVA----SSPQFIALNALSHLLSP---------------DTTHPRLSSLAFPLYMRITEESWFQWNP  111 (425)
Q Consensus        51 ~~d~~~~~~ll~~~~~----~~~~~~a~~~~~~~l~~---------------~~~~~~~~~~a~~lf~~m~~~~~~~~~~  111 (425)
                      ..|..++..+-..|..    .++.+.|+..+.+....               +...++..++|.+.|+...+.+    ++
T Consensus        36 ~g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~----~~  111 (490)
T 2xm6_A           36 SGEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG----LP  111 (490)
T ss_dssp             TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CH
T ss_pred             CCCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CH
Confidence            3455666666666665    56666666666655433               2223557899999999987765    66


Q ss_pred             HHHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----cCCcccHHHHHHHHHHHhhcCC
Q 042756          112 KLVAEIIAFLDK----QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----HDSKRGFDDTYARLNQLVNSSS  183 (425)
Q Consensus       112 ~~~~~ll~~~~~----~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~g~~~~~~~~~~~~~~~~~~~~  183 (425)
                      ..+..|-..|..    .+++++|.+.|++..+.+.   +   ..+..|-..|..    .++   ..+++..+.+....+ 
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~---~---~a~~~Lg~~y~~g~g~~~d---~~~A~~~~~~a~~~~-  181 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGR---D---SGQQSMGDAYFEGDGVTRD---YVMAREWYSKAAEQG-  181 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---H---HHHHHHHHHHHHTSSSCCC---HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC---H---HHHHHHHHHHHcCCCCCCC---HHHHHHHHHHHHHCC-
Confidence            677778888888    7899999999999876532   2   245566677766    455   677777777776654 


Q ss_pred             CCccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCC
Q 042756          184 SVYVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       184 ~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a~~~~~~m~~~g~  255 (425)
                          +...+..+-..|..    .++.++|.+.|++..+.|   +...+..+-..|..    .++.++|.+.|+...+.| 
T Consensus       182 ----~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-  253 (490)
T 2xm6_A          182 ----NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG-  253 (490)
T ss_dssp             ----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT-
T ss_pred             ----CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-
Confidence                23488899999998    899999999999999875   56778888888876    889999999999988875 


Q ss_pred             CcCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH-----HHHHHhhc------cCCch
Q 042756          256 RVDTVCSNMVLSSYGD----HNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTI-----MSMLQDLN------SNDFP  320 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~-----~~~~~~~~------~~~~~  320 (425)
                        +...+..+-..|..    .++.++|..+|++..+.|   +...+..|-..|...     ++..+++.      ..+..
T Consensus       254 --~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~~~  328 (490)
T 2xm6_A          254 --NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGDA  328 (490)
T ss_dssp             --CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTTCH
T ss_pred             --CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcCCH
Confidence              55677777777877    899999999999998775   444555555555553     34444422      11111


Q ss_pred             -hhHH---HHHhhcc---hhhHH-HHHHHHhCCCCcccceeeccccchhc----ccCcchhHHHHHHHHHHHHHh
Q 042756          321 -LSIL---ELTEVLN---EEEVS-VVKELEDSSVLDEAMKWDSGETKLDL----HGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       321 -~~~~---~~~~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~m~~  383 (425)
                       ....   .+...+.   .+.+. .+.+..+.   .+...+..+-..|..    .++.++|     +++|++..+
T Consensus       329 ~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~g~g~~~~~~~A-----~~~~~~A~~  395 (490)
T 2xm6_A          329 TAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK---GEKAAQFNLGNALLQGKGVKKDEQQA-----AIWMRKAAE  395 (490)
T ss_dssp             HHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCCCHHHH-----HHHHHHHHh
Confidence             1111   2222221   12222 22222333   245566666666766    7899999     999999887

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.91  E-value=4.8e-08  Score=95.54  Aligned_cols=198  Identities=9%  Similarity=-0.117  Sum_probs=148.7

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHH
Q 042756           52 RDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAE  131 (425)
Q Consensus        52 ~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~  131 (425)
                      .+...+..+-..+...|++                    .++|++.|++..+.+.  -+...|..+-..|.+.|++++|.
T Consensus       100 ~~a~~~~~lg~~~~~~g~~--------------------~~~A~~~~~~al~~~p--~~~~a~~~lg~~~~~~g~~~~A~  157 (474)
T 4abn_A          100 VEAQALMLKGKALNVTPDY--------------------SPEAEVLLSKAVKLEP--ELVEAWNQLGEVYWKKGDVTSAH  157 (474)
T ss_dssp             CCHHHHHHHHHHHTSSSSC--------------------CHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             hhHHHHHHHHHHHHhcccc--------------------HHHHHHHHHHHHhhCC--CCHHHHHHHHHHHHHcCCHHHHH
Confidence            3555555555555555544                    0555555555444431  25778999999999999999999


Q ss_pred             HHHHHHHHhcCCCchhHHHHHHHHHHHHHhc---------CCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc
Q 042756          132 TLILETLSKLGSRERELVLFYCNLIDSFCKH---------DSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM  202 (425)
Q Consensus       132 ~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~---------g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~  202 (425)
                      +.|++..+..  +.   ...+..+-..|...         |++   +++...+.+.....+   -+...|..+-.+|...
T Consensus       158 ~~~~~al~~~--p~---~~~~~~lg~~~~~~~~~~~~~~~g~~---~~A~~~~~~al~~~p---~~~~~~~~lg~~~~~~  226 (474)
T 4abn_A          158 TCFSGALTHC--KN---KVSLQNLSMVLRQLQTDSGDEHSRHV---MDSVRQAKLAVQMDV---LDGRSWYILGNAYLSL  226 (474)
T ss_dssp             HHHHHHHTTC--CC---HHHHHHHHHHHTTCCCSCHHHHHHHH---HHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhC--CC---HHHHHHHHHHHHHhccCChhhhhhhH---HHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHH
Confidence            9999988753  22   24678888888888         884   455555555443321   1345899999999998


Q ss_pred             --------CChhHHHHHHHHHHHcCCCC----CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          203 --------GQPHEAENLIEEMRVKGLEP----SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       203 --------g~~~~a~~~~~~m~~~g~~p----~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                              |++++|++.|++..+.  .|    +...|..+-.+|.+.|++++|.+.|+...+..- -+...+..+...+.
T Consensus       227 ~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~a~~~l~~~~~  303 (474)
T 4abn_A          227 YFNTGQNPKISQQALSAYAQAEKV--DRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDP-AWPEPQQREQQLLE  303 (474)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHHH--CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHhhccccchHHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence                    9999999999999985  45    788999999999999999999999999887532 25678999999999


Q ss_pred             hcCCHHHHHHHHHHH
Q 042756          271 DHNELSRMVLWLQKM  285 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M  285 (425)
                      ..|++++|.+.+.++
T Consensus       304 ~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          304 FLSRLTSLLESKGKT  318 (474)
T ss_dssp             HHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhccc
Confidence            999999998876554

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.91  E-value=2.7e-07  Score=84.61  Aligned_cols=208  Identities=12%  Similarity=0.020  Sum_probs=150.7

Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHH-------hcCCh-------hHHHHHHHHHHHhcCCCchhHHHHHHHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLD-------KQGQR-------EEAETLILETLSKLGSRERELVLFYCNLID  157 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~-------~~g~~-------~~A~~l~~~m~~~~~~~~~~~~~~y~~li~  157 (425)
                      ++|..+|++....+.  -++..|..+...+.       +.|++       ++|..+|++..+...+   .....|..+..
T Consensus        33 ~~a~~~~~~al~~~p--~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p---~~~~~~~~~~~  107 (308)
T 2ond_A           33 KRVMFAYEQCLLVLG--HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLK---KNMLLYFAYAD  107 (308)
T ss_dssp             HHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTT---TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCc---ccHHHHHHHHH
Confidence            678888888776542  36667777776665       45886       8999999998763222   22346888999


Q ss_pred             HHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hh-HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH-
Q 042756          158 SFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQ-ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGY-  234 (425)
Q Consensus       158 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~-  234 (425)
                      .+.+.|+++   ++...+.+...    ..|+ .. .|..+...+.+.|++++|..+|++..+.+ +++...|....... 
T Consensus       108 ~~~~~~~~~---~A~~~~~~al~----~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~  179 (308)
T 2ond_A          108 YEESRMKYE---KVHSIYNRLLA----IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEY  179 (308)
T ss_dssp             HHHHTTCHH---HHHHHHHHHHT----SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHH
T ss_pred             HHHhcCCHH---HHHHHHHHHHh----ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            999999955   45555555443    2233 22 89999999999999999999999998853 23344554443332 


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCC--HHHHHHHHHHHHHHHHHH
Q 042756          235 GRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG-IPFS--VRTYNSVLNSCSTIMSML  311 (425)
Q Consensus       235 ~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g-~~pd--~~t~~~ll~~~~~~~~~~  311 (425)
                      ...|+.++|.++|+...+.. +-+...|..++..+.+.|++++|..+|++..+.. +.|+  ...|..++....+.|+.+
T Consensus       180 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~  258 (308)
T 2ond_A          180 YCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLA  258 (308)
T ss_dssp             HTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            23799999999999887652 2368899999999999999999999999998863 4663  456777777666666554


Q ss_pred             Hh
Q 042756          312 QD  313 (425)
Q Consensus       312 ~~  313 (425)
                      .+
T Consensus       259 ~a  260 (308)
T 2ond_A          259 SI  260 (308)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.89  E-value=7.7e-07  Score=84.05  Aligned_cols=237  Identities=9%  Similarity=0.086  Sum_probs=168.2

Q ss_pred             HHHhhHHHHHHHHHHhHHh--cCCC----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           31 LTARLTKQGQRFLSSLALA--VTRD----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~--~~~d----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      ...|+.++|.+.|+.....  -.+|    ..++..+-..|...|+++.|...+.+.              ++++......
T Consensus       112 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~a--------------l~~~~~~~~~  177 (378)
T 3q15_A          112 FDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQA--------------LDIYQNHPLY  177 (378)
T ss_dssp             HHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH--------------HHHHHTSTTC
T ss_pred             HHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH--------------HHHHHhCCCc
Confidence            4567889999999998776  3344    467888888899999988888777664              4444432211


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS  182 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~  182 (425)
                        ......+++.+-..|...|++++|.+.|++..+.  ..........++..+-..|...|+++.+.+.+....+.....
T Consensus       178 --~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~  255 (378)
T 3q15_A          178 --SIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREK  255 (378)
T ss_dssp             --HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             --hhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence              0123567888999999999999999999987652  112233334577888899999999665555555444433221


Q ss_pred             CCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCC
Q 042756          183 SSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKG----LEPSGFEYKCIIYGYGRLGL---LEDMERIVNQMESDGT  255 (425)
Q Consensus       183 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~ty~~ll~~~~~~g~---~~~a~~~~~~m~~~g~  255 (425)
                      ... ....++..+-..|.+.|++++|...|++..+..    -......+..+-..|...|+   +++|..+++.   .+.
T Consensus       256 ~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~  331 (378)
T 3q15_A          256 VPD-LLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNL  331 (378)
T ss_dssp             CGG-GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTC
T ss_pred             CCh-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCC
Confidence            111 125688999999999999999999999998752    12224466777777888888   7777777775   332


Q ss_pred             Cc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          256 RV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       256 ~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .| ....+..+...|...|++++|...|++..+
T Consensus       332 ~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          332 HAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33 345677888999999999999999998754

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.86  E-value=3.4e-07  Score=76.71  Aligned_cols=167  Identities=15%  Similarity=0.020  Sum_probs=129.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +...|..+-..+...|+++.|...+.+.+.                     .+  +-++.++..+...|.+.|++++|.+
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~---------------------~~--p~~~~~~~~la~~~~~~~~~~~a~~   60 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLK---------------------AD--PNNVETLLKLGKTYMDIGLPNDAIE   60 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---------------------HC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---------------------hC--CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            567888999999999977777666666542                     22  1267788889999999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      .+......... .   ...+..+...+...++++.+.+.+....+..+      -+...+..+-..|.+.|++++|++.|
T Consensus        61 ~~~~~~~~~~~-~---~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~------~~~~~~~~lg~~~~~~g~~~~A~~~~  130 (184)
T 3vtx_A           61 SLKKFVVLDTT-S---AEAYYILGSANFMIDEKQAAIDALQRAIALNT------VYADAYYKLGLVYDSMGEHDKAIEAY  130 (184)
T ss_dssp             HHHHHHHHCCC-C---HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------TCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHhcCch-h---HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc------cchHHHHHHHHHHHHhCCchhHHHHH
Confidence            99998775332 2   23566777788888996555555554444322      23458999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          213 EEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       213 ~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ++..+.. +-+..+|..+-.+|.+.|++++|.+.|+...+.
T Consensus       131 ~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          131 EKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            9998853 235778999999999999999999999998875

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.86  E-value=3.3e-06  Score=79.24  Aligned_cols=266  Identities=7%  Similarity=-0.099  Sum_probs=170.9

Q ss_pred             HHHHhhHHHHHHHHHHhHHh-cCCCHH----HHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhc
Q 042756           30 CLTARLTKQGQRFLSSLALA-VTRDSK----AASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEE  104 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~-~~~d~~----~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~  104 (425)
                      .+..|++++|.+.++..... ...+..    +++.+-..+...|+++.|...+.+.+              .+....   
T Consensus        24 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al--------------~~~~~~---   86 (373)
T 1hz4_A           24 AINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTE--------------QMARQH---   86 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH--------------HHHHHT---
T ss_pred             HHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH--------------HHHHhc---
Confidence            34578999999999998776 333332    55666677777888888877776643              222221   


Q ss_pred             CCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc----CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 042756          105 SWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL----GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVN  180 (425)
Q Consensus       105 ~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~----~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~  180 (425)
                      +.......++..+-..+...|++++|.+.+++..+..    ....+.....+..+-..+...|+++.+.+.++...+...
T Consensus        87 ~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  166 (373)
T 1hz4_A           87 DVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLS  166 (373)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence            1111123446667788899999999999999876532    211133344566788888999996665555555544433


Q ss_pred             cCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--HHHHH----HHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          181 SSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS--GFEYK----CIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       181 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~ty~----~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      ..... ....+|..+...+...|++++|...+++.....-.++  .....    .....+...|++++|...++......
T Consensus       167 ~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~  245 (373)
T 1hz4_A          167 SYQPQ-QQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPE  245 (373)
T ss_dssp             TSCGG-GGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCC
T ss_pred             ccCcH-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCC
Confidence            22111 1235788888999999999999999999876421211  11111    23345779999999999999876543


Q ss_pred             CCc---CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCCCHH-HHHHHHHHHHHHHHHHHh
Q 042756          255 TRV---DTVCSNMVLSSYGDHNELSRMVLWLQKMKD----SGIPFSVR-TYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       255 ~~~---~~~~yn~li~~~~~~g~~~~A~~l~~~M~~----~g~~pd~~-t~~~ll~~~~~~~~~~~~  313 (425)
                      ..+   ....+..+...+...|++++|..++++...    .|..++.. .+..+-.++...|+..++
T Consensus       246 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  312 (373)
T 1hz4_A          246 FANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDA  312 (373)
T ss_dssp             CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHH
Confidence            211   133577888999999999999999998754    23222221 444444455555555444

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.85  E-value=6.8e-07  Score=74.24  Aligned_cols=165  Identities=10%  Similarity=0.014  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHH
Q 042756           55 KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLI  134 (425)
Q Consensus        55 ~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~  134 (425)
                      ..|..+...+...|+++.|...+.+++..                       .+.+..++..+...+...|++++|.+.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~A~~~~   65 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDA-----------------------DAFDVDVALHLGIAYVKTGAVDRGTELL   65 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCT-----------------------TSCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh-----------------------CccChHHHHHHHHHHHHcCCHHHHHHHH
Confidence            45666777777788777777777666432                       1235778888999999999999999999


Q ss_pred             HHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHH
Q 042756          135 LETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEE  214 (425)
Q Consensus       135 ~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  214 (425)
                      ++..+...    .....+..+...+...|+++.+.+.++...+.   .   ..+...|..+...+.+.|++++|.+.|++
T Consensus        66 ~~~~~~~~----~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---~---~~~~~~~~~~a~~~~~~~~~~~A~~~~~~  135 (186)
T 3as5_A           66 ERSLADAP----DNVKVATVLGLTYVQVQKYDLAVPLLIKVAEA---N---PINFNVRFRLGVALDNLGRFDEAIDSFKI  135 (186)
T ss_dssp             HHHHHHCT----TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---C---TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHhcCC----CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc---C---cHhHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            99887522    22346788889999999955554444444443   2   12446899999999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          215 MRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       215 m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..... +.+..++..+...+.+.|++++|.+.++...+.
T Consensus       136 ~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          136 ALGLR-PNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            98863 345789999999999999999999999988764

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.82  E-value=1.2e-07  Score=97.03  Aligned_cols=165  Identities=12%  Similarity=-0.024  Sum_probs=135.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++..|+.+-..|.+.|++++|++.|++..+.    .|+....|..+-.+|.+.|+++++.+.++...+..+.      +.
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l----~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~------~~   77 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV----FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT------FA   77 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC------CH
Confidence            4678999999999999999999999998875    2233457889999999999965555555544443221      24


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ..|+.+-.+|.+.|++++|++.|++..+.  .| +...|+.+-.+|.+.|++++|.+.|+...+..- -+...|..+...
T Consensus        78 ~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P-~~~~a~~~L~~~  154 (723)
T 4gyw_A           78 DAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP-DFPDAYCNLAHC  154 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHhhhhhH
Confidence            59999999999999999999999999884  45 477999999999999999999999999887531 257899999999


Q ss_pred             HHhcCCHHHHHHHHHHHHh
Q 042756          269 YGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~  287 (425)
                      |...|++++|.+.|++..+
T Consensus       155 l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          155 LQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHHTTCCTTHHHHHHHHHH
T ss_pred             HHhcccHHHHHHHHHHHHH
Confidence            9999999999998888753

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.76  E-value=1.2e-06  Score=79.61  Aligned_cols=175  Identities=11%  Similarity=0.012  Sum_probs=122.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcC--CCchhHHHHHHHHHHHHHhc-CCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLG--SRERELVLFYCNLIDSFCKH-DSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~--~~~~~~~~~y~~li~~~~~~-g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      ..+|+.+-..|.+.|++++|...|++..+...  ........+|+.+-..|... |+++.+.+.++...+..+......-
T Consensus        77 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~  156 (292)
T 1qqe_A           77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVAL  156 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHH
Confidence            56889999999999999999999998765211  11222234678888899986 9966665555555554332211100


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH------HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC---
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG------FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD---  258 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~------~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~---  258 (425)
                      ...+|+.+...|.+.|++++|+..|++..........      ..|..+..++...|++++|...|+...+.  .|+   
T Consensus       157 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~  234 (292)
T 1qqe_A          157 SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFAD  234 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC--------
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCC
Confidence            1347889999999999999999999999885422211      15777888899999999999999987653  232   


Q ss_pred             ---HHhHHHHHHHHH--hcCCHHHHHHHHHHHHh
Q 042756          259 ---TVCSNMVLSSYG--DHNELSRMVLWLQKMKD  287 (425)
Q Consensus       259 ---~~~yn~li~~~~--~~g~~~~A~~l~~~M~~  287 (425)
                         ...+..++.+|.  ..+++++|++.|+++..
T Consensus       235 ~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~  268 (292)
T 1qqe_A          235 SRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (292)
T ss_dssp             ---HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCc
Confidence               223455666664  45678889888877653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.74  E-value=3.6e-06  Score=83.33  Aligned_cols=227  Identities=9%  Similarity=-0.030  Sum_probs=157.9

Q ss_pred             HHHHHHHHHhHHhcCCCHHHHHHHHHHHHh-------cCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCcc
Q 042756           37 KQGQRFLSSLALAVTRDSKAASRLISKFVA-------SSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQW  109 (425)
Q Consensus        37 ~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~-------~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~  109 (425)
                      +.+..+|++.....+.+...|..+...+.+       .|+.+.+..              ..++|..+|++..+.- .+-
T Consensus       255 ~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~--------------~~~~A~~~~~~Al~~~-~p~  319 (530)
T 2ooe_A          255 KRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKL--------------FSDEAANIYERAISTL-LKK  319 (530)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHH--------------HHHHHHHHHHHHTTTT-CSS
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhh--------------hhHHHHHHHHHHHHHh-Ccc
Confidence            356667777776655677888887777765       455441110              1235666666654311 223


Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...+..+...+.+.|++++|.++|++..+..  +... ...|..+...+.+.|+.   +++...+.+.....+. .+..
T Consensus       320 ~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~-~~~~~~~~~~~~~~~~~---~~A~~~~~~Al~~~~~-~~~~  392 (530)
T 2ooe_A          320 NMLLYFAYADYEESRMKYEKVHSIYNRLLAIE--DIDP-TLVYIQYMKFARRAEGI---KSGRMIFKKAREDART-RHHV  392 (530)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS--SSCH-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHTCTTC-CTHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcc--ccCc-hHHHHHHHHHHHHhcCH---HHHHHHHHHHHhccCC-chHH
Confidence            67788889999999999999999999998742  2211 23678888888888884   4555555555433211 1111


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCcC--HHhHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDG-TRVD--TVCSNMV  265 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g-~~~~--~~~yn~l  265 (425)
                      ....+.+ .+...|+.++|..+|++..+.  .| +...|..++..+.+.|+.++|..+|+.....+ ..|+  ...|...
T Consensus       393 ~~~~a~~-~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~  469 (530)
T 2ooe_A          393 YVTAALM-EYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARF  469 (530)
T ss_dssp             HHHHHHH-HHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHH
T ss_pred             HHHHHHH-HHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence            1222222 233689999999999998875  34 57899999999999999999999999998763 2332  5589999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhC
Q 042756          266 LSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      +......|+.+.+.++++++.+.
T Consensus       470 ~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          470 LAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             HHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            99999999999999999998754

>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=98.71  E-value=1.2e-06  Score=68.46  Aligned_cols=129  Identities=10%  Similarity=0.076  Sum_probs=95.1

Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042756          152 YCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII  231 (425)
Q Consensus       152 y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll  231 (425)
                      |..+...+...|+++   ++...+.+.....+   .+...|..+...+...|++++|..+|+++...+ +.+...+..+.
T Consensus         4 ~~~l~~~~~~~~~~~---~A~~~~~~~~~~~~---~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   76 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYD---EAIEYYQKALELDP---RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLG   76 (136)
T ss_dssp             HHHHHHHHHHHTCHH---HHHHHHHHHHHHCT---TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCcHH---HHHHHHHHHHHcCC---cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHH
Confidence            456666777777743   44444444332221   234578888888888899999999999888753 33567888888


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          232 YGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ..+...|++++|.++++.+.+.. +.+...+..+...|...|++++|...|+++.+.
T Consensus        77 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           77 NAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            88999999999999999887754 235778888899999999999999999988754

>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=98.70  E-value=4.4e-06  Score=76.47  Aligned_cols=227  Identities=8%  Similarity=-0.020  Sum_probs=136.1

Q ss_pred             HHhhHHHHHHHHHHhHHhc-------CCCH----HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHH
Q 042756           32 TARLTKQGQRFLSSLALAV-------TRDS----KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMR  100 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~-------~~d~----~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~  100 (425)
                      ..|...+|.+++++..+..       .+|.    ..|+.....|...|+++.|...+.+.              .+++..
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~a--------------l~~~~~   68 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQE--------------AEAHAN   68 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH--------------HHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH--------------HHHHHH
Confidence            3577888888888777652       2332    23444444455555555554444432              223332


Q ss_pred             hhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756          101 ITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus       101 m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      ...   ...-..+|+.+...|.+.|++++|.+.|++..+..  .........++..+-..|.+ |+++.+.+.++...+.
T Consensus        69 ~~~---~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~  144 (307)
T 2ifu_A           69 NRS---LFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAV  144 (307)
T ss_dssp             TTC---HHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHH
T ss_pred             cCC---HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHH
Confidence            211   11124578888888999999999999998866531  11122223467777778877 8866555555554444


Q ss_pred             hhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          179 VNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       179 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      .+......--..+|+.+-..|.+.|++++|+..|++....    +..++ ...+..+..++...|++++|...|+... .
T Consensus       145 ~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~  223 (307)
T 2ifu_A          145 FENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-S  223 (307)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T
T ss_pred             HHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-C
Confidence            3332111111347888888899999999999999888763    22222 2266667777788899999999888876 3


Q ss_pred             CCCcC------HHhHHHHHHHHHhcCCHHHHHH
Q 042756          254 GTRVD------TVCSNMVLSSYGDHNELSRMVL  280 (425)
Q Consensus       254 g~~~~------~~~yn~li~~~~~~g~~~~A~~  280 (425)
                        .|+      ......++.++ ..|+.+.+.+
T Consensus       224 --~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          224 --IPGFSGSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             --STTSTTSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             --CCCCCCCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence              232      22344455555 5666655544

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.69  E-value=8e-06  Score=86.82  Aligned_cols=253  Identities=12%  Similarity=0.059  Sum_probs=167.0

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCC------CCchhhhHHHHHHHhhhcCC
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTT------HPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~------~~~~~~~a~~lf~~m~~~~~  106 (425)
                      +.+..+..+..+.+....      ...+-..+...|.+++|..++.+.-.....      .-+.+++|.++.++.     
T Consensus      1034 kaD~~Rv~eyI~kLd~~d------~~eIA~Iai~lglyEEAf~IYkKa~~~~~A~~VLie~i~nldrAiE~Aerv----- 1102 (1630)
T 1xi4_A         1034 KADRTRVMEYINRLDNYD------APDIANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERC----- 1102 (1630)
T ss_pred             HhChhhHHHHHHHhhhcc------HHHHHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHHHHHhc-----
Confidence            335555555555543211      333556666677777777777775211000      001344455554432     


Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                        -++.+|..+-.++.+.|++++|.+-|.+-      ..+   ..|..++.++.+.|++   +++.+.+.......    
T Consensus      1103 --n~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~---say~eVa~~~~~lGky---EEAIeyL~mArk~~---- 1164 (1630)
T 1xi4_A         1103 --NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDP---SSYMEVVQAANTSGNW---EELVKYLQMARKKA---- 1164 (1630)
T ss_pred             --CCHHHHHHHHHHHHhCCCHHHHHHHHHhc------CCh---HHHHHHHHHHHHcCCH---HHHHHHHHHHHhhc----
Confidence              24668888999999999999999999663      122   2577899999999995   45555554433322    


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL  266 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li  266 (425)
                      ++....+.+..+|++.+++++...+.    .   .|+...|..+-..|...|++++|..+|...         ..|..+.
T Consensus      1165 ~e~~Idt~LafaYAKl~rleele~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA 1228 (1630)
T 1xi4_A         1165 RESYVETELIFALAKTNRLAELEEFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLA 1228 (1630)
T ss_pred             ccccccHHHHHHHHhhcCHHHHHHHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHH
Confidence            22223445999999999988644442    1   456677888999999999999999999984         3799999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhc--------cCCchhhHHHHHhhcchhhHH
Q 042756          267 SSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLN--------SNDFPLSILELTEVLNEEEVS  336 (425)
Q Consensus       267 ~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~  336 (425)
                      ..|++.|++++|.+.+++..      +..+|.-+-.+|...|++..+..        +..+..+++.|.+.|..+++.
T Consensus      1229 ~tLvkLge~q~AIEaarKA~------n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI 1300 (1630)
T 1xi4_A         1229 STLVHLGEYQAAVDGARKAN------STRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELI 1300 (1630)
T ss_pred             HHHHHhCCHHHHHHHHHHhC------CHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999998763      56888888888887777777643        112333344455555544444

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.69  E-value=1.9e-05  Score=74.07  Aligned_cols=239  Identities=12%  Similarity=-0.004  Sum_probs=161.5

Q ss_pred             HHHHhhHHHHHHHHHHhHHh--cCCCH----HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhh
Q 042756           30 CLTARLTKQGQRFLSSLALA--VTRDS----KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITE  103 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~--~~~d~----~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~  103 (425)
                      ....|++++|.+.+++....  -.++.    .+++.+-..+...|+++.|...+.+.+              ++......
T Consensus        63 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al--------------~~~~~~~~  128 (373)
T 1hz4_A           63 LHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAF--------------QLINEQHL  128 (373)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHTTC
T ss_pred             HHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--------------HHHHHhcc
Confidence            34578999999999988776  33333    335667777888888888877776643              23332211


Q ss_pred             cCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC-chhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC
Q 042756          104 ESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSR-ERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS  182 (425)
Q Consensus       104 ~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~-~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~  182 (425)
                      .. .......+..+-..+...|++++|...+++..+..... .+....+|..+-..+...|+++.+.+.++...+.....
T Consensus       129 ~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~  207 (373)
T 1hz4_A          129 EQ-LPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNG  207 (373)
T ss_dssp             TT-STHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS
T ss_pred             cc-CcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcc
Confidence            11 11234566778888999999999999999987643221 11223467788888999999666665555555443322


Q ss_pred             CCCccChhHHH-----HHHHHHHhcCChhHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHcCCCHHHHHHHHHHHHH--
Q 042756          183 SSVYVKRQALK-----SMISGLCEMGQPHEAENLIEEMRVKGLEP---SGFEYKCIIYGYGRLGLLEDMERIVNQMES--  252 (425)
Q Consensus       183 ~~~~p~~~~~~-----~li~~~~~~g~~~~a~~~~~~m~~~g~~p---~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~--  252 (425)
                      ..  |  ..|.     ..+..+...|++++|...+++.......+   ....+..+...+...|++++|...++....  
T Consensus       208 ~~--~--~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~  283 (373)
T 1hz4_A          208 KY--H--SDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENA  283 (373)
T ss_dssp             CC--C--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             Cc--c--hhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            11  1  1222     23345789999999999999887643211   133567788899999999999999998754  


Q ss_pred             --CCCCcCH-HhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          253 --DGTRVDT-VCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       253 --~g~~~~~-~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                        .|..++. ..+..+-.++...|+.++|...|++...
T Consensus       284 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          284 RSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence              2333333 3677778889999999999999998754

>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=98.65  E-value=2.1e-06  Score=66.94  Aligned_cols=130  Identities=12%  Similarity=0.041  Sum_probs=101.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      .|..+...+...|++++|.++|+++.+.... .   ...+..+...+...|+++.   +...+.+.....+   .+...|
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~---~~~~~~~a~~~~~~~~~~~---A~~~~~~~~~~~~---~~~~~~   72 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPR-S---AEAWYNLGNAYYKQGDYDE---AIEYYQKALELDP---RSAEAW   72 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-C---HHHHHHHHHHHHHHTCHHH---HHHHHHHHHHHCT---TCHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCc-c---hhHHHHHHHHHHHhcCHHH---HHHHHHHHHHHCC---CchHHH
Confidence            4667888899999999999999998875321 2   3367788888999999554   4444444433221   234588


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..+...+.+.|++++|.++|+++.... +.+..++..+...+.+.|++++|.+.++.+.+.
T Consensus        73 ~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           73 YNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            999999999999999999999998863 335778889999999999999999999988764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.65  E-value=1.5e-06  Score=78.97  Aligned_cols=170  Identities=9%  Similarity=-0.137  Sum_probs=125.6

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHH
Q 042756          118 IAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSM  195 (425)
Q Consensus       118 l~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l  195 (425)
                      ...|...|++++|.+.|++..+..  ....+....+|+.+-..|.+.|+++++.+.++...+.....+...--..+|+.+
T Consensus        44 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l  123 (292)
T 1qqe_A           44 ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFEL  123 (292)
T ss_dssp             HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            456778999999999998876521  112233345789999999999997766666555555443322111113588999


Q ss_pred             HHHHHhc-CChhHHHHHHHHHHHcC----CCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCH------HhHH
Q 042756          196 ISGLCEM-GQPHEAENLIEEMRVKG----LEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDT------VCSN  263 (425)
Q Consensus       196 i~~~~~~-g~~~~a~~~~~~m~~~g----~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~------~~yn  263 (425)
                      -..|... |++++|+..|++..+..    -.+. ..+|..+...+.+.|++++|...|+...+.......      ..|.
T Consensus       124 g~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  203 (292)
T 1qqe_A          124 GEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFL  203 (292)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Confidence            9999996 99999999999987631    1111 357889999999999999999999998875432222      2578


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .+..++...|++++|...|++..+
T Consensus       204 ~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          204 KKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            888899999999999999999875

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.62  E-value=4.3e-06  Score=72.56  Aligned_cols=153  Identities=10%  Similarity=-0.046  Sum_probs=107.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      |+..+...-..+.+.|++++|.+.|++..+....+..   ..+..+-.++.+.|++   +++...+.+.....+.   +.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~---~~~~~~~~~~~~~~~~---~~A~~~~~~al~~~p~---~~   76 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDS---VTAYNCGVCADNIKKY---KEAADYFDIAIKKNYN---LA   76 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCH---HHHHHHHHHHHHTTCH---HHHHHHHHHHHHTTCS---HH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCc---HHHHHHHHHHHHhhcH---HHHHHHHHHHHHhCcc---hH
Confidence            5567777788888889999999999888765331222   2344477788888884   4444444444433211   34


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-H-------HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC---
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-G-------FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD---  258 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~-------~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~---  258 (425)
                      ..|..+-..|...|++++|.+.|++..+.  .|+ .       ..|..+-..+.+.|++++|.+.|+...+.  .|+   
T Consensus        77 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~  152 (228)
T 4i17_A           77 NAYIGKSAAYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWK  152 (228)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCccc
Confidence            57888888888899999999999888874  333 3       45777777788888999999999888765  344   


Q ss_pred             HHhHHHHHHHHHhcCCH
Q 042756          259 TVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       259 ~~~yn~li~~~~~~g~~  275 (425)
                      ...|..+-..|...|+.
T Consensus       153 ~~~~~~l~~~~~~~~~~  169 (228)
T 4i17_A          153 TDALYSLGVLFYNNGAD  169 (228)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            56777777777766665

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.62  E-value=8.5e-07  Score=90.73  Aligned_cols=165  Identities=15%  Similarity=0.068  Sum_probs=129.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAET  132 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~  132 (425)
                      +..+|+.|-..|.+.|++++|...+.+.+                     +.+  +-+...|..+-..|.+.|++++|.+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl---------------------~l~--P~~~~a~~nLg~~l~~~g~~~eA~~   64 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKAL---------------------EVF--PEFAAAHSNLASVLQQQGKLQEALM   64 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH---------------------HHC--SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHH---------------------HhC--CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            46788888888888887776666666654                     222  1257789999999999999999999


Q ss_pred             HHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          133 LILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       133 l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      .|++..+.    .|+....|..+-.+|.+.|+++++.+.++...+..+.      +...|+.+-.+|.+.|++++|++.|
T Consensus        65 ~~~~Al~l----~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l~P~------~~~a~~~Lg~~~~~~g~~~eAi~~~  134 (723)
T 4gyw_A           65 HYKEAIRI----SPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPA------FADAHSNLASIHKDSGNIPEAIASY  134 (723)
T ss_dssp             HHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99998875    2333457899999999999965555555544443221      2459999999999999999999999


Q ss_pred             HHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          213 EEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       213 ~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ++..+.  .|+ ...|..+..++...|++++|.+.++...+
T Consensus       135 ~~Al~l--~P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          135 RTALKL--KPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHHHHH--CSCCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             HHHHHh--CCCChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence            999884  564 67999999999999999999998887654

>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=98.60  E-value=3.3e-06  Score=77.31  Aligned_cols=173  Identities=6%  Similarity=-0.142  Sum_probs=128.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhc--CCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKL--GSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~--~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      .|......|...|++++|.+.|.+..+..  .........+|+.+...|.+.|+++.+.+.++...+..........-..
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            45556677888999999999998876521  1122333457888999999999988887777776666543322212245


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcC-HH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVK----GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRVD-TV  260 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~~-~~  260 (425)
                      +|+.+-..|.+ |++++|+..|++....    |-.+ ...++..+-..|.+.|++++|...|+...+.    +..++ ..
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  196 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYK  196 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHH
Confidence            88889999988 9999999999988753    1111 1458888999999999999999999988752    22222 23


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          261 CSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       261 ~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                      .|..+...+...|++++|...|++..
T Consensus       197 ~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          197 KCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            67777788888899999999999987

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.54  E-value=1.2e-05  Score=71.44  Aligned_cols=196  Identities=10%  Similarity=-0.035  Sum_probs=135.9

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .++..+-..-..+.+.|++++|.+.|++..+.... .+.....+..+-.+|.+.|+++.+.+.++.+.+..+...   ..
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~---~~   88 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRT-HEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDP---RV   88 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSC-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCT---TH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC-CcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCc---hh
Confidence            35566666788888999999999999998775322 211133567788889999996655555555555432221   11


Q ss_pred             hhHHHHHHHHHHh--------cCChhHHHHHHHHHHHcCCCCC-HHHH-----------------HHHHHHHHcCCCHHH
Q 042756          189 RQALKSMISGLCE--------MGQPHEAENLIEEMRVKGLEPS-GFEY-----------------KCIIYGYGRLGLLED  242 (425)
Q Consensus       189 ~~~~~~li~~~~~--------~g~~~~a~~~~~~m~~~g~~p~-~~ty-----------------~~ll~~~~~~g~~~~  242 (425)
                      ...+..+-.++.+        .|++++|...|++.....  |+ ....                 -.+-..|.+.|++++
T Consensus        89 ~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  166 (261)
T 3qky_A           89 PQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEA  166 (261)
T ss_dssp             HHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHH
Confidence            3467788888888        999999999999998752  33 2223                 455678999999999


Q ss_pred             HHHHHHHHHHCCCC--cCHHhHHHHHHHHHhc----------CCHHHHHHHHHHHHhCCCCCCHH----HHHHHHHHHHH
Q 042756          243 MERIVNQMESDGTR--VDTVCSNMVLSSYGDH----------NELSRMVLWLQKMKDSGIPFSVR----TYNSVLNSCST  306 (425)
Q Consensus       243 a~~~~~~m~~~g~~--~~~~~yn~li~~~~~~----------g~~~~A~~l~~~M~~~g~~pd~~----t~~~ll~~~~~  306 (425)
                      |...|+...+..-.  .....+..+..+|...          |++++|...|++..+.  .|+..    ....+-..+..
T Consensus       167 A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~l~~~~~~  244 (261)
T 3qky_A          167 AAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI--FPDSPLLRTAEELYTRARQR  244 (261)
T ss_dssp             HHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHHHH
Confidence            99999998875321  1345777888888866          8999999999998875  45543    33444444444


Q ss_pred             HHHHHH
Q 042756          307 IMSMLQ  312 (425)
Q Consensus       307 ~~~~~~  312 (425)
                      .++++.
T Consensus       245 ~~~~~~  250 (261)
T 3qky_A          245 LTELEG  250 (261)
T ss_dssp             HHHHHT
T ss_pred             HHHhhh
Confidence            555433

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.50  E-value=8.7e-05  Score=67.16  Aligned_cols=255  Identities=7%  Similarity=-0.033  Sum_probs=153.0

Q ss_pred             cccccchhHHHHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCCh---------HHHHHHHHhhhCCCCCCC
Q 042756           18 CRLRQQRLTLVQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQ---------FIALNALSHLLSPDTTHP   88 (425)
Q Consensus        18 ~~~~~~~~~~~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~---------~~a~~~~~~~l~~~~~~~   88 (425)
                      +..|.---++.+....|....+.+=...+.  ..-+...---+.+++...|.+         ..++.++.+.+..     
T Consensus        11 ~~~~~~lf~ikn~fy~G~yq~~i~e~~~~~--~~~~~~~~~~~~Rs~iAlg~~~~~~~~~~~~~a~~~la~~~~~-----   83 (310)
T 3mv2_B           11 SQDPMDYFNIKQNYYTGNFVQCLQEIEKFS--KVTDNTLLFYKAKTLLALGQYQSQDPTSKLGKVLDLYVQFLDT-----   83 (310)
T ss_dssp             ----CCTHHHHHHHTTTCHHHHTHHHHTSS--CCCCHHHHHHHHHHHHHTTCCCCCCSSSTTHHHHHHHHHHHTT-----
T ss_pred             CCCcHHHHHHHHHHHhhHHHHHHHHHHhcC--ccchHHHHHHHHHHHHHcCCCccCCCCCHHHHHHHHHHHHhcc-----
Confidence            333443334566677777777766222211  112222333344666655433         2355555555431     


Q ss_pred             chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           89 RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        89 ~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                          .|+..|++....+  .++..++-.+..++...|++++|++++.+....+.  .......+..++..+.+.|+.+.+
T Consensus        84 ----~a~~~l~~l~~~~--~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~--~~~~lea~~l~vqi~L~~~r~d~A  155 (310)
T 3mv2_B           84 ----KNIEELENLLKDK--QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDE--AEGTTELLLLAIEVALLNNNVSTA  155 (310)
T ss_dssp             ----TCCHHHHHTTTTS--CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSC--STTHHHHHHHHHHHHHHTTCHHHH
T ss_pred             ----cHHHHHHHHHhcC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCC--CcCcHHHHHHHHHHHHHCCCHHHH
Confidence                1556666665443  34555556788888899999999999988654322  112334677889999999995555


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~  244 (425)
                      .+.++.+.+..+..  +..+..+...+..++..    .++..+|+.+|+++.+.  .|+..+-..++.++.+.|++++|+
T Consensus       156 ~k~l~~~~~~~~d~--~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe  231 (310)
T 3mv2_B          156 STIFDNYTNAIEDT--VSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQ  231 (310)
T ss_dssp             HHHHHHHHHHSCHH--HHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhcCccc--cccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHH
Confidence            55555444432100  00123455666666333    34899999999998764  466555566666899999999999


Q ss_pred             HHHHHHHHC-----CC----CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          245 RIVNQMESD-----GT----RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       245 ~~~~~m~~~-----g~----~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      +.++.+.+.     +-    .-|..+.-.+|......|+  +|.+++.++.+.  .|+..
T Consensus       232 ~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~--~P~hp  287 (310)
T 3mv2_B          232 GIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL--DHEHA  287 (310)
T ss_dssp             HHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT--TCCCH
T ss_pred             HHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh--CCCCh
Confidence            999876643     10    2366777555555555676  888999998875  46554

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.48  E-value=8.5e-06  Score=70.68  Aligned_cols=120  Identities=6%  Similarity=-0.186  Sum_probs=97.4

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      |...|...-..+.+.|++++|.+.|++..+..-.++...+..+-.++.+.|++++|.+.|+...+..- -+...|..+-.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNY-NLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC-SHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCc-chHHHHHHHHH
Confidence            34588888999999999999999999999875447788888899999999999999999999887642 25788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVLNSCSTIMSM  310 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll~~~~~~~~~  310 (425)
                      .|...|++++|+..|++..+.  .|+ ...+..+...+...|..
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~  126 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQK  126 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHH
Confidence            999999999999999998864  343 44445555555555554

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.41  E-value=2.3e-05  Score=67.19  Aligned_cols=168  Identities=14%  Similarity=-0.014  Sum_probs=114.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHH----------------HHHHHHhcCCcccHHHHHHHHHHHhh
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCN----------------LIDSFCKHDSKRGFDDTYARLNQLVN  180 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~----------------li~~~~~~g~~~~~~~~~~~~~~~~~  180 (425)
                      ....+.+.|++++|.+.|++..+.    .|+....|..                +-..|.+.|+++++.+.++...+..+
T Consensus        10 ~g~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p   85 (208)
T 3urz_A           10 KVSAAIEAGQNGQAVSYFRQTIAL----NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAP   85 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH----CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh----CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
Confidence            445667889999999999998764    3333445555                78888999995555544444444322


Q ss_pred             cCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHCCCCc
Q 042756          181 SSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGL--LEDMERIVNQMESDGTRV  257 (425)
Q Consensus       181 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~--~~~a~~~~~~m~~~g~~~  257 (425)
                      .      +...|..+-..|...|++++|...|++..+.  .| +..++..+-.+|...|+  .+.+...+.....  ..|
T Consensus        86 ~------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~--~~~  155 (208)
T 3urz_A           86 N------NVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSS--PTK  155 (208)
T ss_dssp             T------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---C--CCH
T ss_pred             C------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC--CCc
Confidence            1      3458999999999999999999999999885  45 46788888887766654  3445555555432  223


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV  300 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l  300 (425)
                      ....+..+-.++...|++++|...|++..+.  .|+......+
T Consensus       156 ~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~l  196 (208)
T 3urz_A          156 MQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHHH
Confidence            3334444555666789999999999998854  6886544443

>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=98.39  E-value=1.6e-05  Score=72.06  Aligned_cols=167  Identities=12%  Similarity=-0.025  Sum_probs=119.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhH---HHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC---
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSREREL---VLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK---  188 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~---~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~---  188 (425)
                      ...+..+.+.|++++|.+++++..+.... .+..   ...|..+...+...++   .+++...+.+....... .++   
T Consensus        79 ~~~i~~~~~~~~y~~a~~~~~~~l~~~~~-~~~~~~~~~~~~~l~~~~~~~~~---~~~Ai~~~~~al~~~~~-~~~~~~  153 (293)
T 3u3w_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEY-HPEFQQFLQWQYYVAAYVLKKVD---YEYCILELKKLLNQQLT-GIDVYQ  153 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHHHHHHHTTSSC---HHHHHHHHHHHHHTCCC-CSCTTH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHhccccC-ChHHHHHHHHHHHHHHHHHcccC---HHHHHHHHHHHHHHhcc-cccHHH
Confidence            33477889999999999999998764322 2221   2234446666666777   45555555555442111 122   


Q ss_pred             -hhHHHHHHHHHHhcCChhHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc
Q 042756          189 -RQALKSMISGLCEMGQPHEAENLIEEMRVK-----GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRV  257 (425)
Q Consensus       189 -~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~  257 (425)
                       ..+|+.+-..|...|++++|+..|++..+.     +..+. ..+|..+...|.+.|++++|.+.++...+.    +..+
T Consensus       154 ~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~  233 (293)
T 3u3w_A          154 NLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMA  233 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHH
Confidence             347999999999999999999999999842     22233 338889999999999999999999977642    2222


Q ss_pred             C-HHhHHHHHHHHHhcCC-HHHHHHHHHHHH
Q 042756          258 D-TVCSNMVLSSYGDHNE-LSRMVLWLQKMK  286 (425)
Q Consensus       258 ~-~~~yn~li~~~~~~g~-~~~A~~l~~~M~  286 (425)
                      . ..+|..+-..|.+.|+ .++|.+.|++..
T Consensus       234 ~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          234 LIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             THHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            2 6789999999999995 699999998875

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.39  E-value=4e-05  Score=66.48  Aligned_cols=172  Identities=11%  Similarity=-0.019  Sum_probs=111.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++..+-.+...+.+.|++++|.+.|+++.+.... .+.....+..+..+|.+.|+++.+.+.++.+.+..+.... .|  
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~-~~--   78 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPF-GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPN-ID--   78 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTT-HH--
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCc-HH--
Confidence            3444445666677778888888888887764222 1111224556677777888855555555544443322211 01  


Q ss_pred             hHHHHHHHHHH------------------hcCChhHHHHHHHHHHHcCCCCCHH-HH-----------------HHHHHH
Q 042756          190 QALKSMISGLC------------------EMGQPHEAENLIEEMRVKGLEPSGF-EY-----------------KCIIYG  233 (425)
Q Consensus       190 ~~~~~li~~~~------------------~~g~~~~a~~~~~~m~~~g~~p~~~-ty-----------------~~ll~~  233 (425)
                      ..+..+-.++.                  ..|++++|...|++..+.  -|+.. .+                 -.+-..
T Consensus        79 ~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~  156 (225)
T 2yhc_A           79 YVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEY  156 (225)
T ss_dssp             HHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            13333333333                  357899999999999875  34321 22                 234556


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCcC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          234 YGRLGLLEDMERIVNQMESDGTRVD----TVCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       234 ~~~~g~~~~a~~~~~~m~~~g~~~~----~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      |.+.|++++|...|+.+.+..  |+    ...+..+..+|.+.|+.++|.+.|+.+...+
T Consensus       157 ~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          157 YTERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            889999999999999988752  33    3578889999999999999999999888763

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.36  E-value=7.8e-06  Score=69.16  Aligned_cols=162  Identities=12%  Similarity=-0.052  Sum_probs=108.1

Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh
Q 042756          122 DKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE  201 (425)
Q Consensus       122 ~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~  201 (425)
                      ...|++++|.++++.+..  .  +.....++..+-..+...|+++.+.+.++...+.....+.......+++.+-..|..
T Consensus         3 ~~~g~~~~A~~~~~~~~~--~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~   78 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA--H--PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERM   78 (203)
T ss_dssp             ----CHHHHHHHHHHHHT--S--TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHhcC--C--hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence            456888888885554432  1  112244677777888888886665555555555443332222334578888889999


Q ss_pred             cCChhHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc-CHHhHHHHHHHHH
Q 042756          202 MGQPHEAENLIEEMRVK----GLEP--SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRV-DTVCSNMVLSSYG  270 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~----g~~p--~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~-~~~~yn~li~~~~  270 (425)
                      .|++++|.+.|++..+.    +-.|  ....+..+-..+...|++++|...+++..+.    +-.. -..++..+-..|.
T Consensus        79 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  158 (203)
T 3gw4_A           79 AGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQ  158 (203)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence            99999999999887654    2122  2346778888899999999999999877532    2111 2345678888899


Q ss_pred             hcCCHHHHHHHHHHHHh
Q 042756          271 DHNELSRMVLWLQKMKD  287 (425)
Q Consensus       271 ~~g~~~~A~~l~~~M~~  287 (425)
                      ..|++++|.+.|++..+
T Consensus       159 ~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          159 QEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            99999999999988753

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.32  E-value=7.5e-05  Score=72.26  Aligned_cols=253  Identities=11%  Similarity=-0.014  Sum_probs=148.1

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCCh---HHHHHHHHhhhCC---------------CCCCCc
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQ---FIALNALSHLLSP---------------DTTHPR   89 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~---~~a~~~~~~~l~~---------------~~~~~~   89 (425)
                      ...+..|++++|.++|+...+.-  +..++..|-..|...|..   ++|...+.+....               +...+.
T Consensus        11 ~~~~~~g~~~~A~~~~~~aa~~g--~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~   88 (452)
T 3e4b_A           11 NEALKRGDTVTAQQNYQQLAELG--YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEA   88 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHT--CCTGGGTCC----------------------------CHHHHHHHHHTC--CCHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCc
Confidence            34466789999999999987652  333344444445555555   6777766655433               111223


Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhH---HHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREE---AETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR  166 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~---A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~  166 (425)
                      ..++|++.|+.....+.  ++  .+..|-..|...+..++   +.+.+......+.+   .   ....|-..|...+.++
T Consensus        89 ~~~~A~~~~~~Aa~~g~--~~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~---~---a~~~Lg~~y~~~~~~~  158 (452)
T 3e4b_A           89 EHHEAESLLKKAFANGE--GN--TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYP---E---AGLAQVLLYRTQGTYD  158 (452)
T ss_dssp             HHHHHHHHHHHHHHTTC--SS--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCT---T---HHHHHHHHHHHHTCGG
T ss_pred             CHHHHHHHHHHHHHCCC--HH--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCH---H---HHHHHHHHHHcCCCcc
Confidence            56788888888777652  12  45556666666554443   44444444333221   1   3455666677666655


Q ss_pred             cHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcC---ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC----CC
Q 042756          167 GFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMG---QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL----GL  239 (425)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~----g~  239 (425)
                      ...+....+.+....+.   |+  .+..+-..|.+.|   +.++|++.|++..+.| .++...+..+-..|...    ++
T Consensus       159 ~~~~~a~~~~~~a~~~~---~~--a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d  232 (452)
T 3e4b_A          159 QHLDDVERICKAALNTT---DI--CYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPD  232 (452)
T ss_dssp             GGHHHHHHHHHHHTTTC---TT--HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCC
T ss_pred             cCHHHHHHHHHHHHcCC---HH--HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCC
Confidence            44443444444433332   33  8888888899999   9999999999998876 34555556666666554    78


Q ss_pred             HHHHHHHHHHHHHCCCCcCHHhHHHHHHH-H--HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          240 LEDMERIVNQMESDGTRVDTVCSNMVLSS-Y--GDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       240 ~~~a~~~~~~m~~~g~~~~~~~yn~li~~-~--~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      .++|.+.|+... .|   +...+..|-.. |  ...|+.++|.++|++..+.|   +...+..|-..|.
T Consensus       233 ~~~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~  294 (452)
T 3e4b_A          233 EKTAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY  294 (452)
T ss_dssp             HHHHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH
Confidence            999999999877 33   55666666666 4  46889999999999988877   4555555555554

>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=98.31  E-value=6.6e-05  Score=64.51  Aligned_cols=182  Identities=9%  Similarity=0.009  Sum_probs=138.2

Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDT  171 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~  171 (425)
                      .+|++.|+...+.+    ++..+..+-..|...+++++|.+.|++..+.+   .+.   .+..|-..|...|......++
T Consensus         3 ~eA~~~~~~aa~~g----~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~---a~~~lg~~y~~~g~~~~~~~A   72 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG----DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGD---ALALLAQLKIRNPQQADYPQA   72 (212)
T ss_dssp             -CTTHHHHHHHHTT----CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHH---HHHHHHHHTTSSTTSCCHHHH
T ss_pred             chHHHHHHHHHHCC----CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHH---HHHHHHHHHHcCCCCCCHHHH
Confidence            35677777777665    77788888889999999999999999987653   222   455666667663322347788


Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHc----CCCHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLE-PSGFEYKCIIYGYGR----LGLLED  242 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~-p~~~ty~~ll~~~~~----~g~~~~  242 (425)
                      +..+.+....+.     ...+..|-..|..    .+++++|+++|++..+.|-. .+...+..|-..|..    .++.++
T Consensus        73 ~~~~~~A~~~g~-----~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~  147 (212)
T 3rjv_A           73 RQLAEKAVEAGS-----KSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVK  147 (212)
T ss_dssp             HHHHHHHHHTTC-----HHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHH
T ss_pred             HHHHHHHHHCCC-----HHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHH
Confidence            888888765543     2488888888887    88999999999999887532 126788888888888    889999


Q ss_pred             HHHHHHHHHHCCCCcCHHhHHHHHHHHHhc-C-----CHHHHHHHHHHHHhCCC
Q 042756          243 MERIVNQMESDGTRVDTVCSNMVLSSYGDH-N-----ELSRMVLWLQKMKDSGI  290 (425)
Q Consensus       243 a~~~~~~m~~~g~~~~~~~yn~li~~~~~~-g-----~~~~A~~l~~~M~~~g~  290 (425)
                      |.+.|+...+.  ..+...+..|-..|... |     +.++|..+|++..+.|.
T Consensus       148 A~~~~~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          148 ASEYFKGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            99999999886  23555777787788654 3     89999999999988874

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.30  E-value=3.7e-05  Score=64.85  Aligned_cols=170  Identities=11%  Similarity=-0.033  Sum_probs=108.3

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccC
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWN  110 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~  110 (425)
                      +..|++++|.+.++.+.........+++.+-..+...|+++.|...+.+.              +++++....   ....
T Consensus         3 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a--------------l~~~~~~~~---~~~~   65 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQAL--------------QQQAQKSGD---HTAE   65 (203)
T ss_dssp             ----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH--------------HHHHHTTCC---HHHH
T ss_pred             cccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHH--------------HHHHHHcCC---cHHH
Confidence            45788899999655554333346788889999999999988888777764              333333221   2235


Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHh---cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSK---LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~---~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      ..++..+-..+...|++++|.+.+++..+.   .+.........+..+-..+...|+++.+.+.++...+..........
T Consensus        66 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  145 (203)
T 3gw4_A           66 HRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVA  145 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHH
Confidence            567888889999999999999999987653   22112133445677777888888865555554444443332222212


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      -..++..+-..+...|++++|.+.|++..+
T Consensus       146 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          146 IACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            233566777777778888888777776654

>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=98.28  E-value=2.2e-05  Score=65.18  Aligned_cols=159  Identities=9%  Similarity=0.001  Sum_probs=114.1

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      ......+.+.|++++|...|++..+.    .|+....+..+-..+.+.|+   .+++...+.+.....    |+...+..
T Consensus        10 ~~~a~~~~~~g~~~~A~~~~~~al~~----~P~~~~a~~~la~~~~~~g~---~~~A~~~~~~a~~~~----p~~~~~~~   78 (176)
T 2r5s_A           10 LKQVSELLQQGEHAQALNVIQTLSDE----LQSRGDVKLAKADCLLETKQ---FELAQELLATIPLEY----QDNSYKSL   78 (176)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSCHH----HHTSHHHHHHHHHHHHHTTC---HHHHHHHHTTCCGGG----CCHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH----CCCcHHHHHHHHHHHHHCCC---HHHHHHHHHHhhhcc----CChHHHHH
Confidence            34566788899999999999987654    33334467888889999999   556666665554332    22222222


Q ss_pred             HHHH-HHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-CHHhHHHHHHHHHh
Q 042756          195 MISG-LCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-DTVCSNMVLSSYGD  271 (425)
Q Consensus       195 li~~-~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~yn~li~~~~~  271 (425)
                      +... +...+...+|...|++..+.  .| +...+..+-.++...|++++|...|+...+..-.+ +...+..+...|..
T Consensus        79 ~~~~~~~~~~~~~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~  156 (176)
T 2r5s_A           79 IAKLELHQQAAESPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSA  156 (176)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHH
Confidence            2111 22333445678888888774  45 47888999999999999999999999988764322 36689999999999


Q ss_pred             cCCHHHHHHHHHHHH
Q 042756          272 HNELSRMVLWLQKMK  286 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~  286 (425)
                      .|+.++|...|++..
T Consensus       157 ~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          157 LGQGNAIASKYRRQL  171 (176)
T ss_dssp             HCSSCHHHHHHHHHH
T ss_pred             hCCCCcHHHHHHHHH
Confidence            999999999998765

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.28  E-value=3.6e-05  Score=58.87  Aligned_cols=98  Identities=9%  Similarity=0.036  Sum_probs=85.0

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ...|..+...+...|++++|.++|+++.... +.+..++..+...+.+.|++++|..+|+.+.+.. ..+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            3588889999999999999999999998753 3357788999999999999999999999988754 2367889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhC
Q 042756          269 YGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~  288 (425)
                      |...|++++|...|+++.+.
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHh
Confidence            99999999999999998765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.27  E-value=7.9e-05  Score=67.40  Aligned_cols=172  Identities=12%  Similarity=-0.035  Sum_probs=121.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCch--hHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-CccC
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRER--ELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYVK  188 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~--~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p~  188 (425)
                      ..+...+..+...|++++|.+.+++..+.......  ....++..+...+...|+   .+++...+.+....... ..+.
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~A~~~~~~al~~~~~~~~~~  152 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVD---YEYCILELKKLLNQQLTGIDVY  152 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSC---HHHHHHHHHHHHTTCCCSSCTT
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCC---HHHHHHHHHHHHHHHhcCCchH
Confidence            34555788889999999999999887764332111  111233445556677788   45555655555432211 1111


Q ss_pred             --hhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCC
Q 042756          189 --RQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEP--SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTR  256 (425)
Q Consensus       189 --~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p--~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~  256 (425)
                        ..+|+.+-..|...|++++|...|++....    +-.+  ...+|..+-..|.+.|++++|.+.++...+.    +..
T Consensus       153 ~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~  232 (293)
T 2qfc_A          153 QNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSM  232 (293)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcH
Confidence              358999999999999999999999998732    1112  1258899999999999999999999987643    111


Q ss_pred             c-CHHhHHHHHHHHHhcCCHHHH-HHHHHHHH
Q 042756          257 V-DTVCSNMVLSSYGDHNELSRM-VLWLQKMK  286 (425)
Q Consensus       257 ~-~~~~yn~li~~~~~~g~~~~A-~~l~~~M~  286 (425)
                      . -..+|..+-..|.+.|+.++| ...|++..
T Consensus       233 ~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          233 ALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            1 167899999999999999999 77788764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.24  E-value=6.9e-05  Score=66.42  Aligned_cols=173  Identities=6%  Similarity=-0.070  Sum_probs=115.2

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc-cCHHHHHHHHHHHHhcCChhHHH
Q 042756           53 DSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ-WNPKLVAEIIAFLDKQGQREEAE  131 (425)
Q Consensus        53 d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~-~~~~~~~~ll~~~~~~g~~~~A~  131 (425)
                      +...+-.+-..+.+.|+++.|...|.+++                     ....-. .....+..+-.+|.+.|++++|.
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l---------------------~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~   72 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVF---------------------TYGRTHEWAADAQFYLARAYYQNKEYLLAA   72 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHG---------------------GGCSCSTTHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHH---------------------HhCCCCcchHHHHHHHHHHHHHhCcHHHHH
Confidence            45555556666666666555555555544                     332111 12567777889999999999999


Q ss_pred             HHHHHHHHhcCCCchhHHHHHHHHHHHHHh--------cCCcccHHHHHHHHHHHhhcCCCCccChhHH-----------
Q 042756          132 TLILETLSKLGSRERELVLFYCNLIDSFCK--------HDSKRGFDDTYARLNQLVNSSSSVYVKRQAL-----------  192 (425)
Q Consensus       132 ~l~~~m~~~~~~~~~~~~~~y~~li~~~~~--------~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~-----------  192 (425)
                      +.|++..+.... .+.....+..+-.++.+        .|+++.+.+.++.+.+..+...      ..+           
T Consensus        73 ~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~------~~~~a~~~~~~~~~  145 (261)
T 3qky_A           73 SEYERFIQIYQI-DPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHE------LVDDATQKIRELRA  145 (261)
T ss_dssp             HHHHHHHHHCTT-CTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCT------THHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCC-CchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCch------hHHHHHHHHHHHHH
Confidence            999999875322 22223355667777777        7885544444444444322221      133           


Q ss_pred             ------HHHHHHHHhcCChhHHHHHHHHHHHcCCC-C-CHHHHHHHHHHHHcC----------CCHHHHHHHHHHHHHC
Q 042756          193 ------KSMISGLCEMGQPHEAENLIEEMRVKGLE-P-SGFEYKCIIYGYGRL----------GLLEDMERIVNQMESD  253 (425)
Q Consensus       193 ------~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p-~~~ty~~ll~~~~~~----------g~~~~a~~~~~~m~~~  253 (425)
                            ..+-..|.+.|++++|...|++.....-. | ....+..+..+|.+.          |++++|...|+...+.
T Consensus       146 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          146 KLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence                  45678899999999999999999875311 1 245677777888766          8999999999998875

>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=98.24  E-value=1.3e-05  Score=80.08  Aligned_cols=153  Identities=8%  Similarity=-0.075  Sum_probs=85.6

Q ss_pred             chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           89 RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        89 ~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      +.+++|.+.|++..+.+  +-+...+..+-..+.+.|++++|.+.|++..+.    .+.....|..+-..|.+.|+++++
T Consensus         3 g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~lg~~~~~~g~~~~A   76 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRHR--PQDFVAWLMLADAELGMGDTTAGEMAVQRGLAL----HPGHPEAVARLGRVRWTQQRHAEA   76 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT----STTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             ccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHCCCHHHH
Confidence            35667777777766554  224666777777777777777777777776653    122233566677777777774444


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC---CCHHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL---GLLEDMER  245 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~---g~~~~a~~  245 (425)
                      .+.++...+..+      -+...|..+-.+|.+.|++++|.+.|++..+.. .-+...+..+..++...   |+.++|.+
T Consensus        77 ~~~~~~al~~~p------~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           77 AVLLQQASDAAP------EHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             HHHHHHHHHHCT------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             HHHHHHHHhcCC------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHH
Confidence            333333333211      123477777777777777777777777776642 22456677777777777   77777777


Q ss_pred             HHHHHHHCC
Q 042756          246 IVNQMESDG  254 (425)
Q Consensus       246 ~~~~m~~~g  254 (425)
                      .++...+.+
T Consensus       150 ~~~~al~~~  158 (568)
T 2vsy_A          150 QVRAAVAQG  158 (568)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHhcC
Confidence            777776653

>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=98.19  E-value=1.9e-05  Score=80.73  Aligned_cols=169  Identities=6%  Similarity=-0.080  Sum_probs=124.8

Q ss_pred             hhhhHHHHHHHhh--------hcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh
Q 042756           90 LSSLAFPLYMRIT--------EESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK  161 (425)
Q Consensus        90 ~~~~a~~lf~~m~--------~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~  161 (425)
                      ..++|++.|++..        +.+  +-+...+..+-..+.+.|++++|.+.|++..+...    +....|..+-.+|.+
T Consensus       406 ~~~~A~~~~~~al~~~~~~~~~~~--p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p----~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          406 QPVQTLDSLRAARHGALDADGVDF--SESVELPLMEVRALLDLGDVAKATRKLDDLAERVG----WRWRLVWYRAVAELL  479 (681)
T ss_dssp             CHHHHHHHHHHHHTC-------CC--TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC----CCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhhhhccccccccc--ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc----chHHHHHHHHHHHHH
Confidence            5677888777765        322  23556788888899999999999999999887522    223467788888999


Q ss_pred             cCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHH
Q 042756          162 HDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLE  241 (425)
Q Consensus       162 ~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~  241 (425)
                      .|+++++.+.++...+..+..      ...|..+-.+|.+.|++++ .+.|++..+.+ .-+...|..+-.++.+.|+++
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~------~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~  551 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGE------LAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRV  551 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTC------SHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCC------hHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHH
Confidence            999665555555555543222      3489999999999999999 99999998753 225678999999999999999


Q ss_pred             HHHHHHHHHHHCCCCcC-HHhHHHHHHHHHhcCC
Q 042756          242 DMERIVNQMESDGTRVD-TVCSNMVLSSYGDHNE  274 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~-~~~yn~li~~~~~~g~  274 (425)
                      +|.+.|+...+.  .|+ ...|..+..++...|+
T Consensus       552 ~A~~~~~~al~l--~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          552 GAVRTLDEVPPT--SRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHHHHTSCTT--STTHHHHHHHHHHHTC----
T ss_pred             HHHHHHHhhccc--CcccHHHHHHHHHHHHccCC
Confidence            999999987765  344 6778888888877665

>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=98.19  E-value=0.00033  Score=70.91  Aligned_cols=236  Identities=9%  Similarity=-0.005  Sum_probs=153.6

Q ss_pred             HHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHH-HHHHHhhhcCCCccCHHHHHHH
Q 042756           39 GQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAF-PLYMRITEESWFQWNPKLVAEI  117 (425)
Q Consensus        39 a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~-~lf~~m~~~~~~~~~~~~~~~l  117 (425)
                      ...+|++.....+.+...|-....-+...|+.                     +.|. ++|++....  ++.+...+-..
T Consensus       328 v~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~---------------------~~a~r~il~rAi~~--~P~s~~Lwl~~  384 (679)
T 4e6h_A          328 MTYVYMQAAQHVCFAPEIWFNMANYQGEKNTD---------------------STVITKYLKLGQQC--IPNSAVLAFSL  384 (679)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCC---------------------TTHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcH---------------------HHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            34455555554444555665555555555543                     3453 555554432  33466667677


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcC---------CCc---------hhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 042756          118 IAFLDKQGQREEAETLILETLSKLG---------SRE---------RELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLV  179 (425)
Q Consensus       118 l~~~~~~g~~~~A~~l~~~m~~~~~---------~~~---------~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~  179 (425)
                      +...-+.|++++|.++|+...+...         .|.         .....+|...++...+.|..+.+..++....+..
T Consensus       385 a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~  464 (679)
T 4e6h_A          385 SEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLK  464 (679)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTG
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            8888889999999999999876420         111         0123367777888778888555555554443331


Q ss_pred             hcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC--c
Q 042756          180 NSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR--V  257 (425)
Q Consensus       180 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~--~  257 (425)
                         +...+......+.+...+ .++.+.|..+|+...+. ..-+...+...++.....|+.+.|..+|+......-.  -
T Consensus       465 ---~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~  539 (679)
T 4e6h_A          465 ---KLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHL  539 (679)
T ss_dssp             ---GGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTH
T ss_pred             ---CCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHH
Confidence               112222223333333221 35699999999999886 3335566778888888899999999999998876432  2


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~  304 (425)
                      ....|...+.--.+.|+.+.+.++.++|.+.  .|+......+++-|
T Consensus       540 ~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          540 LKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHHHHh
Confidence            4678999999999999999999999999876  46665555555443

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.14  E-value=0.00019  Score=64.84  Aligned_cols=165  Identities=8%  Similarity=-0.026  Sum_probs=124.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...+..+-..+.+.|++++|.+.|++..+..    |+....+..+...+.+.|+   .+++...+.+....    .|+.
T Consensus       116 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~la~~~~~~g~---~~~A~~~l~~~~~~----~p~~  184 (287)
T 3qou_A          116 EEELXAQQAMQLMQESNYTDALPLLXDAWQLS----NQNGEIGLLLAETLIALNR---SEDAEAVLXTIPLQ----DQDT  184 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT----TSCHHHHHHHHHHHHHTTC---HHHHHHHHTTSCGG----GCSH
T ss_pred             chhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC----CcchhHHHHHHHHHHHCCC---HHHHHHHHHhCchh----hcch
Confidence            44556667788889999999999999987752    2223367788899999999   56666666665433    2443


Q ss_pred             hHHH-HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-cCHHhHHHHHH
Q 042756          190 QALK-SMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR-VDTVCSNMVLS  267 (425)
Q Consensus       190 ~~~~-~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~-~~~~~yn~li~  267 (425)
                      .... .....+.+.++.++|...|++..... +.+...+..+-.++...|++++|...|....+..-. .+...+..+..
T Consensus       185 ~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~  263 (287)
T 3qou_A          185 RYQGLVAQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQE  263 (287)
T ss_dssp             HHHHHHHHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHH
Confidence            3222 22333667788999999999988752 335778999999999999999999999999876322 23778999999


Q ss_pred             HHHhcCCHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~  286 (425)
                      .|...|+.++|...|++-.
T Consensus       264 ~~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          264 ILAALGTGDALASXYRRQL  282 (287)
T ss_dssp             HHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHcCCCCcHHHHHHHHH
Confidence            9999999999999888754

>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=98.13  E-value=0.00028  Score=63.75  Aligned_cols=163  Identities=7%  Similarity=-0.080  Sum_probs=111.0

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHH----HHHHHHHHHHhcCChhHHHHHHHHHHHhcCC--CchhHHHHHHHHHHHHHhcC
Q 042756           90 LSSLAFPLYMRITEESWFQWNPK----LVAEIIAFLDKQGQREEAETLILETLSKLGS--RERELVLFYCNLIDSFCKHD  163 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~----~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~--~~~~~~~~y~~li~~~~~~g  163 (425)
                      .+++|.++++.........++..    .|..+...+...|++++|.+.|++..+....  .......+|+.+-..|...|
T Consensus        90 ~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g  169 (293)
T 3u3w_A           90 RYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENG  169 (293)
T ss_dssp             CHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcC
Confidence            45666666666554332333322    3344666667778999999999998873221  11122336889999999999


Q ss_pred             CcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcC
Q 042756          164 SKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEPS-GFEYKCIIYGYGRL  237 (425)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~ty~~ll~~~~~~  237 (425)
                      +++.+.+.++...+.....+...+. ..+|+.+...|.+.|++++|...+++..+.    +..+. ..+|..+-.+|.+.
T Consensus       170 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~  249 (293)
T 3u3w_A          170 YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKL  249 (293)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHh
Confidence            9766665555555443332112222 348999999999999999999999988753    22333 66899999999999


Q ss_pred             C-CHHHHHHHHHHHHH
Q 042756          238 G-LLEDMERIVNQMES  252 (425)
Q Consensus       238 g-~~~~a~~~~~~m~~  252 (425)
                      | +.++|.+.|+....
T Consensus       250 g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          250 EYEEAEIEDAYKKASF  265 (293)
T ss_dssp             TCCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHH
Confidence            9 46999998887654

>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=98.11  E-value=0.00037  Score=59.22  Aligned_cols=131  Identities=7%  Similarity=-0.085  Sum_probs=105.8

Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 042756          152 YCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCII  231 (425)
Q Consensus       152 y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll  231 (425)
                      +..+-..+...|+   .+++...+.+.      +.|+...|..+..+|.+.|++++|...|++..... +.+...|..+-
T Consensus         9 ~~~~g~~~~~~~~---~~~A~~~~~~a------~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg   78 (213)
T 1hh8_A            9 LWNEGVLAADKKD---WKGALDAFSAV------QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRG   78 (213)
T ss_dssp             HHHHHHHHHHTTC---HHHHHHHHHTS------SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHhCC---HHHHHHHHHHH------cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHH
Confidence            4556677788898   56666666655      23566799999999999999999999999998863 33577899999


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCC--------------Cc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          232 YGYGRLGLLEDMERIVNQMESDGT--------------RV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       232 ~~~~~~g~~~~a~~~~~~m~~~g~--------------~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      .+|.+.|++++|.+.|+...+..-              .| +...|..+...|...|++++|...|++..+.  .|+.
T Consensus        79 ~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~  154 (213)
T 1hh8_A           79 MLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM--KSEP  154 (213)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCSG
T ss_pred             HHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc--Cccc
Confidence            999999999999999999887421              11 2378899999999999999999999998865  4543

>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=98.09  E-value=3.9e-05  Score=78.30  Aligned_cols=174  Identities=11%  Similarity=-0.031  Sum_probs=130.0

Q ss_pred             HHHHhhHHHHHHHHHHhH--------HhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHh
Q 042756           30 CLTARLTKQGQRFLSSLA--------LAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRI  101 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~--------~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m  101 (425)
                      .+..++.++|.+.|+...        +..+.+...+..+-..+...|+++.|...+.+.+                    
T Consensus       401 a~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al--------------------  460 (681)
T 2pzi_A          401 ATVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLA--------------------  460 (681)
T ss_dssp             HTTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHH--------------------
T ss_pred             cccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHh--------------------
Confidence            356678899999999987        3344567888888899999987777666666654                    


Q ss_pred             hhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc
Q 042756          102 TEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS  181 (425)
Q Consensus       102 ~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~  181 (425)
                       +.+  +-+...|..+-..+.+.|++++|.+.|++..+...    +....|..+-.+|.+.|++++ .+.++...+..+.
T Consensus       461 -~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P----~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~  532 (681)
T 2pzi_A          461 -ERV--GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFP----GELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG  532 (681)
T ss_dssp             -HHH--CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST----TCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT
T ss_pred             -ccC--cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC----CChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc
Confidence             222  12677888899999999999999999999887522    223367889999999999888 7777776665322


Q ss_pred             CCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCC
Q 042756          182 SSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGL  239 (425)
Q Consensus       182 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~  239 (425)
                            +...|..+-.++.+.|++++|.+.|++..+  +.|+ ...+..+..++...++
T Consensus       533 ------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~--l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          533 ------VISAAFGLARARSAEGDRVGAVRTLDEVPP--TSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             ------CHHHHHHHHHHHHHTTCHHHHHHHHHTSCT--TSTTHHHHHHHHHHHTC----
T ss_pred             ------hHHHHHHHHHHHHHcCCHHHHHHHHHhhcc--cCcccHHHHHHHHHHHHccCC
Confidence                  234899999999999999999999998876  4565 4577777777766554

>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=98.06  E-value=6.6e-05  Score=74.85  Aligned_cols=153  Identities=7%  Similarity=-0.071  Sum_probs=95.6

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcC
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMG  203 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g  203 (425)
                      .|++++|.+.|++..+.    .+.....|..+-..|.+.|++   +++...+.+.....+   -+...|..+-.+|.+.|
T Consensus         2 ~g~~~~A~~~~~~al~~----~p~~~~~~~~lg~~~~~~g~~---~~A~~~~~~al~~~p---~~~~~~~~lg~~~~~~g   71 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH----RPQDFVAWLMLADAELGMGDT---TAGEMAVQRGLALHP---GHPEAVARLGRVRWTQQ   71 (568)
T ss_dssp             -----------------------CCHHHHHHHHHHHHHHTCH---HHHHHHHHHHHTTST---TCHHHHHHHHHHHHHTT
T ss_pred             CccHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCH---HHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHCC
Confidence            36778888888877653    222233567777888888884   444444444443331   13457888888888888


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc---CCHHHHHH
Q 042756          204 QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH---NELSRMVL  280 (425)
Q Consensus       204 ~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~---g~~~~A~~  280 (425)
                      ++++|.+.|++..+.. +-+...+..+-.+|.+.|++++|.+.|+...+..- -+...+..+...+...   |+.++|.+
T Consensus        72 ~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           72 RHAEAAVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLP-EEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhccccHHHHHH
Confidence            8888888888887752 22466888888888888888888888888776532 2567788888888888   88888888


Q ss_pred             HHHHHHhC
Q 042756          281 WLQKMKDS  288 (425)
Q Consensus       281 l~~~M~~~  288 (425)
                      .|++..+.
T Consensus       150 ~~~~al~~  157 (568)
T 2vsy_A          150 QVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            88887654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.05  E-value=0.00019  Score=55.27  Aligned_cols=117  Identities=9%  Similarity=-0.018  Sum_probs=89.9

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ...|..+...+...|++++|...|++..... +.+...+..+...+...|++++|.+.++...+.. +.+...|..+...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHH
Confidence            4578888888899999999999999988752 2357788888889999999999999999887753 2357788888889


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIM  308 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~  308 (425)
                      |...|++++|...|++..+.. ..+...+..+..++...|
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  128 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLR  128 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHh
Confidence            999999999999999887652 224455555555554433

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.03  E-value=0.00017  Score=55.90  Aligned_cols=114  Identities=10%  Similarity=-0.083  Sum_probs=91.3

Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVL  266 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li  266 (425)
                      .+...|..+...+.+.|++++|...|++..... ..+...+..+...+...|++++|.+.++...+.. ..+...|..+.
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la   91 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKA   91 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHH
Confidence            345688999999999999999999999998752 2367889999999999999999999999988753 23678899999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHH
Q 042756          267 SSYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVLNSC  304 (425)
Q Consensus       267 ~~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll~~~  304 (425)
                      ..|...|++++|.+.|++..+.  .|+ ...+..+-..+
T Consensus        92 ~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~  128 (133)
T 2lni_A           92 AALEAMKDYTKAMDVYQKALDL--DSSCKEAADGYQRCM  128 (133)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CGGGTHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHh--CCCchHHHHHHHHHH
Confidence            9999999999999999998764  343 23444444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.03  E-value=0.00017  Score=58.38  Aligned_cols=102  Identities=8%  Similarity=-0.094  Sum_probs=88.8

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      ...|..+-..+.+.|++++|...|++....  .| +...|..+-.+|.+.|++++|...|+...+..- -+...|..+-.
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P-~~~~~~~~lg~  112 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGK-NDYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSS-SCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCC-CCcHHHHHHHH
Confidence            357888889999999999999999999985  44 578999999999999999999999999987642 25788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      +|...|++++|...|++..+.  .||..
T Consensus       113 ~~~~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A          113 CQLRLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCHH
Confidence            999999999999999999875  46654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.02  E-value=0.0038  Score=60.19  Aligned_cols=232  Identities=15%  Similarity=0.129  Sum_probs=128.8

Q ss_pred             HhhH---HHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcC-----ChHHHHHHHHhhhCCCCCCCchh-------------
Q 042756           33 ARLT---KQGQRFLSSLALAVTRDSKAASRLISKFVASS-----PQFIALNALSHLLSPDTTHPRLS-------------   91 (425)
Q Consensus        33 ~~~~---~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~-----~~~~a~~~~~~~l~~~~~~~~~~-------------   91 (425)
                      .|..   ++|.+.|+...+.   +...+..|-..+...+     +.++|...+.+....+... ...             
T Consensus        48 ~g~~~d~~~A~~~~~~A~~~---~~~A~~~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~g~~~-A~~~Lg~~y~~~~~~~  123 (452)
T 3e4b_A           48 TRDPAQIKQAEATYRAAADT---SPRAQARLGRLLAAKPGATEAEHHEAESLLKKAFANGEGN-TLIPLAMLYLQYPHSF  123 (452)
T ss_dssp             --------------------------CHHHHHHHHHTC--CCHHHHHHHHHHHHHHHHTTCSS-CHHHHHHHHHHCGGGC
T ss_pred             cCCCCCHHHHHHHHHHHHhC---CHHHHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHCCCHH-HHHHHHHHHHhCCCCC
Confidence            4555   6777777766543   5555555655454444     5667888887776654321 111             


Q ss_pred             --hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           92 --SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        92 --~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                        ..+.+.+......+    ++.....+-..|...+.++++.+-.....+......+.   .+..|-..|.+.|......
T Consensus       124 ~~~~a~~~~~~a~~~g----~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~~~~---a~~~Lg~~~~~~g~~~~~~  196 (452)
T 3e4b_A          124 PNVNAQQQISQWQAAG----YPEAGLAQVLLYRTQGTYDQHLDDVERICKAALNTTDI---CYVELATVYQKKQQPEQQA  196 (452)
T ss_dssp             TTCCHHHHHHHHHHHT----CTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTTCTT---HHHHHHHHHHHTTCHHHHH
T ss_pred             CCHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHcCCHH---HHHHHHHHHHHcCCcccHH
Confidence              23444444444443    23344456666666675555555444443332222333   4566777777778555577


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc----CChhHHHHHHHHHHHcCCCCCHHHHHHHHHH-H--HcCCCHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEM----GQPHEAENLIEEMRVKGLEPSGFEYKCIIYG-Y--GRLGLLED  242 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~----g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~-~--~~~g~~~~  242 (425)
                      +++..+.+....++   ++...+..+-..|...    +++++|++.|++.. .|   +...+..+-.. +  ...++.++
T Consensus       197 ~A~~~~~~aa~~g~---~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~  269 (452)
T 3e4b_A          197 ELLKQMEAGVSRGT---VTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQ  269 (452)
T ss_dssp             HHHHHHHHHHHTTC---SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHH
T ss_pred             HHHHHHHHHHHCCC---HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHH
Confidence            78888877766653   2333446666666554    68888888888877 33   34455555444 3  45788888


Q ss_pred             HHHHHHHHHHCCCCcCHHhHHHHHHHHHhcC-----CHHHHHHHHHHHH
Q 042756          243 MERIVNQMESDGTRVDTVCSNMVLSSYGDHN-----ELSRMVLWLQKMK  286 (425)
Q Consensus       243 a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g-----~~~~A~~l~~~M~  286 (425)
                      |.+.|+...+.|   +...+..|-..|. .|     ++++|.++|++..
T Consensus       270 A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa  314 (452)
T 3e4b_A          270 MMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV  314 (452)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh
Confidence            888888888776   5667777777776 44     8888888888876

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.02  E-value=0.00015  Score=65.56  Aligned_cols=150  Identities=12%  Similarity=-0.034  Sum_probs=101.5

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      ..++|...|++....+.  -+...+..+...+.+.|++++|.+.|++......  ..  ..........+.+.++.+.+.
T Consensus       132 ~~~~A~~~~~~al~~~P--~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p--~~--~~~~~~~~~~l~~~~~~~~a~  205 (287)
T 3qou_A          132 NYTDALPLLXDAWQLSN--QNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQ--DT--RYQGLVAQIELLXQAADTPEI  205 (287)
T ss_dssp             CHHHHHHHHHHHHHHTT--SCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGC--SH--HHHHHHHHHHHHHHHTSCHHH
T ss_pred             CHHHHHHHHHHHHHhCC--cchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhc--ch--HHHHHHHHHHHHhhcccCccH
Confidence            34445555555444331  2667788899999999999999999998765422  22  112222333355556644444


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLE-PSGFEYKCIIYGYGRLGLLEDMERIVN  248 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~ty~~ll~~~~~~g~~~~a~~~~~  248 (425)
                      +.++...+..+      .+...+..+-..+...|++++|.+.|.+..+..-. .+...+..+...+...|+.++|...++
T Consensus       206 ~~l~~al~~~P------~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r  279 (287)
T 3qou_A          206 QQLQQQVAENP------EDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYR  279 (287)
T ss_dssp             HHHHHHHHHCT------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHhcCC------ccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHH
Confidence            44433333221      23458999999999999999999999999986321 125689999999999999999988887


Q ss_pred             HHH
Q 042756          249 QME  251 (425)
Q Consensus       249 ~m~  251 (425)
                      +-.
T Consensus       280 ~al  282 (287)
T 3qou_A          280 RQL  282 (287)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            644

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.01  E-value=0.00077  Score=58.18  Aligned_cols=156  Identities=11%  Similarity=0.029  Sum_probs=102.0

Q ss_pred             hhhhHHHHHHHhhhcCCCcc-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-------
Q 042756           90 LSSLAFPLYMRITEESWFQW-NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK-------  161 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~-~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~-------  161 (425)
                      .+++|...|+.+.....-.+ ....+..+..+|.+.|++++|.+.|++..+...... .....+-.+-.++.+       
T Consensus        19 ~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~-~~~~a~~~~g~~~~~~~~~~~~   97 (225)
T 2yhc_A           19 NWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHP-NIDYVMYMRGLTNMALDDSALQ   97 (225)
T ss_dssp             CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCT-THHHHHHHHHHHHHHHHC----
T ss_pred             CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCC-cHHHHHHHHHHHHHhhhhhhhh
Confidence            44555555555444321222 245677788999999999999999999887533222 111122233333332       


Q ss_pred             -----------cCCcccHHHHHHHHHHHhhcCCCCccChhHH-----------------HHHHHHHHhcCChhHHHHHHH
Q 042756          162 -----------HDSKRGFDDTYARLNQLVNSSSSVYVKRQAL-----------------KSMISGLCEMGQPHEAENLIE  213 (425)
Q Consensus       162 -----------~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~-----------------~~li~~~~~~g~~~~a~~~~~  213 (425)
                                 .|+   .+++...+.+.....+.. +  ..+                 -.+...|.+.|++++|...|+
T Consensus        98 ~~~~~~~~~~~~~~---~~~A~~~~~~~l~~~P~~-~--~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~  171 (225)
T 2yhc_A           98 GFFGVDRSDRDPQQ---ARAAFSDFSKLVRGYPNS-Q--YTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE  171 (225)
T ss_dssp             ----------CCHH---HHHHHHHHHHHHTTCTTC-T--THHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hhhccchhhcCcHH---HHHHHHHHHHHHHHCcCC-h--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence                       234   566666666665433211 1  122                 234567888999999999999


Q ss_pred             HHHHcCCCCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          214 EMRVKGLEPS----GFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       214 ~m~~~g~~p~----~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      ++.+.  -|+    ...+..+..+|.+.|+.++|.+.++.+...+
T Consensus       172 ~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          172 GMLRD--YPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            99885  343    2568889999999999999999999988864

>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=98.01  E-value=0.00015  Score=55.93  Aligned_cols=113  Identities=9%  Similarity=-0.022  Sum_probs=90.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CcC----HHhHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT--RVD----TVCSN  263 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~--~~~----~~~yn  263 (425)
                      ..|..+...+...|++++|...|++..... +.+...+..+...+...|++++|...++...+..-  .++    ..+|.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            478888889999999999999999998763 34677888999999999999999999998876421  112    77889


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCS  305 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~  305 (425)
                      .+...|...|++++|.+.|++..+.  .|+......+-....
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~  123 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQQAEK  123 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHHHHHH
Confidence            9999999999999999999998875  466655555544433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.97  E-value=0.00054  Score=65.29  Aligned_cols=213  Identities=11%  Similarity=0.005  Sum_probs=136.2

Q ss_pred             HHHHhcCChHHHHHHHHhhhCCCCCCCch------hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHH
Q 042756           62 SKFVASSPQFIALNALSHLLSPDTTHPRL------SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLIL  135 (425)
Q Consensus        62 ~~~~~~~~~~~a~~~~~~~l~~~~~~~~~------~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~  135 (425)
                      ..+.+.|++.+|.+.+.+++.........      ......            .....+..+...|.+.|++++|.+++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~------------~~~~al~~l~~~y~~~~~~~~a~~~~~   79 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRN------------EQETSILELGQLYVTMGAKDKLREFIP   79 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHH------------HHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhh------------hHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            44566677777877777776544322210      000000            011246678999999999999999999


Q ss_pred             HHHHhcCCC-chhHHHHHHHHHH-HHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHH
Q 042756          136 ETLSKLGSR-ERELVLFYCNLID-SFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIE  213 (425)
Q Consensus       136 ~m~~~~~~~-~~~~~~~y~~li~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  213 (425)
                      ...+..... ...........+. .+...|+.+.+.+.+...............-..++..+...|...|++++|..+++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~  159 (434)
T 4b4t_Q           80 HSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALIN  159 (434)
T ss_dssp             HTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHH
Confidence            876532222 2111111222333 33345665444444444444333322222234588899999999999999999999


Q ss_pred             HHHHc--C--CCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCcC--HHhHHHHHHHHHhcCCHHHHHHHH
Q 042756          214 EMRVK--G--LEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRVD--TVCSNMVLSSYGDHNELSRMVLWL  282 (425)
Q Consensus       214 ~m~~~--g--~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~~--~~~yn~li~~~~~~g~~~~A~~l~  282 (425)
                      +....  +  -.| ...+|..++..|...|+++.|..+++.....    +..+.  ...|..+...+...|++++|...|
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~  239 (434)
T 4b4t_Q          160 DLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYF  239 (434)
T ss_dssp             HHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHH
T ss_pred             HHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            98754  1  122 2458899999999999999999999876532    22211  466777788888999999999988


Q ss_pred             HHHH
Q 042756          283 QKMK  286 (425)
Q Consensus       283 ~~M~  286 (425)
                      .+..
T Consensus       240 ~~a~  243 (434)
T 4b4t_Q          240 FESF  243 (434)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8764

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.96  E-value=0.00018  Score=57.59  Aligned_cols=106  Identities=11%  Similarity=-0.017  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcC--CCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLG--SRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~--~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      ..++..+-..+...|++++|.+.+++..+...  ........++..+-..+...|+++.+.+.++...+...........
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~   88 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHH
Confidence            44677788888889999999999888765211  1111112244555555666666444443333333332222111111


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~  216 (425)
                      ...+..+-..+...|++++|.+.|++..
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~  116 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHL  116 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            2344444555555555555555554443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.96  E-value=3.4e-05  Score=62.30  Aligned_cols=52  Identities=8%  Similarity=-0.199  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDME  244 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~  244 (425)
                      +|..+-.+|.+.|++++|+..|++..+.  .| +..+|..+-..|.+.|+.++|.
T Consensus        67 a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa  119 (150)
T 4ga2_A           67 AHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRA  119 (150)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHH
T ss_pred             HHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHH
Confidence            5555555555555555555555555442  23 2344555555555555554433

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.96  E-value=0.0003  Score=63.55  Aligned_cols=138  Identities=9%  Similarity=-0.043  Sum_probs=97.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCC--CchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-CccChh
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSKLGS--RERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYVKRQ  190 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~--~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p~~~  190 (425)
                      +..+...+...|++++|.+.|++..+....  .......+|+.+-..|...|+++.+.+.++...+.....+. ......
T Consensus       118 ~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~  197 (293)
T 2qfc_A          118 QYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVK  197 (293)
T ss_dssp             HHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHH
Confidence            334556677889999999999987753211  12222447888999999999966655555555433232211 111235


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCC-HHHHHHHHHHHHcCCCHHHH-HHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKG----LEPS-GFEYKCIIYGYGRLGLLEDM-ERIVNQME  251 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~-~~ty~~ll~~~~~~g~~~~a-~~~~~~m~  251 (425)
                      +|+.+...|.+.|++++|+..|++..+..    .... ..+|..+-.+|.+.|+.++| ...++...
T Consensus       198 ~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          198 VRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            89999999999999999999999987532    1111 66889999999999999999 77777654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.96  E-value=0.00022  Score=60.92  Aligned_cols=139  Identities=10%  Similarity=-0.062  Sum_probs=91.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      ..+-..|.+.|++++|.+.|++..+..    |.....+..+-..|...|+++++.+.++...+.-+.      +..+|..
T Consensus        58 ~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~------~~~a~~~  127 (208)
T 3urz_A           58 TELALAYKKNRNYDKAYLFYKELLQKA----PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEAD------NLAANIF  127 (208)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT------CHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC------CHHHHHH
Confidence            348888999999999999999988752    222446788999999999965555555555444222      2348888


Q ss_pred             HHHHHHhcCC--hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          195 MISGLCEMGQ--PHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       195 li~~~~~~g~--~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      +-.+|...|+  .+.+...|+....  ..|....+-..-.++...|++++|...|+...+.  .|+......+.+
T Consensus       128 lg~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~l~~  198 (208)
T 3urz_A          128 LGNYYYLTAEQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKTLDK  198 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHHHHH
Confidence            8888866653  4455666655432  2233333444455667789999999999998875  577655544433

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.95  E-value=0.00036  Score=54.35  Aligned_cols=102  Identities=10%  Similarity=-0.123  Sum_probs=84.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|...-..|.+.|++++|++.|++..+.. +-+...|..+-.+|.+.|++++|.+.|+...+..- .+...|..+-.+|
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS-KFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh-hhhHHHHHHHHHH
Confidence            477788888999999999999999988752 33578899999999999999999999998887542 3578899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHH
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      ...|++++|.+.|++..+.  .|+..
T Consensus        92 ~~~~~~~~A~~~~~~al~l--~P~~~  115 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQV--DPSNE  115 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCH
T ss_pred             HHCCCHHHHHHHHHHHHHH--CcCCH
Confidence            9999999999999998764  56543

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.95  E-value=0.00014  Score=59.99  Aligned_cols=113  Identities=6%  Similarity=-0.064  Sum_probs=81.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHcCCCH--HHHHHHHHHHHHCCCCcCHHhHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYG-YGRLGLL--EDMERIVNQMESDGTRVDTVCSNMVL  266 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~-~~~~g~~--~~a~~~~~~m~~~g~~~~~~~yn~li  266 (425)
                      ..|..+...|...|++++|...|++..... +.+...+..+..+ +...|++  ++|...|+...+..- .+...|..+.
T Consensus        45 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la  122 (177)
T 2e2e_A           45 EQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTRAMIDKALALDS-NEITALMLLA  122 (177)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhCC-CcHHHHHHHH
Confidence            478888888888888888888888887642 2255677777777 7788887  888888888876532 2567788888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          267 SSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       267 ~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      ..|...|++++|...|++..+.  .|+......++....+
T Consensus       123 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~i~~  160 (177)
T 2e2e_A          123 SDAFMQANYAQAIELWQKVMDL--NSPRINRTQLVESINM  160 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHT--CCTTSCHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhh--CCCCccHHHHHHHHHH
Confidence            8888999999999999988764  3443333444444433

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.93  E-value=0.00019  Score=64.88  Aligned_cols=135  Identities=10%  Similarity=-0.026  Sum_probs=97.7

Q ss_pred             HHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 042756          172 YARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLE-PSGFEYKCIIYGYGRLGLLEDMERIVNQM  250 (425)
Q Consensus       172 ~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~ty~~ll~~~~~~g~~~~a~~~~~~m  250 (425)
                      ...+.+....+   .++..++..+..++...|++++|++++.+-...|-. -+...+..++..+.+.|+.+.|.+.++.|
T Consensus        86 ~~~l~~l~~~~---~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           86 IEELENLLKDK---QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             CHHHHHTTTTS---CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC---CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444444332   234446668889999999999999999998665432 25668889999999999999999999999


Q ss_pred             HHCCCCc-----CHHhHHHHHHHHH--h--cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          251 ESDGTRV-----DTVCSNMVLSSYG--D--HNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       251 ~~~g~~~-----~~~~yn~li~~~~--~--~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .+.  .|     +..+...|..+++  .  .++..+|..+|+++.+.  .|+..+-..+++++.+.|+++.+
T Consensus       163 ~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eA  230 (310)
T 3mv2_B          163 TNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEA  230 (310)
T ss_dssp             HHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHH
T ss_pred             Hhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHH
Confidence            875  45     3566666666633  2  34899999999998765  46655556666666666766554

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.93  E-value=0.00074  Score=57.31  Aligned_cols=106  Identities=8%  Similarity=0.006  Sum_probs=68.6

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCC-----
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSS-----  183 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~-----  183 (425)
                      |++..+..+...|.+.|++++|.+.|++..+..    +.....|..+-..|.+.|+++.+.+.++...+..+...     
T Consensus        35 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  110 (213)
T 1hh8_A           35 PHSRICFNIGCMYTILKNMTEAEKAFTRSINRD----KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYK  110 (213)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECG
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----ccchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHH
Confidence            466777888888888888888888888877652    12233567777888888885544444444444322211     


Q ss_pred             ----CCcc-ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          184 ----SVYV-KRQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       184 ----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                          ...| ....|..+..+|.+.|++++|.+.|++..+.
T Consensus       111 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A          111 ILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             GGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence                0111 1247777777888888888888888877764

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.91  E-value=0.00055  Score=51.99  Aligned_cols=63  Identities=10%  Similarity=0.017  Sum_probs=40.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..|..+...+.+.|++++|..+|+++.... +.+..++..+...|...|++++|.+.|+...+.
T Consensus        44 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           44 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            356666666666666667766666666542 224556666666677777777777777666554

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.90  E-value=0.00083  Score=54.20  Aligned_cols=121  Identities=7%  Similarity=-0.078  Sum_probs=89.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|..+...+...|++++|...|++..... +.+..++..+..++...|++++|.+.++...+.. +.+...|..+...|
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            377788888888999999999999887752 2357788888888999999999999999887753 23577888888899


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH--HHHHHHHHHHHHh
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSVRTYNSV--LNSCSTIMSMLQD  313 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l--l~~~~~~~~~~~~  313 (425)
                      ...|++++|...|++..+.. ..+...+..+  ...+...|+++++
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A  136 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERA  136 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999987642 1233344333  3335556666555

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.89  E-value=0.00023  Score=57.62  Aligned_cols=93  Identities=8%  Similarity=-0.177  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHH--HHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNM--VLSS  268 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~--li~~  268 (425)
                      .|..+..++...|++++|.+.|++..... +.+...|..+..++.+.|++++|.+.|+...+..- .+...+..  +...
T Consensus        49 ~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~  126 (166)
T 1a17_A           49 YYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNK  126 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            44555555555555555555555555431 12344555555555555666666655555554321 12223322  2222


Q ss_pred             HHhcCCHHHHHHHHHHH
Q 042756          269 YGDHNELSRMVLWLQKM  285 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M  285 (425)
                      +...|++++|.+.+.+.
T Consensus       127 ~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A          127 IVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccch
Confidence            45556666666665544

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.86  E-value=0.00074  Score=50.71  Aligned_cols=98  Identities=9%  Similarity=-0.111  Sum_probs=83.9

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ...|..+...+...|++++|.+.|++..... +.+...+..+...+.+.|++++|...++...+..- .+...|..+...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHHHH
Confidence            3478888899999999999999999998753 23677888899999999999999999999887642 367889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhC
Q 042756          269 YGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~  288 (425)
                      |...|++++|.+.|++..+.
T Consensus        82 ~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHhhHHHHHHHHHHHHHc
Confidence            99999999999999998864

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.85  E-value=0.00063  Score=52.51  Aligned_cols=97  Identities=8%  Similarity=-0.082  Sum_probs=83.3

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|..+-..+.+.|++++|...|++..+.. +.+...|..+-.+|.+.|++++|...|+...+..- .+...|..+-.+|
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHH
Confidence            477888888999999999999999998753 33578999999999999999999999999887642 3578899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhC
Q 042756          270 GDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~  288 (425)
                      ...|++++|...|++..+.
T Consensus        83 ~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           83 IAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHh
Confidence            9999999999999998753

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.85  E-value=0.00092  Score=54.35  Aligned_cols=119  Identities=10%  Similarity=-0.101  Sum_probs=93.5

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      +...|..+-..+.+.|++++|++.|++..+.. .-+...|..+-.+|.+.|++++|...|+...+..- -+...|..+-.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDP-KYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            45688889999999999999999999998853 22678999999999999999999999999887642 35889999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSG-IPFSVRTYNSVLNSCSTIM  308 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g-~~pd~~t~~~ll~~~~~~~  308 (425)
                      .|...|++++|...|++..+.. -.++......+..+..+.+
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~  129 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEAEGNGGSDAMKRGLETTKRKIE  129 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHH
Confidence            9999999999999999987532 2233333444444433333

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.84  E-value=0.0009  Score=53.36  Aligned_cols=146  Identities=12%  Similarity=-0.062  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHH
Q 042756           55 KAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLI  134 (425)
Q Consensus        55 ~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~  134 (425)
                      .++..+-..+...|+++.|...+.+.+              +++.....   ......++..+-..+...|++++|.+.+
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al--------------~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~   72 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRL--------------LIAKEFGD---KAAERIAYSNLGNAYIFLGEFETASEYY   72 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH--------------HHHHHHTC---HHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHH--------------HHHHHhCC---chHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            456777777888888888877776643              23332211   1122357888899999999999999999


Q ss_pred             HHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH
Q 042756          135 LETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI  212 (425)
Q Consensus       135 ~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  212 (425)
                      ++..+.  .....+.....+..+-..+...|+++.+.+.++...+..............+..+-..|...|++++|.+.+
T Consensus        73 ~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  152 (164)
T 3ro3_A           73 KKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFA  152 (164)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHH
Confidence            997652  112222334467778888999999766666555555543332222122346777778888888888888888


Q ss_pred             HHHHH
Q 042756          213 EEMRV  217 (425)
Q Consensus       213 ~~m~~  217 (425)
                      ++..+
T Consensus       153 ~~a~~  157 (164)
T 3ro3_A          153 EKHLE  157 (164)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77654

>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=97.83  E-value=0.00065  Score=56.07  Aligned_cols=130  Identities=13%  Similarity=0.077  Sum_probs=68.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHH-HHhcCCcccHHHHHHHHHHHhhcCCCCcc-
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDS-FCKHDSKRGFDDTYARLNQLVNSSSSVYV-  187 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~-~~~~g~~~~~~~~~~~~~~~~~~~~~~~p-  187 (425)
                      +...+..+-..+.+.|++++|...|++..+...  .+.   .+..+... +.+.+....   +...+.+.....    | 
T Consensus        39 ~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~---~~~~~~~~~~~~~~~~~~---a~~~~~~al~~~----P~  106 (176)
T 2r5s_A           39 RGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNS---YKSLIAKLELHQQAAESP---ELKRLEQELAAN----PD  106 (176)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHH---HHHHHHHHHHHHHHTSCH---HHHHHHHHHHHS----TT
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChH---HHHHHHHHHHHhhcccch---HHHHHHHHHHhC----CC
Confidence            455566666667777777777777766544321  111   11111101 111111111   223333332211    2 


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      +...+..+-.++...|++++|...|++..+..-.+ +...+..+...+...|+.++|...|+...
T Consensus       107 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          107 NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            23466777777777777777777777776643221 24566777777777777777777776544

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.79  E-value=0.0026  Score=49.51  Aligned_cols=98  Identities=11%  Similarity=-0.045  Sum_probs=85.4

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLS  267 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~  267 (425)
                      +...|..+-..+.+.|++++|...|++..... +.+...|..+-.++...|++++|...++...+..- .+...|..+-.
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHHHH
Confidence            45689999999999999999999999988753 23577899999999999999999999999887642 36788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHh
Q 042756          268 SYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~  287 (425)
                      .|...|++++|...|++..+
T Consensus        86 ~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHH
Confidence            99999999999999999864

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.79  E-value=0.00038  Score=51.86  Aligned_cols=97  Identities=8%  Similarity=-0.152  Sum_probs=83.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc--CHHhHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV--DTVCSNMVLS  267 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~--~~~~yn~li~  267 (425)
                      ..|..+...+.+.|++++|...|++..+.. ..+...+..+-.++.+.|++++|.+.|+...+.. ..  +...|..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~   84 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKAD   84 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHH
Confidence            478888899999999999999999998753 3357788899999999999999999999988763 22  5788999999


Q ss_pred             HHHhc-CCHHHHHHHHHHHHhC
Q 042756          268 SYGDH-NELSRMVLWLQKMKDS  288 (425)
Q Consensus       268 ~~~~~-g~~~~A~~l~~~M~~~  288 (425)
                      .|... |++++|.+.|++....
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           85 ALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHhCCHHHHHHHHHHHhhc
Confidence            99999 9999999999998765

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.77  E-value=0.00047  Score=55.34  Aligned_cols=98  Identities=9%  Similarity=-0.051  Sum_probs=81.7

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ...+..+-..+.+.|++++|...|++..... +.+...|..+-.+|...|++++|.+.|+...+..- -+...|..+-.+
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~   98 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDI-XEPRFPFHAAEC   98 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHH
Confidence            3477778888999999999999999988752 23677888888999999999999999999887532 357788889999


Q ss_pred             HHhcCCHHHHHHHHHHHHhC
Q 042756          269 YGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~  288 (425)
                      |...|++++|...|++..+.
T Consensus        99 ~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           99 LLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHH
Confidence            99999999999999998753

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.77  E-value=0.0012  Score=50.62  Aligned_cols=119  Identities=6%  Similarity=-0.103  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHH
Q 042756          149 VLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYK  228 (425)
Q Consensus       149 ~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~  228 (425)
                      ...+..+...+...|+++   ++...+.+.....+   .+...|..+...+...|++++|.+.|++..... +.+...+.
T Consensus        12 ~~~~~~~~~~~~~~~~~~---~A~~~~~~~~~~~~---~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~   84 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFE---AAVHFYGKAIELNP---ANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYG   84 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHH---HHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             hHHHHHHHHHHHHccCHH---HHHHHHHHHHHcCC---CCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHH
Confidence            345666777777777744   44444444332211   134578888888888999999999998888752 23467888


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCH
Q 042756          229 CIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNEL  275 (425)
Q Consensus       229 ~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~  275 (425)
                      .+...+.+.|++++|.+.|+...+..- .+...+..+...+.+.|+.
T Consensus        85 ~~~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           85 RMGLALSSLNKHVEAVAYYKKALELDP-DNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHHhcC
Confidence            888888999999999999988876532 2566777777777776653

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.76  E-value=0.00066  Score=52.82  Aligned_cols=106  Identities=14%  Similarity=0.091  Sum_probs=83.9

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCcC----HHhH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDG--TRVD----TVCS  262 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g--~~~~----~~~y  262 (425)
                      ..+..+-..+.+.|++++|++.|++..+.  .| +...|..+-.+|.+.|++++|.+.|+...+..  ..++    ..+|
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            37788888999999999999999998874  44 47789999999999999999999999876531  1111    3467


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHH
Q 042756          263 NMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNS  299 (425)
Q Consensus       263 n~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~  299 (425)
                      ..+-.+|...|++++|++.|++..+.  .||..+...
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~~  121 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVKK  121 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHHH
Confidence            77888889999999999999997763  566655443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.74  E-value=0.0011  Score=52.19  Aligned_cols=102  Identities=12%  Similarity=-0.048  Sum_probs=86.9

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHH
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS----GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSN  263 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn  263 (425)
                      +...|..+...+.+.|++++|.+.|++..+.  .|+    ...+..+-.+|...|++++|.+.++...+.. ..+...|.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHH
Confidence            4568889999999999999999999999874  566    6788889999999999999999999887753 23678888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      .+...|...|++++|...|++..+.  .|+.
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~--~p~~  132 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSL--EPKN  132 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH--CSSC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc--CCCc
Confidence            9999999999999999999998764  4543

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.74  E-value=0.00098  Score=61.57  Aligned_cols=95  Identities=3%  Similarity=-0.220  Sum_probs=78.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|..+-.+|.+.|++++|+..|++..+.. +.+...|..+-.+|...|++++|...|+...+..- -+...+..+...+
T Consensus       197 ~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~  274 (336)
T 1p5q_A          197 ASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYP-NNKAAKTQLAVCQ  274 (336)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHH
Confidence            488999999999999999999999998853 23677899999999999999999999998887532 2577888899999


Q ss_pred             HhcCCHHHH-HHHHHHHH
Q 042756          270 GDHNELSRM-VLWLQKMK  286 (425)
Q Consensus       270 ~~~g~~~~A-~~l~~~M~  286 (425)
                      .+.|+.++| ..+|++|.
T Consensus       275 ~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          275 QRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999888 44666664

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.73  E-value=0.00027  Score=56.90  Aligned_cols=137  Identities=11%  Similarity=-0.051  Sum_probs=95.2

Q ss_pred             chhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           89 RLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        89 ~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      +.+++|+..|......+  +-++..+-.+-..|.+.|++++|.+.|++..+.    .|.....|..+-..|.+.|+++.+
T Consensus        11 ~~~e~ai~~~~~a~~~~--p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~----~p~~~~a~~~lg~~~~~~~~~~~A   84 (150)
T 4ga2_A           11 ADVERYIASVQGSTPSP--RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV----QERDPKAHRFLGLLYELEENTDKA   84 (150)
T ss_dssp             HHHHHHHHHHHHHSCSH--HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             ChHHHHHHHHHHhcccC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCchHHH
Confidence            35677777777654432  113334556888899999999999999998875    223344788999999999996555


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHH-HHHHHcCCCC-CHHHHHHHHHHHHcCCC
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLI-EEMRVKGLEP-SGFEYKCIIYGYGRLGL  239 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~-~~m~~~g~~p-~~~ty~~ll~~~~~~g~  239 (425)
                      .+.++...+..+.      +..+|..+-..|.+.|+.++|.+.| ++..+.  .| +..+|...-..+.+.|+
T Consensus        85 ~~~~~~al~~~p~------~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           85 VECYRRSVELNPT------QKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHCTT------CHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHhCCC------CHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhCc
Confidence            5555554443221      2458999999999999998877764 776663  45 45677776666666664

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.72  E-value=0.00058  Score=52.73  Aligned_cols=80  Identities=5%  Similarity=-0.176  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .|..+...|...|++++|.+.|++..+.. ..+...+..+..++.+.|++++|.+.|+...+..- -+...+..+...+.
T Consensus        52 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~  129 (133)
T 2lni_A           52 LYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDS-SCKEAADGYQRCMM  129 (133)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCG-GGTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCC-CchHHHHHHHHHHH
Confidence            55555555555666666666666555531 12345555566666666666666666665554321 12344444444444


Q ss_pred             hc
Q 042756          271 DH  272 (425)
Q Consensus       271 ~~  272 (425)
                      ..
T Consensus       130 ~~  131 (133)
T 2lni_A          130 AQ  131 (133)
T ss_dssp             HH
T ss_pred             Hh
Confidence            33

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.72  E-value=0.0095  Score=54.00  Aligned_cols=223  Identities=8%  Similarity=-0.036  Sum_probs=146.2

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHH
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLV  114 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~  114 (425)
                      ..++|+++++.+...-+-+..+||.--..+...+.                   ..+++++++++.+...+.-  +..+|
T Consensus        48 ~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~-------------------~~~~eeL~~~~~~L~~nPk--~y~aW  106 (306)
T 3dra_A           48 YSERALHITELGINELASHYTIWIYRFNILKNLPN-------------------RNLYDELDWCEEIALDNEK--NYQIW  106 (306)
T ss_dssp             CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTT-------------------SCHHHHHHHHHHHHHHCTT--CCHHH
T ss_pred             CCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHccc-------------------ccHHHHHHHHHHHHHHCcc--cHHHH
Confidence            44567777777776544456667766666665551                   1455566666665554422  33334


Q ss_pred             HHHHHHH----Hhc---CChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          115 AEIIAFL----DKQ---GQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       115 ~~ll~~~----~~~---g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      +.--..+    .+.   +++++++++++.+.+.    .|.+..+|+.---.+.+.|.++ ..+.++.+.++.....   -
T Consensus       107 ~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~----~pkny~aW~~R~~vl~~l~~~~-~~~EL~~~~~~i~~d~---~  178 (306)
T 3dra_A          107 NYRQLIIGQIMELNNNDFDPYREFDILEAMLSS----DPKNHHVWSYRKWLVDTFDLHN-DAKELSFVDKVIDTDL---K  178 (306)
T ss_dssp             HHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHCT---T
T ss_pred             HHHHHHHHHHHHhccccCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHhcccC-hHHHHHHHHHHHHhCC---C
Confidence            4333333    444   7899999999999875    2222345666666666777754 1244455555543331   2


Q ss_pred             ChhHHHHHHHHHHhcCC------hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH-HHHHHHHHHHHHCC--CCcC
Q 042756          188 KRQALKSMISGLCEMGQ------PHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLL-EDMERIVNQMESDG--TRVD  258 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~------~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~-~~a~~~~~~m~~~g--~~~~  258 (425)
                      |-..|+.--..+.+.+.      ++++++.++++.... +-|...|+-.-..+.+.|+. +.+..+.+...+.+  -..+
T Consensus       179 N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s  257 (306)
T 3dra_A          179 NNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTS  257 (306)
T ss_dssp             CHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESC
T ss_pred             CHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCC
Confidence            44588877777777776      889999999988753 33778888888888888874 44555666655432  1347


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          259 TVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       259 ~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ...+..+.+.|.+.|+.++|.++++.+.+
T Consensus       258 ~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          258 SFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            88999999999999999999999999875

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.72  E-value=0.00014  Score=61.50  Aligned_cols=95  Identities=9%  Similarity=-0.072  Sum_probs=53.5

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|..+-.+|.+.|++++|+..|++..... +.+...+..+-.+|...|++++|.+.|+...+.. +-+...+..+...+
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  166 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCV  166 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHH
Confidence            466666677777777777777777766642 2245566666666777777777777777665542 12455566666666


Q ss_pred             HhcCCHHHHH-HHHHHHH
Q 042756          270 GDHNELSRMV-LWLQKMK  286 (425)
Q Consensus       270 ~~~g~~~~A~-~l~~~M~  286 (425)
                      ...|+.+++. ..|..|.
T Consensus       167 ~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          167 NKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             HHHHHHHC----------
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence            6555555554 3444443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.72  E-value=0.00066  Score=53.82  Aligned_cols=97  Identities=8%  Similarity=-0.038  Sum_probs=81.4

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..+..+-..+.+.|++++|...|++..... +.+...|..+-.+|.+.|++++|...|+...+..- -+...|..+-.+|
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~   96 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDI-NEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHHHHH
Confidence            466677788899999999999999988752 23677888888999999999999999999887642 3677888899999


Q ss_pred             HhcCCHHHHHHHHHHHHhC
Q 042756          270 GDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~  288 (425)
                      ...|++++|...|++..+.
T Consensus        97 ~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            9999999999999998754

>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=97.71  E-value=0.0054  Score=52.30  Aligned_cols=178  Identities=11%  Similarity=-0.018  Sum_probs=121.7

Q ss_pred             HHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHH
Q 042756           39 GQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEII  118 (425)
Q Consensus        39 a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll  118 (425)
                      |.+.|+...+.  -+..++..|-..|...++.++|...+.                     ...+.+    ++..+..+-
T Consensus         5 A~~~~~~aa~~--g~~~a~~~lg~~~~~~~~~~~A~~~~~---------------------~a~~~g----~~~a~~~lg   57 (212)
T 3rjv_A            5 PGSQYQQQAEA--GDRRAQYYLADTWVSSGDYQKAEYWAQ---------------------KAAAQG----DGDALALLA   57 (212)
T ss_dssp             TTHHHHHHHHT--TCHHHHHHHHHHHHHHTCHHHHHHHHH---------------------HHHHTT----CHHHHHHHH
T ss_pred             HHHHHHHHHHC--CCHHHHHHHHHHHhcCCCHHHHHHHHH---------------------HHHHcC----CHHHHHHHH
Confidence            44555555443  677777777777777665555554444                     444444    555666666


Q ss_pred             HHHHhcC----ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh----cCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          119 AFLDKQG----QREEAETLILETLSKLGSRERELVLFYCNLIDSFCK----HDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       119 ~~~~~~g----~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~----~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ..|.. +    +.++|.+.|++..+.+   .+   ..+..|-..|..    .++   ..+++..+.+....++. .-+..
T Consensus        58 ~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~---~a~~~Lg~~y~~g~g~~~d---~~~A~~~~~~A~~~~~~-~~~~~  126 (212)
T 3rjv_A           58 QLKIR-NPQQADYPQARQLAEKAVEAG---SK---SGEIVLARVLVNRQAGATD---VAHAITLLQDAARDSES-DAAVD  126 (212)
T ss_dssp             HHTTS-STTSCCHHHHHHHHHHHHHTT---CH---HHHHHHHHHHTCGGGSSCC---HHHHHHHHHHHTSSTTS-HHHHH
T ss_pred             HHHHc-CCCCCCHHHHHHHHHHHHHCC---CH---HHHHHHHHHHHcCCCCccC---HHHHHHHHHHHHHcCCC-cchHH
Confidence            66766 6    8999999999986642   22   245566666665    445   78888888888765531 00135


Q ss_pred             HHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC------CCHHHHHHHHHHHHHCCCC
Q 042756          191 ALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL------GLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       191 ~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~------g~~~~a~~~~~~m~~~g~~  256 (425)
                      .++.|-..|..    .+++++|+..|++..+.  .++...+..+-..|.+.      .+.++|.+.|+...+.|..
T Consensus       127 a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          127 AQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             HHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            88899999998    88999999999999886  23445666676676543      3899999999998887753

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.70  E-value=0.00035  Score=57.64  Aligned_cols=119  Identities=7%  Similarity=-0.044  Sum_probs=60.4

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHH-HHhc
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISG-LCEM  202 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~-~~~~  202 (425)
                      .|++++|.+.|++..+...    .....|..+-..|...|+++.+.+.++...+..+.      +...|..+..+ +...
T Consensus        23 ~~~~~~A~~~~~~al~~~p----~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~------~~~~~~~la~~l~~~~   92 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRANP----QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE------NAELYAALATVLYYQA   92 (177)
T ss_dssp             ----CCCCHHHHHHHHHCC----SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS------CHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHHHHhCC----CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC------CHHHHHHHHHHHHHhc
Confidence            4555666666655544311    11224455555566666644333333333332211      22355555555 5566


Q ss_pred             CCh--hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          203 GQP--HEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       203 g~~--~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      |++  ++|...|++..... +-+...+..+...|...|++++|...|+...+.
T Consensus        93 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           93 SQHMTAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             TTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CCcchHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            666  66666666666542 123455666666666677777777777666654

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.69  E-value=0.002  Score=61.29  Aligned_cols=207  Identities=6%  Similarity=-0.118  Sum_probs=134.5

Q ss_pred             HHHHHhhHHHHHHHHHHhHHh-cC-CC---------------HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchh
Q 042756           29 QCLTARLTKQGQRFLSSLALA-VT-RD---------------SKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLS   91 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~-~~-~d---------------~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~   91 (425)
                      ..+..|..++|.+.|..+.+. .. .+               ..++..+...|...|+++.+.+.+.+.+.         
T Consensus        13 ~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~---------   83 (434)
T 4b4t_Q           13 RLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTE---------   83 (434)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHH---------
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---------
Confidence            345678999999999998876 21 12               13477888999999988888887777532         


Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                           ++..+....   ....+.+.+-..+...|+.+.|.+++.+....  ..........++..+...|...|+++.+.
T Consensus        84 -----~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  155 (434)
T 4b4t_Q           84 -----YMMQFAKSK---TVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSL  155 (434)
T ss_dssp             -----HHHTSCHHH---HHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             -----HHHHccchH---HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHH
Confidence                 111111110   01112222333334568899999998887542  11112222346788999999999965555


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc----CCCCC--HHHHHHHHHHHHcCCCHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK----GLEPS--GFEYKCIIYGYGRLGLLEDM  243 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~ty~~ll~~~~~~g~~~~a  243 (425)
                      +.+..+.........-.-...+|..++..|...|++++|..++++....    +..|.  ...+..+...+...|++++|
T Consensus       156 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A  235 (434)
T 4b4t_Q          156 ALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTA  235 (434)
T ss_dssp             HHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHH
Confidence            5555444433332222223468999999999999999999999987653    22222  34677777888999999999


Q ss_pred             HHHHHHHHH
Q 042756          244 ERIVNQMES  252 (425)
Q Consensus       244 ~~~~~~m~~  252 (425)
                      ...|.+..+
T Consensus       236 ~~~~~~a~~  244 (434)
T 4b4t_Q          236 FSYFFESFE  244 (434)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988877654

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.69  E-value=0.0013  Score=60.71  Aligned_cols=119  Identities=8%  Similarity=-0.158  Sum_probs=99.7

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----------------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS----------------GFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----------------~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..|..+-..|.+.|++++|...|++.....  |+                ...|..+-.+|.+.|++++|...|+...+.
T Consensus       148 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          148 TIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            478888888889999999999999888753  33                479999999999999999999999999876


Q ss_pred             CCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHh
Q 042756          254 GTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       254 g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~  313 (425)
                      . +.+...|..+-.+|...|++++|...|++..+.  .| +...+..+-..+...++..++
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            4 237889999999999999999999999998875  34 456777777788888877654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.65  E-value=0.0005  Score=55.51  Aligned_cols=104  Identities=13%  Similarity=-0.008  Sum_probs=78.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...+..+-..+.+.|++++|.+.|++..+.    .|.....|..+-.+|.+.|+++++.+.++...+..+..      .
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~----~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~------~  104 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY----DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKND------Y  104 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSC------C
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCC------c
Confidence            3445667778889999999999999998875    22224467888999999999666555555555543322      3


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF  225 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  225 (425)
                      ..|..+-.+|.+.|++++|...|++..+.  .||..
T Consensus       105 ~~~~~lg~~~~~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A          105 TPVFHTGQCQLRLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCHH
Confidence            48999999999999999999999999885  45543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.63  E-value=0.00085  Score=52.14  Aligned_cols=95  Identities=15%  Similarity=0.009  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      .+...-..|.+.|++++|.+.|++..+.    .|.....|..+-.+|.+.|+++++.+.++...+.-+      .+...|
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~----~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p------~~~~a~   84 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKR----DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS------KFIKGY   84 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------TCHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh------hhhHHH
Confidence            3444555566666666666666665543    111122445555555555553333333322222211      112355


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      ..+-.+|...|++++|.+.|++..+
T Consensus        85 ~~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           85 IRKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5555555555555555555555554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.61  E-value=0.0016  Score=50.53  Aligned_cols=110  Identities=9%  Similarity=-0.023  Sum_probs=68.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hh
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQ  190 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~  190 (425)
                      ..+..+-..+.+.|++++|++.|++..+.    .|.....|..+-.+|.+.|+++.+.+.++...+..+......+. ..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~----~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~   84 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIEL----DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAK   84 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh----CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHH
Confidence            34556777788888888888888887764    22224467778888888888655555555544443332111111 23


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEY  227 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty  227 (425)
                      +|..+-.++...|++++|++.|++....  .||..+.
T Consensus        85 ~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~  119 (127)
T 4gcn_A           85 AMSRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELV  119 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHH
Confidence            5666667777777888888877776653  4554443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.57  E-value=0.0012  Score=64.09  Aligned_cols=62  Identities=10%  Similarity=0.050  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCC--CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          226 EYKCIIYGYGRLGLLEDMERIVNQMES-----DGT--RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       226 ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~--~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +++.|-..|...|++++|+.++++..+     .|-  .-...+.+.+-.++...|.+++|+.+|.++++
T Consensus       395 ~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          395 AVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555554443322     121  11234445555666666666777777766654

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.56  E-value=0.0036  Score=55.81  Aligned_cols=216  Identities=8%  Similarity=-0.075  Sum_probs=123.0

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHH-------HHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHH---HHHHh
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRL-------ISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFP---LYMRI  101 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~l-------l~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~---lf~~m  101 (425)
                      ..++..+|.+.|......-+-....|+-+       ...+.+.+....++..+.+.+.-.   |+.+.....   +|.++
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~---p~~l~a~~~~~g~y~~~   94 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQIS---MSTLNARIAIGGLYGDI   94 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCC---GGGGCCEEECCTTTCCC
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCC---hhhhhhhhccCCccccc
Confidence            46788999999999988755567888777       344444444444444444443211   000000000   00000


Q ss_pred             hhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc
Q 042756          102 TEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS  181 (425)
Q Consensus       102 ~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~  181 (425)
                      . ....+++ ...-.....+...|++++|.++|+.+...    .+... ..-.+-..+.+.+++++   +...+......
T Consensus        95 ~-~~v~~r~-dl~LayA~~L~~~g~y~eA~~~l~~~~~~----~p~~~-~~~~~a~l~~~~~r~~d---A~~~l~~a~~~  164 (282)
T 4f3v_A           95 T-YPVTSPL-AITMGFAACEAAQGNYADAMEALEAAPVA----GSEHL-VAWMKAVVYGAAERWTD---VIDQVKSAGKW  164 (282)
T ss_dssp             E-EECSSHH-HHHHHHHHHHHHHTCHHHHHHHHTSSCCT----TCHHH-HHHHHHHHHHHTTCHHH---HHHHHTTGGGC
T ss_pred             c-cccCCHh-HHHHHHHHHHHHCCCHHHHHHHHHHHHhc----CCchH-HHHHHHHHHHHcCCHHH---HHHHHHHhhcc
Confidence            0 0001111 23444667788899999999999887653    12222 23344457778888544   44444333211


Q ss_pred             CCCCcc--ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          182 SSSVYV--KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       182 ~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                         ..|  ....+..+-.++.+.|++++|++.|++.......|.  .......-.++.+.|+.++|..+|+++....  |
T Consensus       165 ---~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~--P  239 (282)
T 4f3v_A          165 ---PDKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH--P  239 (282)
T ss_dssp             ---SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--C
T ss_pred             ---CCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--C
Confidence               111  123666777888888888888888888875443354  2244555567778888888888888887753  4


Q ss_pred             CHHhHHHH
Q 042756          258 DTVCSNMV  265 (425)
Q Consensus       258 ~~~~yn~l  265 (425)
                      +...+..|
T Consensus       240 ~~~~~~aL  247 (282)
T 4f3v_A          240 EPKVAAAL  247 (282)
T ss_dssp             CHHHHHHH
T ss_pred             cHHHHHHH
Confidence            44444433

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.56  E-value=0.015  Score=52.74  Aligned_cols=209  Identities=6%  Similarity=-0.083  Sum_probs=142.4

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcC--ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH----Hhc-
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQG--QREEAETLILETLSKLGSRERELVLFYCNLIDSF----CKH-  162 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g--~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~----~~~-  162 (425)
                      ..++|+++++.+...+.  -+..+|+.--..+...|  ++++++++++.+..... ..   ..+|+.--..+    .+. 
T Consensus        48 ~s~~aL~~t~~~L~~nP--~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nP-k~---y~aW~~R~~iL~~~~~~l~  121 (306)
T 3dra_A           48 YSERALHITELGINELA--SHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNE-KN---YQIWNYRQLIIGQIMELNN  121 (306)
T ss_dssp             CSHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCT-TC---CHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHCc--HHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCc-cc---HHHHHHHHHHHHHHHHhcc
Confidence            34567777777665541  14455676667777778  99999999999887522 12   22454433333    444 


Q ss_pred             --CCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChh--HHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC
Q 042756          163 --DSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH--EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG  238 (425)
Q Consensus       163 --g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~--~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g  238 (425)
                        ++   ..+.+..+.++....+   -+-.+|+.---.+.+.|.++  ++++.++++.+... -|...|+.--....+.|
T Consensus       122 ~~~~---~~~EL~~~~~~l~~~p---kny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~  194 (306)
T 3dra_A          122 NDFD---PYREFDILEAMLSSDP---KNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKK  194 (306)
T ss_dssp             TCCC---THHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSG
T ss_pred             ccCC---HHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcc
Confidence              45   4555566666554332   23458888888888889888  99999999998643 26677777666677777


Q ss_pred             C------HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHH-HHHHHHHHHhCC--CCCCHHHHHHHHHHHHHHHH
Q 042756          239 L------LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSR-MVLWLQKMKDSG--IPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       239 ~------~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~-A~~l~~~M~~~g--~~pd~~t~~~ll~~~~~~~~  309 (425)
                      +      ++++.+.++....... -|...|+-+-..+.+.|+..+ +..+..+..+.+  -..+...+..+...|.+.|+
T Consensus       195 ~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~  273 (306)
T 3dra_A          195 HLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKK  273 (306)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTC
T ss_pred             ccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCC
Confidence            6      8999999999887654 389999999999999888544 555777665432  13466778888888776555


Q ss_pred             HHH
Q 042756          310 MLQ  312 (425)
Q Consensus       310 ~~~  312 (425)
                      .++
T Consensus       274 ~~~  276 (306)
T 3dra_A          274 YNE  276 (306)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.55  E-value=0.001  Score=50.97  Aligned_cols=114  Identities=7%  Similarity=-0.052  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-h
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-R  189 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~  189 (425)
                      +..+..+...+...|++++|...|++..+...    .....+..+...|...|+++.+.+.++...+..+......+. .
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~----~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~   79 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDP----TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIA   79 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC----ccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHH
Confidence            34566677778888888888888888776521    112356677777777787555554444444443221100000 4


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCI  230 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~l  230 (425)
                      .+|..+..+|.+.|++++|.+.|++..+.  .|+......+
T Consensus        80 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l  118 (131)
T 1elr_A           80 KAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKC  118 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHH
Confidence            46677777777777777777777777664  3444444333

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.55  E-value=0.0014  Score=63.80  Aligned_cols=109  Identities=9%  Similarity=-0.047  Sum_probs=80.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHH----hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLS----KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-  184 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~----~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-  184 (425)
                      ...+++.|...|...|++++|+.++++..+    ..++..|+...+++.|-..|...|+++++...++...+......+ 
T Consensus       350 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~  429 (490)
T 3n71_A          350 VLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGP  429 (490)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            456899999999999999999999988754    466677888889999999999999977766655554444333211 


Q ss_pred             CccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          185 VYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       185 ~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      --|+ ..+.+.+-.++...+.+++|..+|.++++.
T Consensus       430 ~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          430 SHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            0132 245666777777888888888888888763

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.55  E-value=0.0023  Score=49.16  Aligned_cols=101  Identities=11%  Similarity=-0.070  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC---HHhHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSG----FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD---TVCSN  263 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~---~~~yn  263 (425)
                      .+..+...+.+.|++++|...|++.....  |+.    ..+..+-.++.+.|++++|...|+...+..-. +   ...+.
T Consensus         4 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~   80 (129)
T 2xev_A            4 TAYNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLL   80 (129)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHH
Confidence            34456677888999999999999998753  332    47777888999999999999999998875321 2   56788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH
Q 042756          264 MVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRT  296 (425)
Q Consensus       264 ~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t  296 (425)
                      .+..+|...|++++|...|++..+.  .|+...
T Consensus        81 ~la~~~~~~g~~~~A~~~~~~~~~~--~p~~~~  111 (129)
T 2xev_A           81 KLGLSQYGEGKNTEAQQTLQQVATQ--YPGSDA  111 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--STTSHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH--CCCChH
Confidence            8889999999999999999998875  365443

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.54  E-value=0.0045  Score=51.92  Aligned_cols=120  Identities=8%  Similarity=-0.143  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCC-CC---C-----------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGL-EP---S-----------GFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p---~-----------~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .+..+-..+.+.|++++|...|++.....- .|   .           ...|..+-.+|.+.|++++|...++...+.. 
T Consensus        40 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-  118 (198)
T 2fbn_A           40 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-  118 (198)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-
Confidence            666777778888888888888888876421 11   1           2788889999999999999999999988753 


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHh
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~  313 (425)
                      ..+...|..+-.+|...|++++|.+.|++..+.  .| +...+..+-.++...++..++
T Consensus       119 p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~  175 (198)
T 2fbn_A          119 KNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNKLKEARKK  175 (198)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHC-
T ss_pred             cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHHHHHHH
Confidence            236788999999999999999999999998765  34 455666666666666655443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.52  E-value=0.0059  Score=54.40  Aligned_cols=196  Identities=8%  Similarity=-0.056  Sum_probs=128.9

Q ss_pred             CchhhhHHHHHHHhhhcCCCccCHHHHHHH-------HHHHHhcCChhHHHHHHHHHHH------------hcCC-----
Q 042756           88 PRLSSLAFPLYMRITEESWFQWNPKLVAEI-------IAFLDKQGQREEAETLILETLS------------KLGS-----  143 (425)
Q Consensus        88 ~~~~~~a~~lf~~m~~~~~~~~~~~~~~~l-------l~~~~~~g~~~~A~~l~~~m~~------------~~~~-----  143 (425)
                      ++..+.|.+.|.+..+.+.-  .+..|..+       ...+.+.++..++...+..-..            .+..     
T Consensus        19 ~~d~~~A~~~F~~a~~~dP~--~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           19 PMSEARSLDLFTEITNYDES--ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT--CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             CCCHHHHHHHHHHHHHhChh--hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            45778888889888776633  44455555       3444444445554443333222            0000     


Q ss_pred             --CchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 042756          144 --RERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLE  221 (425)
Q Consensus       144 --~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  221 (425)
                        .+++  ..+-.+...+...|+   .+++.+.+......+    |+.....++-..+.+.+++++|+..|+...... .
T Consensus        97 ~v~~r~--dl~LayA~~L~~~g~---y~eA~~~l~~~~~~~----p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d  166 (282)
T 4f3v_A           97 PVTSPL--AITMGFAACEAAQGN---YADAMEALEAAPVAG----SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-D  166 (282)
T ss_dssp             ECSSHH--HHHHHHHHHHHHHTC---HHHHHHHHTSSCCTT----CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-C
T ss_pred             ccCCHh--HHHHHHHHHHHHCCC---HHHHHHHHHHHHhcC----CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-C
Confidence              0111  133456777888999   566777666654432    443366666678899999999999998543321 1


Q ss_pred             CC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 042756          222 PS--GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVD--TVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTY  297 (425)
Q Consensus       222 p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~--~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~  297 (425)
                      |.  ...+..+-.++.+.|++++|...|++.......|.  .......-.++.+.|+.++|..+|+++...  .|+...+
T Consensus       167 ~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~~~  244 (282)
T 4f3v_A          167 KFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPKVA  244 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHHHH
T ss_pred             cccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHH
Confidence            11  23677788899999999999999999886443253  346777788889999999999999999875  5763333

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.50  E-value=0.00027  Score=54.03  Aligned_cols=87  Identities=14%  Similarity=0.040  Sum_probs=66.3

Q ss_pred             hcCChhHHHHHHHHHHHcCC-CC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHH
Q 042756          201 EMGQPHEAENLIEEMRVKGL-EP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRM  278 (425)
Q Consensus       201 ~~g~~~~a~~~~~~m~~~g~-~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A  278 (425)
                      ..|++++|+..|++..+.+. .| +...+..+-.+|.+.|++++|.+.|+...+..- -+...|..+..+|...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFP-NHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CchHHHHHHHHHHHHcCCHHHH
Confidence            35788999999999887542 13 356788888889999999999999998887642 2577888888999999999999


Q ss_pred             HHHHHHHHhC
Q 042756          279 VLWLQKMKDS  288 (425)
Q Consensus       279 ~~l~~~M~~~  288 (425)
                      +..|++..+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999987654

>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=97.46  E-value=0.0096  Score=60.23  Aligned_cols=188  Identities=8%  Similarity=-0.022  Sum_probs=129.9

Q ss_pred             HHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHH-HHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           94 AFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAE-TLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        94 a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~-~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      +..+|++.....  +-++..|-.....+.+.|+.++|. ++|+..... .+..   ...|-..+...-+.|+++.+.+++
T Consensus       328 v~~~Ye~aL~~~--p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s---~~Lwl~~a~~ee~~~~~e~aR~iy  401 (679)
T 4e6h_A          328 MTYVYMQAAQHV--CFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNS---AVLAFSLSEQYELNTKIPEIETTI  401 (679)
T ss_dssp             HHHHHHHHHHHT--TTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTC---HHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHc--CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCC---HHHHHHHHHHHHHhCCHHHHHHHH
Confidence            445566655443  235666766777777889999996 999998753 2222   335667778888889977777777


Q ss_pred             HHHHHHhhcCC----CCcc------------ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc-C-CCCCHHHHHHHHHHH
Q 042756          173 ARLNQLVNSSS----SVYV------------KRQALKSMISGLCEMGQPHEAENLIEEMRVK-G-LEPSGFEYKCIIYGY  234 (425)
Q Consensus       173 ~~~~~~~~~~~----~~~p------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g-~~p~~~ty~~ll~~~  234 (425)
                      +.+.+......    .-.|            ...+|-..+....+.|..+.|..+|.+..+. + ..+..+...+.+.-.
T Consensus       402 ek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~  481 (679)
T 4e6h_A          402 LSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYH  481 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Confidence            66665431000    0002            1237888899989999999999999999876 2 334444444444322


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 042756          235 GRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       235 ~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g  289 (425)
                      + .++.+.|.++|+...+. +.-+...|...++.....|+.+.|..+|++.....
T Consensus       482 ~-~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~  534 (679)
T 4e6h_A          482 I-SKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKI  534 (679)
T ss_dssp             T-TSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTS
T ss_pred             h-CCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence            2 35699999999988875 33466778888998889999999999999988763

>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=97.45  E-value=0.00096  Score=59.89  Aligned_cols=65  Identities=15%  Similarity=-0.078  Sum_probs=33.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      +...|..+-..|.+.|++++|.+.+++..+.    .+.....+..+-.+|...|+++++.+.+....+.
T Consensus        37 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~----~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           37 VAVYYTNRALCYLKMQQPEQALADCRRALEL----DGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4555555666666666666666666665442    1112234555556666666644444444443333

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.42  E-value=0.0016  Score=50.05  Aligned_cols=95  Identities=12%  Similarity=-0.036  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .+..+-..+.+.|++++|...|++..+.  .| +...|..+-.++.+.|++++|...|+...+..- -+...|..+...|
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~~~~~la~~~   95 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSH   95 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHH
Confidence            5666778889999999999999999885  34 677888899999999999999999999887642 2577889999999


Q ss_pred             HhcCCHHHHHHHHHHHHhC
Q 042756          270 GDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~  288 (425)
                      ...|++++|...|++..+.
T Consensus        96 ~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           96 TNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHC-
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            9999999999999998753

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.39  E-value=0.0018  Score=51.81  Aligned_cols=99  Identities=11%  Similarity=-0.094  Sum_probs=71.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...+..+-..+.+.|++++|...|++..+..    |.....|..+-.+|.+.|+++++.+.++...+..+.      +.
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~------~~   89 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD----HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX------EP   89 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT------CT
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC----cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC------Cc
Confidence            44556667788889999999999999887652    222335677888888999965555555554444222      23


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ..|..+-.+|...|++++|...|++..+.
T Consensus        90 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           90 RFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            48888888999999999999999888764

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.38  E-value=0.0025  Score=49.01  Aligned_cols=95  Identities=11%  Similarity=-0.095  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      .+..+-..+.+.|++++|.+.|++..+..    |.....|..+-.+|.+.|+++++.+.++...+..+.      +...|
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~----p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~------~~~~~   75 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA----PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN------FVRAY   75 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC----CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC------cHHHH
Confidence            44445556666677777777776665531    111234555666666666643333333333332111      12355


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      ..+-.++...|++++|...|++..+
T Consensus        76 ~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           76 IRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCHHHHHHHHHHHHH
Confidence            5666666666666666666665554

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.36  E-value=0.0025  Score=49.62  Aligned_cols=100  Identities=14%  Similarity=-0.026  Sum_probs=75.8

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .++..+..+-..+.+.|++++|...|++..+...    .....|..+...+...|+++.+.+.++...+..+.      +
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~----~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~------~   76 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNP----LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ------S   76 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------C
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCc----CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch------h
Confidence            4677888899999999999999999999877522    22346788888899999965555555444443211      3


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ...|..+-.+|...|++++|...|++..+.
T Consensus        77 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           77 VKAHFFLGQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            458889999999999999999999988764

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.35  E-value=0.0022  Score=50.66  Aligned_cols=98  Identities=8%  Similarity=-0.075  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ...+..+-..+.+.|++++|.+.|++.....    |.....|..+-.+|.+.|+++.+.+.++...+..+.      +..
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~------~~~   87 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCMLD----HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN------EPR   87 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CTH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHhC----CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC------CcH
Confidence            3445556777888999999999999987652    222336777888889999965555555555444222      224


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      .|..+-.+|...|++++|...|++....
T Consensus        88 ~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           88 FPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7888888999999999999999988764

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.34  E-value=0.0054  Score=45.73  Aligned_cols=96  Identities=14%  Similarity=0.026  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..+..+...+...|++++|.+.|++..+.... .   ...+..+...+.+.|+++.+.+.++...+.   .+   .+...
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~---~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---~~---~~~~~   74 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLDPH-N---HVLYSNRSAAYAKKGDYQKAYEDGCKTVDL---KP---DWGKG   74 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-C---HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CT---TCHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-c---HHHHHHHHHHHHhhccHHHHHHHHHHHHHh---Cc---ccHHH
Confidence            34455556666666777776666666543111 1   223445555555555533333222222222   10   12235


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                      |..+..++...|++++|.+.|++..+
T Consensus        75 ~~~~a~~~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           75 YSRKAAALEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            55555555555555555555555544

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.31  E-value=0.0028  Score=51.38  Aligned_cols=99  Identities=9%  Similarity=-0.016  Sum_probs=64.7

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      ++..+..+-..+.+.|++++|.+.|++..+..    +.....|..+-.+|.+.|+++++.+.++...+..+.      +.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~------~~   79 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA----PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK------YS   79 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC------CH
Confidence            45566777777888888888888888877642    222335667777777778754444444443333211      23


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ..|..+-.+|.+.|++++|.+.|++..+.
T Consensus        80 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           80 KAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            47777777777888888888888777664

>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=97.26  E-value=0.0041  Score=55.67  Aligned_cols=93  Identities=12%  Similarity=-0.017  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .+..+-..+.+.|++++|...|++....  .| +...|..+-.+|.+.|++++|.+.++...+.. .-+...|+.+-.+|
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   82 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQ   82 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            5555556666666666666666666553  23 45556666666666666666666666655432 12455566666666


Q ss_pred             HhcCCHHHHHHHHHHHH
Q 042756          270 GDHNELSRMVLWLQKMK  286 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~  286 (425)
                      ...|++++|...|++..
T Consensus        83 ~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           83 LEMESYDEAIANLQRAY   99 (281)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            66666666666666554

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.23  E-value=0.016  Score=46.68  Aligned_cols=112  Identities=11%  Similarity=-0.014  Sum_probs=86.4

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHc-------CC---------CC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVK-------GL---------EP-SGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------g~---------~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ..+...-..+.+.|++++|+..|.+....       .-         .| +...|..+-.+|.+.|++++|...++...+
T Consensus        12 ~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~   91 (162)
T 3rkv_A           12 EALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLK   91 (162)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHh
Confidence            36777778888889999999988888764       00         12 235788889999999999999999999887


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHH
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVR-TYNSVLNSC  304 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~-t~~~ll~~~  304 (425)
                      .. +.+...|..+-.+|...|++++|...|++..+.  .|+.. .....+..+
T Consensus        92 ~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~l~~~  141 (162)
T 3rkv_A           92 RE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAASVVAREMKIV  141 (162)
T ss_dssp             HS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHH
T ss_pred             cC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCHHHHHHHHHHH
Confidence            64 236888999999999999999999999998765  56654 444444433

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.19  E-value=0.0088  Score=57.68  Aligned_cols=118  Identities=7%  Similarity=-0.156  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----------------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS----------------GFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----------------~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      .|+.+-..|.+.|++++|...|++..+..  |+                ...|..+-.+|.+.|++++|...++...+..
T Consensus       270 ~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          270 IVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            77788888888999999999998887742  22                5788888999999999999999999888754


Q ss_pred             CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHHHHHHHHHh
Q 042756          255 TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       255 ~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll~~~~~~~~~~~~  313 (425)
                      - .+...|..+-.+|...|++++|...|++..+.  .|+ ...+..+-..+.+.++..++
T Consensus       348 p-~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a  404 (457)
T 1kt0_A          348 S-ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNER  404 (457)
T ss_dssp             T-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHH
T ss_pred             C-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            2 36788899999999999999999999998764  453 35666666667776666544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.14  E-value=0.0055  Score=45.25  Aligned_cols=26  Identities=12%  Similarity=-0.009  Sum_probs=14.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLS  139 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~  139 (425)
                      +..+...+.+.|++++|...|++..+
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~   34 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQ   34 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            33355555566666666666665544

>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=97.11  E-value=0.0066  Score=48.98  Aligned_cols=110  Identities=9%  Similarity=-0.080  Sum_probs=84.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-------------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-------------GFEYKCIIYGYGRLGLLEDMERIVNQMESD----  253 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-------------~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----  253 (425)
                      .+...-..+.+.|++++|+..|++..+.  .|+             ...|..+-.++.+.|++++|...++...+.    
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~   90 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   90 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcc
Confidence            5666667788889999999999988774  333             238889999999999999999999988764    


Q ss_pred             -CCCcC-HHhH----HHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCCCHHHHHHHHH
Q 042756          254 -GTRVD-TVCS----NMVLSSYGDHNELSRMVLWLQKMKD-----SGIPFSVRTYNSVLN  302 (425)
Q Consensus       254 -g~~~~-~~~y----n~li~~~~~~g~~~~A~~l~~~M~~-----~g~~pd~~t~~~ll~  302 (425)
                       .+.|+ ...|    ...-.++...|++++|+..|++..+     .|+.+........+.
T Consensus        91 ~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~~~~  150 (159)
T 2hr2_A           91 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAI  150 (159)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHHHHH
T ss_pred             ccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH
Confidence             22454 5677    8888999999999999999999863     566666555554443

>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=97.06  E-value=0.012  Score=55.03  Aligned_cols=120  Identities=10%  Similarity=-0.067  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc--------------CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVK--------------GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .|..+-..+.+.|++++|++.|++..+.              ...| +...|..+-.+|.+.|++++|.+.++...+.. 
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  303 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  303 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-
Confidence            6788888999999999999999998761              1223 35688899999999999999999999998754 


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHh
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .-+...|..+-.+|...|++++|.+.|++..+.  .| +...+..+-..+...++..++
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            236788999999999999999999999998765  45 445566666666665555443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.02  E-value=0.016  Score=45.32  Aligned_cols=103  Identities=12%  Similarity=-0.034  Sum_probs=64.3

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      .+...+..+...+.+.|++++|.+.|++..+... ..+.....|..+...|.+.|+++++.+.++...+..+      .+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~------~~   98 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDA-TPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDG------GD   98 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTS------CC
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcc-cchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCc------cC
Confidence            4677788888889999999999999999876421 1111123556666667777774443333333333211      12


Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ...|..+..+|...|++++|...|++....
T Consensus        99 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           99 VKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            346666667777777777777777776653

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.01  E-value=0.0025  Score=48.41  Aligned_cols=88  Identities=13%  Similarity=0.094  Sum_probs=43.4

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcC
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMG  203 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g  203 (425)
                      .|++++|+..|++..+.+. ..|.....+..+-..|.+.|+++++.+.++...+..+.      +...+..+..++.+.|
T Consensus         3 ~g~~~~A~~~~~~al~~~~-~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~------~~~~~~~l~~~~~~~g   75 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGL-QGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN------HQALRVFYAMVLYNLG   75 (117)
T ss_dssp             ----CCCHHHHHHHHSSCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHHcCC-CCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC------chHHHHHHHHHHHHcC
Confidence            4666667777766654321 12333445556666666666643333333333222111      1235666666666666


Q ss_pred             ChhHHHHHHHHHHHc
Q 042756          204 QPHEAENLIEEMRVK  218 (425)
Q Consensus       204 ~~~~a~~~~~~m~~~  218 (425)
                      ++++|...|++....
T Consensus        76 ~~~~A~~~~~~al~~   90 (117)
T 3k9i_A           76 RYEQGVELLLKIIAE   90 (117)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            666666666665543

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.98  E-value=0.0095  Score=57.45  Aligned_cols=95  Identities=5%  Similarity=-0.124  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ..|+.+-.+|.+.|++++|+..|++..+.. +-+...|..+-.+|...|++++|...|+...+..- -+...|..+...+
T Consensus       318 ~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~  395 (457)
T 1kt0_A          318 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP-QNKAARLQISMCQ  395 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHH
Confidence            488999999999999999999999998853 23577899999999999999999999999887532 2567888888999


Q ss_pred             HhcCCHHHHHH-HHHHHH
Q 042756          270 GDHNELSRMVL-WLQKMK  286 (425)
Q Consensus       270 ~~~g~~~~A~~-l~~~M~  286 (425)
                      .+.|+.++|.+ ++..|.
T Consensus       396 ~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          396 KKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            99998887764 556664

>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=96.96  E-value=0.0067  Score=58.90  Aligned_cols=114  Identities=5%  Similarity=-0.128  Sum_probs=77.8

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      -..+.+.|++++|.+.|++..+.  .| +..+|..+-.+|.+.|++++|.+.++...+..- -+...|..+-.+|...|+
T Consensus        13 g~~~~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~~~~~g~   89 (477)
T 1wao_1           13 ANDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNMALGK   89 (477)
T ss_dssp             SSSTTTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCC
Confidence            33456678888888888887774  34 467788888888888888888888888777532 256778888888888888


Q ss_pred             HHHHHHHHHHHHhCCCCCC-HHHHHHHHHH--HHHHHHHHHhh
Q 042756          275 LSRMVLWLQKMKDSGIPFS-VRTYNSVLNS--CSTIMSMLQDL  314 (425)
Q Consensus       275 ~~~A~~l~~~M~~~g~~pd-~~t~~~ll~~--~~~~~~~~~~~  314 (425)
                      +++|.+.|++..+.  .|+ ...+..+-.+  +.+.|+++++.
T Consensus        90 ~~eA~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~  130 (477)
T 1wao_1           90 FRAALRDYETVVKV--KPHDKDAKMKYQECNKIVKQKAFERAI  130 (477)
T ss_dssp             HHHHHHHHHHHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC-
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            88888888887653  232 2233333333  56666666553

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.94  E-value=0.004  Score=47.79  Aligned_cols=93  Identities=11%  Similarity=-0.088  Sum_probs=68.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHH
Q 042756          116 EIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSM  195 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l  195 (425)
                      .+-..+.+.|++++|...|++..+.    .|.....|..+-.++.+.|+++.+.+.++...+..+.      +...|..+
T Consensus        22 ~~g~~~~~~g~~~~A~~~~~~al~~----~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~------~~~~~~~l   91 (121)
T 1hxi_A           22 EEGLSMLKLANLAEAALAFEAVCQK----EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK------DIAVHAAL   91 (121)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC------CHHHHHHH
Confidence            3566788999999999999998875    2222346778888899999965555555544443221      23488899


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHc
Q 042756          196 ISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       196 i~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      ..+|.+.|++++|...|++..+.
T Consensus        92 a~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           92 AVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999999998763

>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=96.90  E-value=0.14  Score=47.05  Aligned_cols=224  Identities=8%  Similarity=-0.019  Sum_probs=134.6

Q ss_pred             hHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHH
Q 042756           35 LTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLV  114 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~  114 (425)
                      ..++|+++++.+...-+-+..+||.--..+...+.                    .+++++++++.+...+ . -+..+|
T Consensus        69 ~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~--------------------~l~eEL~~~~~~L~~n-P-Kny~aW  126 (349)
T 3q7a_A           69 KSERALELTEIIVRMNPAHYTVWQYRFSLLTSLNK--------------------SLEDELRLMNEFAVQN-L-KSYQVW  126 (349)
T ss_dssp             CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC--------------------CHHHHHHHHHHHHHTT-C-CCHHHH
T ss_pred             CCHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhh--------------------hHHHHHHHHHHHHHhC-C-CcHHHH
Confidence            34556666666665533455556655555544441                    3556666666665544 1 366667


Q ss_pred             HHHHHHHHhc-C-ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc-----cHHHHHHHHHHHhhcCCCCcc
Q 042756          115 AEIIAFLDKQ-G-QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR-----GFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       115 ~~ll~~~~~~-g-~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~-----~~~~~~~~~~~~~~~~~~~~p  187 (425)
                      +.--..+.+. + +.++++++++.+.+.    .+.+...|+.-.-.+.+.|..+     ...+.++...++.....   -
T Consensus       127 ~hR~wlL~~l~~~~~~~EL~~~~k~L~~----dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp---~  199 (349)
T 3q7a_A          127 HHRLLLLDRISPQDPVSEIEYIHGSLLP----DPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG---R  199 (349)
T ss_dssp             HHHHHHHHHHCCSCCHHHHHHHHHHTSS----CTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT---T
T ss_pred             HHHHHHHHHhcCCChHHHHHHHHHHHHh----CCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC---C
Confidence            7666666665 6 788999999988764    2222334554333333333322     12355555555554331   2


Q ss_pred             ChhHHHHHHHHHHhcCC-------hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH--------------------
Q 042756          188 KRQALKSMISGLCEMGQ-------PHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLL--------------------  240 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~-------~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~--------------------  240 (425)
                      |-..|+-.-..+.+.+.       ++++++.+++..... +-|...|+-+--.+.+.|+-                    
T Consensus       200 N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (349)
T 3q7a_A          200 NNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDI  278 (349)
T ss_dssp             CHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC-------
T ss_pred             CHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccc
Confidence            44588888888888776       688899888888752 23667777665555555542                    


Q ss_pred             HHHHHHHHHHHHCC-----CCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          241 EDMERIVNQMESDG-----TRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       241 ~~a~~~~~~m~~~g-----~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      .+...+..++...+     -.++.....-|.+.|...|+.++|.++++.+.+.
T Consensus       279 ~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          279 ETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             -------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            22333333333222     1367889999999999999999999999998643

>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=96.82  E-value=0.23  Score=45.65  Aligned_cols=204  Identities=7%  Similarity=-0.130  Sum_probs=130.8

Q ss_pred             hhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhc-C-CcccH
Q 042756           92 SLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQG-QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKH-D-SKRGF  168 (425)
Q Consensus        92 ~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g-~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~-g-~~~~~  168 (425)
                      ++|+++++.+...+.  -+..+|+.--..+...| .+++++++++.+...    .|....+|+.---.+.+. + +   .
T Consensus        71 e~AL~lt~~~L~~nP--~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~----nPKny~aW~hR~wlL~~l~~~~---~  141 (349)
T 3q7a_A           71 ERALELTEIIVRMNP--AHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQ----NLKSYQVWHHRLLLLDRISPQD---P  141 (349)
T ss_dssp             HHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHT----TCCCHHHHHHHHHHHHHHCCSC---C
T ss_pred             HHHHHHHHHHHHhCc--hhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh----CCCcHHHHHHHHHHHHHhcCCC---h
Confidence            456666666655441  24556666666666777 599999999998864    222234566655555555 5 4   3


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChh--------HHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC-
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPH--------EAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL-  239 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~--------~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~-  239 (425)
                      ++.+..+.++....+   -|-.+|+--.-.+.+.|.++        ++++.++++.+... -|...|+.--..+.+.++ 
T Consensus       142 ~~EL~~~~k~L~~dp---kNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~l~~~  217 (349)
T 3q7a_A          142 VSEIEYIHGSLLPDP---KNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVSRPGA  217 (349)
T ss_dssp             HHHHHHHHHHTSSCT---TCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTTSTTC
T ss_pred             HHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcccc
Confidence            566677777664432   24457777666666666666        99999999998642 367788888888888876 


Q ss_pred             ------HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCH--------------------HHHHHHHHHHHhCC----
Q 042756          240 ------LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNEL--------------------SRMVLWLQKMKDSG----  289 (425)
Q Consensus       240 ------~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~--------------------~~A~~l~~~M~~~g----  289 (425)
                            ++++.+.++....... -|...|+-+-..+.+.|+.                    .+..++..++...+    
T Consensus       218 ~~~~~~~~eELe~~~~aI~~~P-~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (349)
T 3q7a_A          218 ETSSRSLQDELIYILKSIHLIP-HNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPED  296 (349)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSS
T ss_pred             ccchHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccc
Confidence                  7889999988887543 3788999888888777764                    23333333333221    


Q ss_pred             -CCCCHHHHHHHHHHHHHHHH
Q 042756          290 -IPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       290 -~~pd~~t~~~ll~~~~~~~~  309 (425)
                       -.++......|.+.|...|+
T Consensus       297 ~~~~s~~al~~l~d~~~~~~~  317 (349)
T 3q7a_A          297 TPLPVPLALEYLADSFIEQNR  317 (349)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTC
T ss_pred             cCCCcHHHHHHHHHHHHhcCC
Confidence             13566777777777765443

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.82  E-value=0.0012  Score=49.20  Aligned_cols=63  Identities=14%  Similarity=0.077  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..|..+-..+.+.|++++|.+.|++..+.. +.+...+..+-.++.+.|++++|.+.|+...+.
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            355566666666666666666666665531 124455666666666666666666666665543

>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=96.77  E-value=0.0026  Score=61.87  Aligned_cols=91  Identities=8%  Similarity=-0.180  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      ..|+.+-.+|.+.|++++|++.|++..+.  .| +..+|..+-.+|.+.|++++|.+.|+...+..- -+...+..+-.+
T Consensus        41 ~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p-~~~~~~~~l~~~  117 (477)
T 1wao_1           41 IYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQEC  117 (477)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            36666666666666666666666666653  23 345666666666666666666666666554321 123344444444


Q ss_pred             --HHhcCCHHHHHHHHH
Q 042756          269 --YGDHNELSRMVLWLQ  283 (425)
Q Consensus       269 --~~~~g~~~~A~~l~~  283 (425)
                        +.+.|++++|+++++
T Consensus       118 ~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1          118 NKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHHhcccc
Confidence              566666667766666

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.75  E-value=0.051  Score=41.29  Aligned_cols=95  Identities=11%  Similarity=0.021  Sum_probs=70.0

Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC----HHHHHH
Q 042756          154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS----GFEYKC  229 (425)
Q Consensus       154 ~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~ty~~  229 (425)
                      .+-..+.+.|+++.+.+.++.+.+..+..   ......+..+-.++.+.|++++|...|++.....  |+    ...+..
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~---~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~   81 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELYPNG---VYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLK   81 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSSS---TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHCCCC---cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHH
Confidence            45566778899555444444444332211   1111378888899999999999999999998853  43    567888


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +-.++.+.|++++|...|+...+.
T Consensus        82 la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           82 LGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            889999999999999999998875

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.75  E-value=0.023  Score=42.65  Aligned_cols=102  Identities=5%  Similarity=-0.086  Sum_probs=70.3

Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 042756          206 HEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM  285 (425)
Q Consensus       206 ~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M  285 (425)
                      ++|++.|++..+.. +.+...+..+-..|.+.|++++|.+.|+...+.. ..+...|..+-..|...|++++|...|++.
T Consensus         2 ~~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            2 QAITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CCHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45667777776642 2356788888888888889988888888877653 235678888888889999999999998887


Q ss_pred             HhCC-CCCCHHHHHHHHHHHHHHHH
Q 042756          286 KDSG-IPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       286 ~~~g-~~pd~~t~~~ll~~~~~~~~  309 (425)
                      .+.. -.++......+...+...+.
T Consensus        80 l~~~~~~~~~~~~~~l~~~l~~l~~  104 (115)
T 2kat_A           80 LAAAQSRGDQQVVKELQVFLRRLAR  104 (115)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHhccccccHHHHHHHHHHHHHhcc
Confidence            6431 12344555555555444443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.70  E-value=0.019  Score=53.67  Aligned_cols=138  Identities=12%  Similarity=-0.058  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      ..+..+-..+.+.|++++|.+.|++..+.    .+.    ..       ....   .++...    ..+      -+...
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~----~~~----~~-------~~~~---~~~~~~----~~~------~~~~~  275 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRY----VEG----SR-------AAAE---DADGAK----LQP------VALSC  275 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH----HHH----HH-------HHSC---HHHHGG----GHH------HHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHH----hhc----Cc-------cccC---hHHHHH----HHH------HHHHH
Confidence            34666788888999999999999887652    000    00       0111   111111    100      11238


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      |+.+-.+|.+.|++++|++.+++..+.  .| +...|..+-.+|.+.|++++|.+.|+...+..- -+...+..+-..+.
T Consensus       276 ~~nla~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P-~~~~~~~~l~~~~~  352 (370)
T 1ihg_A          276 VLNIGACKLKMSDWQGAVDSCLEALEI--DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAP-EDKAIQAELLKVKQ  352 (370)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            888888888999999999999988874  34 567888888889999999999999988876531 25677777888888


Q ss_pred             hcCCHHHHHH
Q 042756          271 DHNELSRMVL  280 (425)
Q Consensus       271 ~~g~~~~A~~  280 (425)
                      ..++.+++.+
T Consensus       353 ~~~~~~~a~k  362 (370)
T 1ihg_A          353 KIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8888777754

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.61  E-value=0.026  Score=45.30  Aligned_cols=116  Identities=16%  Similarity=0.086  Sum_probs=71.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      +..+...-..+.+.|++++|.+.|.+..+..               .......+....+  ...+.   +      -+..
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~---------------~~~~~~~~~~~~~--~~~~~---~------~~~~   64 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRL---------------DTLILREKPGEPE--WVELD---R------KNIP   64 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH---------------HHHHHTSCTTSHH--HHHHH---H------THHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH---------------HHhcccCCCCHHH--HHHHH---H------HHHH
Confidence            3456667778889999999999998876420               0000011111110  01000   0      1122


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      .|..+-.+|.+.|++++|+..+++..... +.+...|..+-.+|...|++++|...|+...+.
T Consensus        65 ~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           65 LYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            67777777777888888888877777642 224667777777788888888888887777664

>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=96.59  E-value=0.097  Score=40.93  Aligned_cols=110  Identities=7%  Similarity=-0.113  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDM  243 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a  243 (425)
                      ..+++..+.+....++.   +  .+  +-..|...+.+++|++.|++..+.|   +...+..+-..|..    .++.++|
T Consensus        11 ~~~A~~~~~~aa~~g~~---~--a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A           11 LKKAIQYYVKACELNEM---F--GC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHTTCT---T--HH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             HHHHHHHHHHHHcCCCH---h--hh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHH
Confidence            56677777777665532   2  44  6666777788899999999999876   66788888888887    8899999


Q ss_pred             HHHHHHHHHCCCCcCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCC
Q 042756          244 ERIVNQMESDGTRVDTVCSNMVLSSYGD----HNELSRMVLWLQKMKDSGI  290 (425)
Q Consensus       244 ~~~~~~m~~~g~~~~~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g~  290 (425)
                      .+.|+...+.|   +...+..|-..|..    .++.++|..+|++..+.|.
T Consensus        81 ~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           81 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            99999999876   67778888888888    8999999999999988873

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.46  E-value=0.044  Score=40.27  Aligned_cols=70  Identities=10%  Similarity=-0.073  Sum_probs=59.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          222 PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       222 p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      ++...+..+-..+.+.|++++|.+.|+...+.. +.+...|..+-.+|...|++++|+..|++..+.  .|+.
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~   71 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTA   71 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSST
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCc
Confidence            345678888899999999999999999988753 236788999999999999999999999998864  4654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.42  E-value=0.042  Score=38.71  Aligned_cols=61  Identities=10%  Similarity=0.030  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      .|..+-..+.+.|++++|...|++..+.. +.+...+..+-.++.+.|++++|.+.|+...+
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            55555555666666666666666655432 12344555555555555666666555555544

>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=96.41  E-value=0.02  Score=54.57  Aligned_cols=85  Identities=9%  Similarity=-0.157  Sum_probs=69.3

Q ss_pred             cCChhHHHHHHHHHHHc---CC---CCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCC-Cc-CHHhHHHHHH
Q 042756          202 MGQPHEAENLIEEMRVK---GL---EPS-GFEYKCIIYGYGRLGLLEDMERIVNQMES-----DGT-RV-DTVCSNMVLS  267 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~---g~---~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~-~~-~~~~yn~li~  267 (425)
                      .|++++|+.++++..+.   -+   .|+ ..+++.+..+|...|++++|+.++++..+     .|- .| ...+||.|-.
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            57899999999988763   12   233 45899999999999999999999998764     221 23 3688999999


Q ss_pred             HHHhcCCHHHHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~  286 (425)
                      .|...|++++|+.+|++..
T Consensus       391 ~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          391 LYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhccCHHHHHHHHHHHH
Confidence            9999999999999999875

>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=96.40  E-value=0.032  Score=53.20  Aligned_cols=109  Identities=12%  Similarity=-0.036  Sum_probs=81.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcC---CCC----CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----C-CCc-CH
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKG---LEP----SGFEYKCIIYGYGRLGLLEDMERIVNQMESD-----G-TRV-DT  259 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g---~~p----~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~-----g-~~~-~~  259 (425)
                      ..+..+.+.|++++|+.++++..+..   +.|    ...+++.+..+|...|++++|+.++++..+-     | -.| ..
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            34566778899999999999998642   223    2458999999999999999999999977642     2 123 36


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCCCCHHHHHHHHH
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKD---SGIPFSVRTYNSVLN  302 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~---~g~~pd~~t~~~ll~  302 (425)
                      .+|+.|-..|...|++++|+.+|++..+   .-..||......+.+
T Consensus       372 ~~l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~  417 (429)
T 3qwp_A          372 VQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLIL  417 (429)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChHHHHHHH
Confidence            8899999999999999999999998753   233455544444433

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.34  E-value=0.015  Score=53.47  Aligned_cols=98  Identities=10%  Similarity=-0.093  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH------------------HHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGF------------------EYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------------------ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      .|..+-..+.+.|++++|...|++....  .|+..                  .|..+-.+|.+.|++++|...++...+
T Consensus       181 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~  258 (338)
T 2if4_A          181 RRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLT  258 (338)
T ss_dssp             HHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5666667777788888888888887653  34433                  788888889999999999999998876


Q ss_pred             CCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 042756          253 DGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS  293 (425)
Q Consensus       253 ~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd  293 (425)
                      .. ..+...|..+-.+|...|++++|...|++..+.  .|+
T Consensus       259 ~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~  296 (338)
T 2if4_A          259 EE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APD  296 (338)
T ss_dssp             HC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCC
Confidence            53 236788899999999999999999999987653  454

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.29  E-value=0.4  Score=46.50  Aligned_cols=177  Identities=10%  Similarity=-0.008  Sum_probs=112.6

Q ss_pred             hhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHH
Q 042756           91 SSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDD  170 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~  170 (425)
                      .+.+..+|++.....  +.++..|-..+..+.+.|+++.|.++|++....  +....   .|-    +|+.....+   +
T Consensus       195 ~~Rv~~~ye~al~~~--p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~---l~~----~y~~~~e~~---~  260 (493)
T 2uy1_A          195 ESRMHFIHNYILDSF--YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMF---LSL----YYGLVMDEE---A  260 (493)
T ss_dssp             HHHHHHHHHHHHHHT--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSH---HHH----HHHHHTTCT---H
T ss_pred             HHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHH---HHH----HHHhhcchh---H
Confidence            345677888876653  245777777788888999999999999998877  33322   111    233322211   2


Q ss_pred             HHHHHHHHhhcCC-------CCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHH--HHHHHHcCCCHH
Q 042756          171 TYARLNQLVNSSS-------SVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKC--IIYGYGRLGLLE  241 (425)
Q Consensus       171 ~~~~~~~~~~~~~-------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~--ll~~~~~~g~~~  241 (425)
                      .++.+.+......       ........|-..+....+.+..+.|..+|++....+  .+...|..  .+.... .++.+
T Consensus       261 ~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~  337 (493)
T 2uy1_A          261 VYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRA  337 (493)
T ss_dssp             HHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSH
T ss_pred             HHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChH
Confidence            2333332211000       001112478888888888889999999999992222  23444443  333322 23799


Q ss_pred             HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 042756          242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM  285 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M  285 (425)
                      .|.++|+...+.. .-+...|...++-....|+.+.|..+|++.
T Consensus       338 ~ar~ife~al~~~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          338 TPYNIFSSGLLKH-PDSTLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999887742 123455777888888899999999999997

>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=96.29  E-value=0.028  Score=53.63  Aligned_cols=92  Identities=3%  Similarity=-0.085  Sum_probs=41.2

Q ss_pred             CChhHHHHHHHHHHH----hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCC-CCccC-hhHHHHHHHH
Q 042756          125 GQREEAETLILETLS----KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSS-SVYVK-RQALKSMISG  198 (425)
Q Consensus       125 g~~~~A~~l~~~m~~----~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~-~~~p~-~~~~~~li~~  198 (425)
                      |++++|+.++++..+    ..++..+....+++.|..+|...|+++++...++...+.....- .--|+ ..+||.|-..
T Consensus       312 g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          312 KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            455666666555433    23333444444555555555555554443333333322222110 01122 2345555555


Q ss_pred             HHhcCChhHHHHHHHHHH
Q 042756          199 LCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~  216 (425)
                      |...|++++|+.+|++..
T Consensus       392 ~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHH
Confidence            555555555555555443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.29  E-value=0.033  Score=40.78  Aligned_cols=83  Identities=2%  Similarity=-0.121  Sum_probs=46.9

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHH
Q 042756          223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSG-IPFSVRTYNSVL  301 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g-~~pd~~t~~~ll  301 (425)
                      +...+..+-.+|.+.|++++|.+.|+...+..- -+...|..+-.+|...|++++|.+.|++..+.. -.++.....-+.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~   84 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDP-DYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQ   84 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHH
Confidence            344556666666666666666666666655431 135566666667777777777777766654321 123444444444


Q ss_pred             HHHHH
Q 042756          302 NSCST  306 (425)
Q Consensus       302 ~~~~~  306 (425)
                      ..+.+
T Consensus        85 ~~l~~   89 (100)
T 3ma5_A           85 DAKLK   89 (100)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44433

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.29  E-value=0.021  Score=52.58  Aligned_cols=95  Identities=7%  Similarity=-0.041  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-CHHhHHHHHHH-
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-DTVCSNMVLSS-  268 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~yn~li~~-  268 (425)
                      .|+.+-.+|.+.|++++|+..|++..+.. .-+...|..+-.+|...|++++|.+.|+...+.  .| +...++.+... 
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~  308 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALA  308 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHH
Confidence            88999999999999999999999998753 236789999999999999999999999988754  23 44555555555 


Q ss_pred             HHhcCCHHHHHHHHHHHHhC
Q 042756          269 YGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       269 ~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ....+..+++.++|.+|...
T Consensus       309 ~~~~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          309 EQEKALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             --------------------
T ss_pred             HHHHHHHHHHHHHHHHhhCC
Confidence            33456678888899888643

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.20  E-value=0.06  Score=37.84  Aligned_cols=78  Identities=8%  Similarity=0.009  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHH
Q 042756          224 GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLN  302 (425)
Q Consensus       224 ~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~  302 (425)
                      ...+..+-..+.+.|++++|.+.|+...+.. +.+...|..+-..|...|++++|...|++..+.  .| +...+..+-.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~p~~~~~~~~l~~   85 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCCHHHHHHHHH
Confidence            4577888889999999999999999988753 236788999999999999999999999998765  34 3444444433


Q ss_pred             HH
Q 042756          303 SC  304 (425)
Q Consensus       303 ~~  304 (425)
                      .+
T Consensus        86 ~~   87 (91)
T 1na3_A           86 AK   87 (91)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.12  E-value=0.094  Score=42.16  Aligned_cols=27  Identities=11%  Similarity=-0.059  Sum_probs=19.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHh
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSK  140 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~  140 (425)
                      +...-..+.+.|++++|.+.|++..+-
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l   40 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEI   40 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence            444556677788888888888887664

>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=95.93  E-value=0.38  Score=44.36  Aligned_cols=75  Identities=7%  Similarity=-0.137  Sum_probs=42.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 042756          222 PSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSV  300 (425)
Q Consensus       222 p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~l  300 (425)
                      .+..+|..+-..+...|++++|...++.....+  |+...|..+-..+.-.|++++|.+.|++....  .|...||...
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~~  349 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYWI  349 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHHH
Confidence            345555555555555566666666666665553  55555555555556666666666666655433  4555555443

>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=95.84  E-value=0.18  Score=48.03  Aligned_cols=70  Identities=9%  Similarity=-0.137  Sum_probs=55.3

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHH----hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLS----KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLV  179 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~----~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~  179 (425)
                      ...+++.+...|...|++++|+.++++..+    ..++..|....+++.|-..|...|+++++...++...+..
T Consensus       328 ~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~i~  401 (429)
T 3qwp_A          328 QLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIM  401 (429)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            456899999999999999999999998764    4566777878889999999999999766655555444443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=95.68  E-value=1.7  Score=42.09  Aligned_cols=125  Identities=13%  Similarity=0.082  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHH
Q 042756          150 LFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYK  228 (425)
Q Consensus       150 ~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~  228 (425)
                      ..|...++...+.+..+.+.+++.   +. ... ...+......+.+.... .++.+.|..+|+...+.-  |+ ...+.
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~---~A-~~~-~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~  358 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFI---EL-GNE-GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKE  358 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHH---HH-TTS-CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHH---Hh-hCC-CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHH
Confidence            456777777777777444444444   43 111 12222222223333333 336999999999998753  33 34456


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          229 CIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       229 ~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ..++...+.|+.+.|..+|+...     .....|...+.-=...|+.+.+.++++++..
T Consensus       359 ~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          359 EFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            67777788999999999999973     2678899999888889999999999998763

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=95.56  E-value=0.24  Score=38.60  Aligned_cols=111  Identities=6%  Similarity=-0.130  Sum_probs=61.7

Q ss_pred             ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh----
Q 042756          126 QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE----  201 (425)
Q Consensus       126 ~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~----  201 (425)
                      +.++|.+.|++..+.+.+ .     ..  |-..|...+.   .+++++.+.+....++     ...++.|-..|..    
T Consensus        10 d~~~A~~~~~~aa~~g~~-~-----a~--lg~~y~~g~~---~~~A~~~~~~Aa~~g~-----~~a~~~Lg~~y~~G~g~   73 (138)
T 1klx_A           10 DLKKAIQYYVKACELNEM-F-----GC--LSLVSNSQIN---KQKLFQYLSKACELNS-----GNGCRFLGDFYENGKYV   73 (138)
T ss_dssp             HHHHHHHHHHHHHHTTCT-T-----HH--HHHHTCTTSC---HHHHHHHHHHHHHTTC-----HHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHcCCCH-h-----hh--HHHHHHcCCC---HHHHHHHHHHHHcCCC-----HHHHHHHHHHHHcCCCC
Confidence            455666666665554321 1     11  2233333333   3445555555544432     2255666666665    


Q ss_pred             cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCC
Q 042756          202 MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a~~~~~~m~~~g~  255 (425)
                      .+++++|+++|++..+.|   +...+..+-..|..    .++.++|.+.|+.-.+.|.
T Consensus        74 ~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           74 KKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             CccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            567777777777776654   45556666666666    6677777777777766653

>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=95.53  E-value=1.4  Score=40.12  Aligned_cols=156  Identities=6%  Similarity=-0.051  Sum_probs=105.5

Q ss_pred             hhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCC-h
Q 042756          127 REEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQ-P  205 (425)
Q Consensus       127 ~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~-~  205 (425)
                      +++++.+++.+...    .|....+|+.---.+.+.++. ..++.+..+.++....+   -|-.+|+----.+...|. .
T Consensus        90 l~~EL~~~~~~L~~----~PKny~aW~hR~wlL~~l~~~-~~~~EL~~~~k~l~~dp---rNy~AW~~R~~vl~~l~~~~  161 (331)
T 3dss_A           90 VKAELGFLESCLRV----NPKSYGTWHHRCWLLSRLPEP-NWARELELCARFLEADE---RNFHCWDYRRFVAAQAAVAP  161 (331)
T ss_dssp             HHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHCSSC-CHHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHHHHh----CCCCHHHHHHHHHHHhccCcc-cHHHHHHHHHHHHHhCC---CCHHHHHHHHHHHHHhCcCH
Confidence            67888888888764    222233566655666666642 14555555555554332   244588888777888888 5


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC--------------CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          206 HEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL--------------GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       206 ~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~--------------g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      +++++.++++.+... -|...|+..-..+.+.              +.++++.+.++....... -|...|+-+-..+.+
T Consensus       162 ~eel~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P-~d~SaW~Y~r~ll~~  239 (331)
T 3dss_A          162 AEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDP-NDQSAWFYHRWLLGA  239 (331)
T ss_dssp             HHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHh
Confidence            899999999998642 3566776655554443              457889999988876542 378888877766666


Q ss_pred             c-----------CCHHHHHHHHHHHHhCCCCCCH
Q 042756          272 H-----------NELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       272 ~-----------g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      .           +.++++++.++++.+.  .||.
T Consensus       240 ~~~~~~~~~~~~~~l~~el~~~~elle~--~pd~  271 (331)
T 3dss_A          240 GSGRCELSVEKSTVLQSELESCKELQEL--EPEN  271 (331)
T ss_dssp             SSCGGGCCHHHHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             ccCccccchHHHHHHHHHHHHHHHHHhh--Cccc
Confidence            5           4578999999999865  5765

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.53  E-value=0.12  Score=38.55  Aligned_cols=80  Identities=9%  Similarity=-0.073  Sum_probs=54.7

Q ss_pred             hHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHH
Q 042756           93 LAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTY  172 (425)
Q Consensus        93 ~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~  172 (425)
                      .|+..|++..+.+  +-+...+..+-..|.+.|++++|.+.|++..+...    .....|..+-.+|.+.|+++++.+.+
T Consensus         3 ~a~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p----~~~~~~~~la~~~~~~g~~~~A~~~~   76 (115)
T 2kat_A            3 AITERLEAMLAQG--TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDP----TYSVAWKWLGKTLQGQGDRAGARQAW   76 (115)
T ss_dssp             CHHHHHHHHHTTT--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC----CcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4566666665543  23677788888888999999999999988876522    22335677888888888865555555


Q ss_pred             HHHHHH
Q 042756          173 ARLNQL  178 (425)
Q Consensus       173 ~~~~~~  178 (425)
                      +...+.
T Consensus        77 ~~al~~   82 (115)
T 2kat_A           77 ESGLAA   82 (115)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            544443

>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=95.39  E-value=0.057  Score=43.38  Aligned_cols=106  Identities=7%  Similarity=-0.071  Sum_probs=71.5

Q ss_pred             HhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC----------HHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          200 CEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL----------LEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       200 ~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~----------~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      .+.+.+++|.+.+++..+.+ +-+...|..+-.++...++          +++|...|++..+..-. +...|+.+-.+|
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~ay   90 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAY   90 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHHH
Confidence            34455666777776666542 2245566656556665554          45888888877765321 567788888888


Q ss_pred             Hhc-----------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHH
Q 042756          270 GDH-----------NELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMS  309 (425)
Q Consensus       270 ~~~-----------g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~  309 (425)
                      ...           |++++|++.|++..+.  .|+...|...+...-+...
T Consensus        91 ~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~~~~ka~e  139 (158)
T 1zu2_A           91 TSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMTAKAPQ  139 (158)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHTHHH
T ss_pred             HHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHhCHh
Confidence            766           4899999999998864  7888888777776655444

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.38  E-value=0.086  Score=38.42  Aligned_cols=63  Identities=16%  Similarity=-0.003  Sum_probs=52.3

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 042756          189 RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES  252 (425)
Q Consensus       189 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~  252 (425)
                      ...|..+-.+|.+.|++++|+..|++..+.. +-+...|..+-.+|.+.|++++|.+.|+...+
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4578888899999999999999999988753 22456888889999999999999999987765

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.29  E-value=0.59  Score=48.01  Aligned_cols=151  Identities=9%  Similarity=-0.045  Sum_probs=79.8

Q ss_pred             HHHHhhHHHHHH-HHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCC--CCCCchhhhHHHHHHHhhhcCC
Q 042756           30 CLTARLTKQGQR-FLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPD--TTHPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        30 ~l~~~~~~~a~~-~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~--~~~~~~~~~a~~lf~~m~~~~~  106 (425)
                      .+..+++++|.+ ++..+     ++......++..+.+.|..+.|+.+...-..+-  ....+.++.|+++.+.+     
T Consensus       609 ~~~~~~~~~a~~~~l~~i-----~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~~~f~~~l~~~~~~~A~~~~~~~-----  678 (814)
T 3mkq_A          609 LTLRGEIEEAIENVLPNV-----EGKDSLTKIARFLEGQEYYEEALNISPDQDQKFELALKVGQLTLARDLLTDE-----  678 (814)
T ss_dssp             HHHTTCHHHHHHHTGGGC-----CCHHHHHHHHHHHHHTTCHHHHHHHCCCHHHHHHHHHHHTCHHHHHHHHTTC-----
T ss_pred             HHHhCCHHHHHHHHHhcC-----CchHHHHHHHHHHHhCCChHHheecCCCcchheehhhhcCCHHHHHHHHHhh-----
Confidence            355667777766 44322     212233777777777787777665442110000  00001344455443322     


Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                        .+...|..+-..+.+.|+++.|++.|..+..            |..+...|...|+.+.+.++.+....   .+    
T Consensus       679 --~~~~~W~~la~~al~~~~~~~A~~~y~~~~d------------~~~l~~l~~~~~~~~~~~~~~~~a~~---~~----  737 (814)
T 3mkq_A          679 --SAEMKWRALGDASLQRFNFKLAIEAFTNAHD------------LESLFLLHSSFNNKEGLVTLAKDAET---TG----  737 (814)
T ss_dssp             --CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC------------HHHHHHHHHHTTCHHHHHHHHHHHHH---TT----
T ss_pred             --CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC------------hhhhHHHHHHcCCHHHHHHHHHHHHH---cC----
Confidence              2556777777777788888888887777631            34455555556664333332222222   11    


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEM  215 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m  215 (425)
                          -++.-..+|.+.|++++|.+++.++
T Consensus       738 ----~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          738 ----KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             ----CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             ----chHHHHHHHHHcCCHHHHHHHHHHc
Confidence                4455555666666666666665543

>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=95.26  E-value=0.74  Score=42.38  Aligned_cols=55  Identities=7%  Similarity=-0.175  Sum_probs=29.5

Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHh
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSCSTIMSMLQD  313 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~  313 (425)
                      .+..+|.++-..+...|++++|...+++....+  |+...|..+-..+.-.|+.+.+
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA  329 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREA  329 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHH
Confidence            355566665555555566666666666665553  5554444443444444444444

>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=95.19  E-value=0.74  Score=45.45  Aligned_cols=176  Identities=7%  Similarity=-0.053  Sum_probs=115.9

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCC----------hhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQ----------REEAETLILETLSKLGSRERELVLFYCNLIDSF  159 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~----------~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~  159 (425)
                      ..++|++.++.+...+.  -+..+|+.-=..+.+.|+          ++++.++++++.+.    .|....+|+.---.+
T Consensus        44 ~~eeal~~~~~~l~~nP--~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~----~pK~y~aW~hR~w~l  117 (567)
T 1dce_A           44 LDESVLELTSQILGANP--DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV----NPKSYGTWHHRCWLL  117 (567)
T ss_dssp             CSHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH----CTTCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCc--hhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHh----CCCCHHHHHHHHHHH
Confidence            44667777777766542  144456655555555555          88999999998875    222234566666666


Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcC-ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC-
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMG-QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL-  237 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~-  237 (425)
                      .+.++.+ .++++..+.++.....   -+-.+|+---..+.+.| ..+++++.++++.+... -|...|+..-..+.+. 
T Consensus       118 ~~l~~~~-~~~el~~~~k~l~~d~---~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p-~n~saW~~r~~ll~~l~  192 (567)
T 1dce_A          118 SRLPEPN-WARELELCARFLEADE---RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLH  192 (567)
T ss_dssp             HTCSSCC-HHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHS
T ss_pred             HHccccc-HHHHHHHHHHHHhhcc---ccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCC-CCccHHHHHHHHHHhhc
Confidence            7777321 3455555555544331   24458888888888888 88999999999887532 2566777666665552 


Q ss_pred             -------------CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHH
Q 042756          238 -------------GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSR  277 (425)
Q Consensus       238 -------------g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~  277 (425)
                                   +.++++.+.++......- -|...|+-+-..+.+.++.++
T Consensus       193 ~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P-~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          193 PQPDSGPQGRLPENVLLKELELVQNAFFTDP-NDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CCCCSSSCCSSCHHHHHHHHHHHHHHHHHCS-SCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccccccccccHHHHHHHHHHHHHHHhhCC-CCccHHHHHHHHHhcCCCccc
Confidence                         557889888888776532 368889988888887777444

>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=94.95  E-value=0.77  Score=45.35  Aligned_cols=171  Identities=6%  Similarity=-0.063  Sum_probs=117.3

Q ss_pred             hcCC-hhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCc-------ccHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          123 KQGQ-REEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSK-------RGFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       123 ~~g~-~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~-------~~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      +.|. -++|.+.++++...    .|....+|+.--..+.+.|+.       +..++++..+.+.....+.   +-.+|+.
T Consensus        40 ~~~~~~eeal~~~~~~l~~----nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK---~y~aW~h  112 (567)
T 1dce_A           40 QAGELDESVLELTSQILGA----NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK---SYGTWHH  112 (567)
T ss_dssp             HTTCCSHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT---CHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHH----CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC---CHHHHHH
Confidence            3444 56789999998875    222233565544444444441       1145566666666544322   2348888


Q ss_pred             HHHHHHhcC--ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          195 MISGLCEMG--QPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG-LLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       195 li~~~~~~g--~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g-~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      ---.+.+.|  +++++++.++++.+... -|...|+.---++.+.| .++++.+.++.+.+.... |...|+..-..+.+
T Consensus       113 R~w~l~~l~~~~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~-n~saW~~r~~ll~~  190 (567)
T 1dce_A          113 RCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQ  190 (567)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCC-CccHHHHHHHHHHh
Confidence            888888899  66999999999998642 26778888777788888 899999999999887543 78889888887766


Q ss_pred             c--------------CCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHH
Q 042756          272 H--------------NELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSC  304 (425)
Q Consensus       272 ~--------------g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~  304 (425)
                      .              +.+++|++++++.+..  .| |...|...--.+
T Consensus       191 l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~--~P~~~saW~y~~~ll  236 (567)
T 1dce_A          191 LHPQPDSGPQGRLPENVLLKELELVQNAFFT--DPNDQSAWFYHRWLL  236 (567)
T ss_dssp             HSCCCCSSSCCSSCHHHHHHHHHHHHHHHHH--CSSCSHHHHHHHHHH
T ss_pred             hcccccccccccccHHHHHHHHHHHHHHHhh--CCCCccHHHHHHHHH
Confidence            3              5578999999988764  34 445565554433

>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=94.75  E-value=0.043  Score=44.08  Aligned_cols=117  Identities=7%  Similarity=-0.049  Sum_probs=67.6

Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc-------cHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          122 DKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR-------GFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       122 ~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~-------~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      .+.+++++|.+.++...+..    |.....|..+-.++.+.++++       .++++...+++.+.-.+.   +...|+.
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~----P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~---~~~A~~~   85 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN----PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK---KDEAVWC   85 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT---CHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC---cHHHHHH
Confidence            44556777777777666541    111224555555555555433       133555555555443211   2347777


Q ss_pred             HHHHHHhc-----------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          195 MISGLCEM-----------GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       195 li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +-.+|...           |++++|++.|++..+  +.|+...|...+...      +.|-+++-.....
T Consensus        86 LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~~------~ka~el~~~~~~~  147 (158)
T 1zu2_A           86 IGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT------AKAPQLHAEAYKQ  147 (158)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH------HTHHHHHHHHHHS
T ss_pred             HHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHHH------HhCHhccCccccc
Confidence            88888766           489999999999888  578777776665532      3344444444443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.73  E-value=1.1  Score=34.63  Aligned_cols=138  Identities=12%  Similarity=0.024  Sum_probs=82.4

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc
Q 042756          123 KQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM  202 (425)
Q Consensus       123 ~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~  202 (425)
                      -.|.+++..++..+..+...      ..-||=+|.-....-+   .+..++.+.....-.. +.|- .-.-.++++|++.
T Consensus        19 ldG~v~qGveii~k~~~ssn------i~E~NW~ICNiiD~a~---C~y~v~vLd~IGkiFD-is~C-~NlKrVi~C~~~~   87 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKSST------KSEYNWFICNLLESID---CRYMFQVLDKIGSYFD-LDKC-QNLKSVVECGVIN   87 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHHSC------HHHHTHHHHHHHHHCC---HHHHHHHHHHHGGGSC-GGGC-SCTHHHHHHHHHT
T ss_pred             HhhhHHHHHHHHHHHcCCCC------ccccceeeeecchhhc---hhHHHHHHHHHhhhcC-cHhh-hcHHHHHHHHHHh
Confidence            35888899999998876421      1234556666666666   6667777776653322 1110 0223344444443


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWL  282 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~  282 (425)
                      +.                  +..-+...++....+|.-+.-.++..++.. +.+|++...-.+-.+|.+.|+..+|.+++
T Consensus        88 n~------------------~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl  148 (172)
T 1wy6_A           88 NT------------------LNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLL  148 (172)
T ss_dssp             TC------------------CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cc------------------hHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHH
Confidence            32                  233445556667777777777777777533 23456666667777777777777777777


Q ss_pred             HHHHhCCC
Q 042756          283 QKMKDSGI  290 (425)
Q Consensus       283 ~~M~~~g~  290 (425)
                      .+.-+.|+
T Consensus       149 ~~AC~kG~  156 (172)
T 1wy6_A          149 IEACKKGE  156 (172)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhhh
Confidence            77777765

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=94.60  E-value=0.41  Score=49.20  Aligned_cols=131  Identities=13%  Similarity=0.084  Sum_probs=86.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKS  194 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~  194 (425)
                      ..++..+.+.|..++|.++.+.-         .      .-.......|+   +++|++.....        .+...|..
T Consensus       633 ~~~~~~l~~~~~~~~a~~~~~~~---------~------~~f~~~l~~~~---~~~A~~~~~~~--------~~~~~W~~  686 (814)
T 3mkq_A          633 TKIARFLEGQEYYEEALNISPDQ---------D------QKFELALKVGQ---LTLARDLLTDE--------SAEMKWRA  686 (814)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCCCH---------H------HHHHHHHHHTC---HHHHHHHHTTC--------CCHHHHHH
T ss_pred             HHHHHHHHhCCChHHheecCCCc---------c------hheehhhhcCC---HHHHHHHHHhh--------CcHhHHHH
Confidence            55777777888888887765321         1      01223345677   55666654332        23459999


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      +-..+.+.|+++.|.+.|.++..         |..+...|...|+.+...++-+.....|-      ++.-..+|.+.|+
T Consensus       687 la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~~------~~~A~~~~~~~g~  751 (814)
T 3mkq_A          687 LGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTGK------FNLAFNAYWIAGD  751 (814)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTTC------HHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcCc------hHHHHHHHHHcCC
Confidence            99999999999999999998754         44555566667777776666666555542      4555566667777


Q ss_pred             HHHHHHHHHHHH
Q 042756          275 LSRMVLWLQKMK  286 (425)
Q Consensus       275 ~~~A~~l~~~M~  286 (425)
                      +++|+++|.++.
T Consensus       752 ~~~a~~~~~~~~  763 (814)
T 3mkq_A          752 IQGAKDLLIKSQ  763 (814)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcC
Confidence            777777776654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=94.33  E-value=0.13  Score=36.90  Aligned_cols=55  Identities=20%  Similarity=0.165  Sum_probs=32.5

Q ss_pred             HHHHhcCChhHHHHHHHHHHHcCCCC-CHH-HHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          197 SGLCEMGQPHEAENLIEEMRVKGLEP-SGF-EYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~-ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ..+.+.|++++|.+.|++..+.  .| +.. .+..+-.+|.+.|++++|.+.|+...+.
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQT--EPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH--CSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3455566666666666666553  23 334 5556666666666666666666665554

>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=94.09  E-value=3.3  Score=37.56  Aligned_cols=223  Identities=6%  Similarity=-0.115  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCC---hHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHH
Q 042756           36 TKQGQRFLSSLALAVTRDSKAASRLISKFVASSP---QFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPK  112 (425)
Q Consensus        36 ~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~---~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~  112 (425)
                      .++|+++++.+...-+-+..+||.-=..+...+.   .+...              ..+++++.+++.+...+.  -+..
T Consensus        46 s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~--------------~~l~~EL~~~~~~L~~~P--Kny~  109 (331)
T 3dss_A           46 DESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESA--------------ALVKAELGFLESCLRVNP--KSYG  109 (331)
T ss_dssp             SHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHH--------------HHHHHHHHHHHHHHHHCT--TCHH
T ss_pred             CHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhh--------------HHHHHHHHHHHHHHHhCC--CCHH
Confidence            3457777777665433345556544333332211   11110              135667788888776552  3677


Q ss_pred             HHHHHHHHHHhcC--ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          113 LVAEIIAFLDKQG--QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       113 ~~~~ll~~~~~~g--~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      +|+.--..+.+.|  .++++.++++.+.+..    +.+...|+.---.+.+.|..  .++.++.+.++.....   -|..
T Consensus       110 aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d----prNy~AW~~R~~vl~~l~~~--~~eel~~~~~~I~~~p---~N~S  180 (331)
T 3dss_A          110 TWHHRCWLLSRLPEPNWARELELCARFLEAD----ERNFHCWDYRRFVAAQAAVA--PAEELAFTDSLITRNF---SNYS  180 (331)
T ss_dssp             HHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCC--HHHHHHHHHHHHHHCS---CCHH
T ss_pred             HHHHHHHHHhccCcccHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHhCcC--HHHHHHHHHHHHHHCC---CCHH
Confidence            7777777777777  4899999999998762    22234566666666666763  3455555555554331   2445


Q ss_pred             HHHHHHHHHHhc--------------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC-----------CCHHHHHH
Q 042756          191 ALKSMISGLCEM--------------GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL-----------GLLEDMER  245 (425)
Q Consensus       191 ~~~~li~~~~~~--------------g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~-----------g~~~~a~~  245 (425)
                      .|+-.-..+.+.              +.++++++.+.+..... +-|...|+-+--.+.+.           +.++++.+
T Consensus       181 AW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~  259 (331)
T 3dss_A          181 SWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELE  259 (331)
T ss_dssp             HHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHH
Confidence            787766666654              45788999999888742 23566776554444444           45788999


Q ss_pred             HHHHHHHCCCCcCHHhHHHHHHHH-----HhcCCHHHHHHHHHHHHh
Q 042756          246 IVNQMESDGTRVDTVCSNMVLSSY-----GDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       246 ~~~~m~~~g~~~~~~~yn~li~~~-----~~~g~~~~A~~l~~~M~~  287 (425)
                      .++++.+..  ||. .|+.+-.+.     ...|..+++...+.++++
T Consensus       260 ~~~elle~~--pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          260 SCKELQELE--PEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHHC--TTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhhC--ccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            999998763  553 454322222     235666777777777765

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=93.23  E-value=2.3  Score=32.90  Aligned_cols=143  Identities=13%  Similarity=0.154  Sum_probs=82.7

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ...++.|.++++.++.....+.  .+..-||.+|--...+-+-+....+++.+                     ..-  +
T Consensus        15 K~~ildG~v~qGveii~k~~~s--sni~E~NW~ICNiiD~a~C~y~v~vLd~I---------------------Gki--F   69 (172)
T 1wy6_A           15 KKFLLDGYIDEGVKIVLEITKS--STKSEYNWFICNLLESIDCRYMFQVLDKI---------------------GSY--F   69 (172)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--SCHHHHTHHHHHHHHHCCHHHHHHHHHHH---------------------GGG--S
T ss_pred             HHHHHhhhHHHHHHHHHHHcCC--CCccccceeeeecchhhchhHHHHHHHHH---------------------hhh--c
Confidence            5568889999999998888764  67778888888777776555555555443                     211  1


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV  187 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p  187 (425)
                        |.          ...|++..+...|-.+..     ...   ..+.-++.+...|..|++++...-+..    .  ..|
T Consensus        70 --Di----------s~C~NlKrVi~C~~~~n~-----~se---~vd~ALd~lv~~~KkDqLdki~~~~l~----n--~~~  123 (172)
T 1wy6_A           70 --DL----------DKCQNLKSVVECGVINNT-----LNE---HVNKALDILVIQGKRDKLEEIGREILK----N--NEV  123 (172)
T ss_dssp             --CG----------GGCSCTHHHHHHHHHTTC-----CCH---HHHHHHHHHHHTTCHHHHHHHHHHHC--------CCS
T ss_pred             --Cc----------HhhhcHHHHHHHHHHhcc-----hHH---HHHHHHHHHHHhccHhHHHHHHHHHhc----c--CCC
Confidence              21          223444444444433321     111   235556666667775555544443211    1  223


Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKGLE  221 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  221 (425)
                      +....-.+-+||.+.|+..+|.++..+..++|++
T Consensus       124 ~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A          124 SASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             ChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            4445556667777777777777777777776653

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=92.45  E-value=0.49  Score=33.71  Aligned_cols=58  Identities=10%  Similarity=0.068  Sum_probs=48.8

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCcCHH-hHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          230 IIYGYGRLGLLEDMERIVNQMESDGTRVDTV-CSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       230 ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~-~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ....+.+.|++++|.+.|+...+..- .+.. .|..+-..|...|++++|.+.|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEP-VGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCS-STHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            34567889999999999999887632 2556 8899999999999999999999998865

>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=91.96  E-value=1.9  Score=38.14  Aligned_cols=127  Identities=6%  Similarity=-0.069  Sum_probs=76.1

Q ss_pred             HHHHhcCCCchhHHHHHHHHHHHHHhc--CCccc---HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhc-----CCh
Q 042756          136 ETLSKLGSRERELVLFYCNLIDSFCKH--DSKRG---FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEM-----GQP  205 (425)
Q Consensus       136 ~m~~~~~~~~~~~~~~y~~li~~~~~~--g~~~~---~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~-----g~~  205 (425)
                      +...+..+...+...+..+....+...  |++..   +.++...+.+...-.+. ..+...|..+...|.+.     |+.
T Consensus       142 ~~l~~~~~~dve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAleLDP~-~~~GsA~~~LG~lY~~vPp~~gGd~  220 (301)
T 3u64_A          142 KVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPS-YQEGAVWNVLTKFYAAAPESFGGGM  220 (301)
T ss_dssp             HHHTTCCGGGHHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHSCTTTTCCH
T ss_pred             HHHHHcCccccHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHHhCCC-cccCHHHHHHHHHHHhCCCccCCCH
Confidence            333333333444343333333345543  44443   33444444444432211 12356888888888884     888


Q ss_pred             hHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHCCCC--cCHHhHHHH
Q 042756          206 HEAENLIEEMRVKGLEP--SGFEYKCIIYGYGRL-GLLEDMERIVNQMESDGTR--VDTVCSNMV  265 (425)
Q Consensus       206 ~~a~~~~~~m~~~g~~p--~~~ty~~ll~~~~~~-g~~~~a~~~~~~m~~~g~~--~~~~~yn~l  265 (425)
                      ++|.+.|++..+.  .|  +..++...-..+++. |+.+++.+.++........  |+....|.+
T Consensus       221 ekA~~~ferAL~L--nP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan~~  283 (301)
T 3u64_A          221 EKAHTAFEHLTRY--CSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVIL  283 (301)
T ss_dssp             HHHHHHHHHHHHH--CCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHHHH
Confidence            8888888888874  45  366777777778774 8888888888888877655  665544443

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=91.72  E-value=3.2  Score=32.80  Aligned_cols=93  Identities=6%  Similarity=-0.036  Sum_probs=63.5

Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHCCCCc--CHHhHHHHHHHHHhcCCHHHHH
Q 042756          205 PHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG---LLEDMERIVNQMESDGTRV--DTVCSNMVLSSYGDHNELSRMV  279 (425)
Q Consensus       205 ~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g---~~~~a~~~~~~m~~~g~~~--~~~~yn~li~~~~~~g~~~~A~  279 (425)
                      +..+.+-|.+....|- ++..+--.+--++++.+   +++++..+|++..+.. .|  +...+-.|--+|.+.|++++|.
T Consensus        14 l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            4556666666666554 56666666666777777   6778888888887764 23  3455555666778999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHH
Q 042756          280 LWLQKMKDSGIPFSVRTYNSVL  301 (425)
Q Consensus       280 ~l~~~M~~~g~~pd~~t~~~ll  301 (425)
                      +.++...+.  .|+-.--..+.
T Consensus        92 ~y~~~lL~i--eP~n~QA~~Lk  111 (152)
T 1pc2_A           92 KYVRGLLQT--EPQNNQAKELE  111 (152)
T ss_dssp             HHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHhc--CCCCHHHHHHH
Confidence            999998864  67554433333

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=91.51  E-value=2.9  Score=32.89  Aligned_cols=53  Identities=11%  Similarity=0.120  Sum_probs=30.9

Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      ++.++|.++|+.+.+..-+- ...|...-.--.++|+++.|.+++..-...+-+
T Consensus        74 ~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k  126 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAV  126 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB
T ss_pred             cCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC
Confidence            56666666666665543222 445544455555666666666666666665544

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=91.42  E-value=3.8  Score=33.28  Aligned_cols=104  Identities=12%  Similarity=0.094  Sum_probs=76.9

Q ss_pred             HHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 042756          156 IDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYG  235 (425)
Q Consensus       156 i~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~  235 (425)
                      .....+.|+   ++.+++...+..        +...|..|-....+.|+++-|.+.|.+..         -|..+.-.|.
T Consensus        12 F~LAL~lg~---l~~A~e~a~~l~--------~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~---------D~~~L~~Ly~   71 (177)
T 3mkq_B           12 FDLALEYGN---LDAALDEAKKLN--------DSITWERLIQEALAQGNASLAEMIYQTQH---------SFDKLSFLYL   71 (177)
T ss_dssp             HHHHHHTTC---HHHHHHHHHHHC--------CHHHHHHHHHHHHHTTCHHHHHHHHHHTT---------CHHHHHHHHH
T ss_pred             HHHHHhcCC---HHHHHHHHHHhC--------CHHHHHHHHHHHHHcCChHHHHHHHHHhC---------CHHHHHHHHH
Confidence            344556788   566666665541        23499999999999999999999999864         3566666777


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 042756          236 RLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKM  285 (425)
Q Consensus       236 ~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M  285 (425)
                      -.|+.+.-.++-+.-..+|      -+|.-...+.-.|+++++.++|.+.
T Consensus        72 ~tg~~e~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           72 VTGDVNKLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HHTCHHHHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HhCCHHHHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHC
Confidence            7888887777766655554      2777778888899999999988653

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=90.89  E-value=3.9  Score=33.18  Aligned_cols=96  Identities=13%  Similarity=0.044  Sum_probs=59.5

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .++.|.++-+.+   +    +...|..|-....+.|+++-|++.|....      +      |..+.-.|.-.|+.+++.
T Consensus        20 ~l~~A~e~a~~l---~----~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~------D------~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           20 NLDAALDEAKKL---N----DSITWERLIQEALAQGNASLAEMIYQTQH------S------FDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             CHHHHHHHHHHH---C----CHHHHHHHHHHHHHTTCHHHHHHHHHHTT------C------HHHHHHHHHHHTCHHHHH
T ss_pred             CHHHHHHHHHHh---C----CHHHHHHHHHHHHHcCChHHHHHHHHHhC------C------HHHHHHHHHHhCCHHHHH
Confidence            455555554443   1    45567778888888888888888888753      1      355666666677743322


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEM  215 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  215 (425)
                      ..   .......+        -+|.-..++.-.|+++++.++|.+.
T Consensus        81 kl---a~iA~~~g--------~~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           81 KM---QNIAQTRE--------DFGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HH---HHHHHHTT--------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HH---HHHHHHCc--------cHHHHHHHHHHcCCHHHHHHHHHHC
Confidence            22   22222222        5677777777888888888887543

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.30  E-value=12  Score=35.33  Aligned_cols=180  Identities=11%  Similarity=0.122  Sum_probs=116.9

Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh-cCCCC
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVN-SSSSV  185 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~-~~~~~  185 (425)
                      ..++......++..|.+.|+++...+.+.-+.++.+.........-+.++..+......+ ...-...+..... ..+.+
T Consensus        52 ~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai~~~V~~~~~~l~~~~~~d-~~~~~~~i~~l~~vte~ki  130 (445)
T 4b4t_P           52 LASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLKSSKSLD-LNTRISVIETIRVVTENKI  130 (445)
T ss_dssp             TTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHHHHHHHHHHHHHHHHCTTH-HHHHHHHHHCCSSSSSCCC
T ss_pred             hhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCchh-HHHHHHHHHHHHHHhccch
Confidence            567888999999999999999999888887776655544332222233333333333322 1111112211110 01112


Q ss_pred             cc---ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc--CCCCC---HHHHHHHHHHHHcCCCHHHHHHHHHHHHH----C
Q 042756          186 YV---KRQALKSMISGLCEMGQPHEAENLIEEMRVK--GLEPS---GFEYKCIIYGYGRLGLLEDMERIVNQMES----D  253 (425)
Q Consensus       186 ~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p~---~~ty~~ll~~~~~~g~~~~a~~~~~~m~~----~  253 (425)
                      +.   ......-|...|-..|++.+|.+++.++...  |.-+.   ...|...+..|...+++..|..+......    .
T Consensus       131 flE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~  210 (445)
T 4b4t_P          131 FVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKN  210 (445)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhccc
Confidence            22   2234466788899999999999999998753  32221   33677788899999999999999998642    2


Q ss_pred             CCCcC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          254 GTRVD--TVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       254 g~~~~--~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ...|+  ..-|..++..+...+++.+|.+.|.+.-+
T Consensus       211 ~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          211 PKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             SCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            22232  45677888888899999999998888743

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=90.25  E-value=1.8  Score=31.43  Aligned_cols=30  Identities=10%  Similarity=0.189  Sum_probs=16.4

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ....|..|..+|.+.|++++|..++++..+
T Consensus        45 ~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A           45 KVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            344555555555555555555555555543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=89.55  E-value=2.6  Score=30.62  Aligned_cols=66  Identities=8%  Similarity=-0.091  Sum_probs=55.6

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC------CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          188 KRQALKSMISGLCEMGQPHEAENLIEEMRVKG------LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       188 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g------~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +..-+..|-..+.+.|+++.|...|++..+.-      -.+....+..+-.++.+.|+++.|..+++...+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            44567788999999999999999999987641      1245678999999999999999999999998875

>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=89.11  E-value=3.6  Score=36.39  Aligned_cols=114  Identities=12%  Similarity=-0.029  Sum_probs=83.1

Q ss_pred             cChhHHHHHHHHH-Hhc--C------ChhHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHcC-----CCHHHHHHHHHH
Q 042756          187 VKRQALKSMISGL-CEM--G------QPHEAENLIEEMRVKGLEPS---GFEYKCIIYGYGRL-----GLLEDMERIVNQ  249 (425)
Q Consensus       187 p~~~~~~~li~~~-~~~--g------~~~~a~~~~~~m~~~g~~p~---~~ty~~ll~~~~~~-----g~~~~a~~~~~~  249 (425)
                      +....|..++.+- ...  |      ....|..++++..+  +-|+   ...|..+-..|.+.     |+.++|++.|++
T Consensus       152 ve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAle--LDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~fer  229 (301)
T 3u64_A          152 VGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACD--LWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEH  229 (301)
T ss_dssp             HHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHH--HCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHH--hCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHH
Confidence            3445777777644 442  3      23456666666655  4566   56899999999995     999999999999


Q ss_pred             HHHCCCCcCHHhHHHHHHHHHhc-CCHHHHHHHHHHHHhCCCC--CCHHHHHHHHH
Q 042756          250 MESDGTRVDTVCSNMVLSSYGDH-NELSRMVLWLQKMKDSGIP--FSVRTYNSVLN  302 (425)
Q Consensus       250 m~~~g~~~~~~~yn~li~~~~~~-g~~~~A~~l~~~M~~~g~~--pd~~t~~~ll~  302 (425)
                      -.+.+-.-+..++....+.+++. |+.++|.+.+++.......  |+....+.+-+
T Consensus       230 AL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan~~~q  285 (301)
T 3u64_A          230 LTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQ  285 (301)
T ss_dssp             HHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHHHHHH
T ss_pred             HHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHHHHHH
Confidence            88864222478888888999985 9999999999999987666  77655555443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=88.52  E-value=23  Score=38.02  Aligned_cols=204  Identities=12%  Similarity=0.104  Sum_probs=109.5

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhh-cCCCccCHHHHHHHHHHHHhcCChhHH
Q 042756           52 RDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITE-ESWFQWNPKLVAEIIAFLDKQGQREEA  130 (425)
Q Consensus        52 ~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~-~~~~~~~~~~~~~ll~~~~~~g~~~~A  130 (425)
                      .+...-=.+-.++...|++++|...|.+.-..-+........-.. +..+.. ......-+.-|..++..|-+.|.++.|
T Consensus       840 ~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~-~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~v  918 (1139)
T 4fhn_B          840 SDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLRE-FQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDA  918 (1139)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHH-HHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHH
T ss_pred             CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcc-cccccccccccccHHHHHHHHHHHHHHcCCHHHH
Confidence            344332234455666799999999998863221111111111111 111211 111223445688899999999999999


Q ss_pred             HHHHHHHHHhcCCCchhH-HHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHH
Q 042756          131 ETLILETLSKLGSREREL-VLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAE  209 (425)
Q Consensus       131 ~~l~~~m~~~~~~~~~~~-~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~  209 (425)
                      .++-....+......++. ...|..+.+++...|++++   |+..+..+....  ..  ......+|...|..|..+.-.
T Consensus       919 i~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~---Ay~aL~~~pd~~--~r--~~cLr~LV~~lce~~~~~~L~  991 (1139)
T 4fhn_B          919 LEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDA---AHVALMVLSTTP--LK--KSCLLDFVNQLTKQGKINQLL  991 (1139)
T ss_dssp             HHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGG---GGHHHHHHHHSS--SC--HHHHHHHHHHHHHHCCHHHHH
T ss_pred             HHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHH---HHHHHHhCCCHH--HH--HHHHHHHHHHHHhCCChhhhh
Confidence            887666555443333322 2257788888888898554   445454443332  11  236667777777766654433


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCcCHHhHHHHHHHHHhcCCHHHHHH-HHHHHH
Q 042756          210 NLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG--TRVDTVCSNMVLSSYGDHNELSRMVL-WLQKMK  286 (425)
Q Consensus       210 ~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g--~~~~~~~yn~li~~~~~~g~~~~A~~-l~~~M~  286 (425)
                      .                       +--.|..++..+++..-.+..  +.....-|..|-.-+...|++.+|-. +|+...
T Consensus       992 ~-----------------------lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmYe~~~ 1048 (1139)
T 4fhn_B          992 N-----------------------YSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIYEKLS 1048 (1139)
T ss_dssp             H-----------------------HTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             C-----------------------CCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHHHHHH
Confidence            2                       112444555555554332211  01112346777777778888766544 455443

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=88.30  E-value=5.3  Score=28.37  Aligned_cols=65  Identities=6%  Similarity=-0.061  Sum_probs=32.7

Q ss_pred             CHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          223 SGFEYKCIIYGYGRLGL---LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~g~---~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      |...+..+-.++...++   .++|..+++...+..- -+......+-..+.+.|++++|...|+++.+.
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp-~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEP-YNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCc-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            33444444444432322   4556666665554321 13444555555556666666666666666543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=88.27  E-value=4.3  Score=32.08  Aligned_cols=88  Identities=9%  Similarity=0.043  Sum_probs=54.8

Q ss_pred             hhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCcc--ChhHHHHHHHHHHhcCC
Q 042756          127 REEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYV--KRQALKSMISGLCEMGQ  204 (425)
Q Consensus       127 ~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p--~~~~~~~li~~~~~~g~  204 (425)
                      +..+++-|.+..+.+. ++..   +.-.+--++++.......+++...+.+.....   .|  ....+-.+--+|.+.|+
T Consensus        14 l~~~~~~y~~e~~~~~-~~~~---~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~---~p~~~rd~lY~LAv~~~kl~~   86 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS-VSKS---TQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG---SKEEQRDYVFYLAVGNYRLKE   86 (152)
T ss_dssp             HHHHHHHHHHHHHTTC-CCHH---HHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS---CHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHccCC-CcHH---HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC---CccchHHHHHHHHHHHHHccC
Confidence            4556666666554322 2332   22345556777776666777777777776653   23  23355556666788888


Q ss_pred             hhHHHHHHHHHHHcCCCCC
Q 042756          205 PHEAENLIEEMRVKGLEPS  223 (425)
Q Consensus       205 ~~~a~~~~~~m~~~g~~p~  223 (425)
                      +++|.+.++...+  +.|+
T Consensus        87 Y~~A~~y~~~lL~--ieP~  103 (152)
T 1pc2_A           87 YEKALKYVRGLLQ--TEPQ  103 (152)
T ss_dssp             HHHHHHHHHHHHH--HCTT
T ss_pred             HHHHHHHHHHHHh--cCCC
Confidence            8888888888887  4563

>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=87.36  E-value=2.7  Score=39.11  Aligned_cols=69  Identities=10%  Similarity=-0.022  Sum_probs=48.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH-----hCCCCCCHHHH
Q 042756          228 KCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMK-----DSGIPFSVRTY  297 (425)
Q Consensus       228 ~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~-----~~g~~pd~~t~  297 (425)
                      ..++.++...|+.++|...+..+.... +.+...|-.+|.+|.+.|+..+|++.|++..     +-|+.|+..+-
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            345566677788888777777665432 3367788888888888888888888887764     35788876653

>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=85.44  E-value=6.3  Score=31.05  Aligned_cols=109  Identities=11%  Similarity=0.069  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHhcCCh------hHHHHHHHHHHHcCCCCCHH----HHHHHHHH---HHcCCCHHHHHHHHHHHHHCCCCc
Q 042756          191 ALKSMISGLCEMGQP------HEAENLIEEMRVKGLEPSGF----EYKCIIYG---YGRLGLLEDMERIVNQMESDGTRV  257 (425)
Q Consensus       191 ~~~~li~~~~~~g~~------~~a~~~~~~m~~~g~~p~~~----ty~~ll~~---~~~~g~~~~a~~~~~~m~~~g~~~  257 (425)
                      +|=..+.-.-+.|+.      ++..++|++.... ++|+..    .|.-|.--   +-..+|+++|.++|+.+.+. .+-
T Consensus        15 ~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~-hKk   92 (161)
T 4h7y_A           15 DWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN-CKK   92 (161)
T ss_dssp             HHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH-CTT
T ss_pred             HHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH-hHH
Confidence            666677777767777      7888888877663 566422    12111111   12337999999999999876 333


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLN  302 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~  302 (425)
                      -...|-....--.+.|++.+|.+++.+.+..+-+| ...+...|+
T Consensus        93 FAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~-~~~le~a~~  136 (161)
T 4h7y_A           93 FAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP-LEMLEIALR  136 (161)
T ss_dssp             BHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc-HHHHHHHHH
Confidence            37888888888889999999999999999877555 344444443

>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=83.97  E-value=5.1  Score=37.25  Aligned_cols=70  Identities=10%  Similarity=0.009  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCcCHHh
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES-----DGTRVDTVC  261 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~~  261 (425)
                      +...++.++...|++++|.......... -+-+...|..+|.++.+.|+..+|.+.|+...+     .|+.|+..+
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            5667788899999999999998888764 234788999999999999999999999998754     489888654

>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=83.48  E-value=7.4  Score=28.22  Aligned_cols=33  Identities=18%  Similarity=0.200  Sum_probs=13.5

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          219 GLEPSGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       219 g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      .+.|+.....+.++||-+.+|+..|.++|+..+
T Consensus        40 DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK   72 (109)
T 1v54_E           40 DLVPEPKIIDAALRACRRLNDFASAVRILEVVK   72 (109)
T ss_dssp             SBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            334444444444444444444444444444333

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.20  E-value=12  Score=35.12  Aligned_cols=101  Identities=12%  Similarity=0.118  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh---
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR---  189 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~---  189 (425)
                      +...+...|.+.|+++.|.+.|.++.......... ...+-.+|..+...+++..+.............+..  |+.   
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~k-id~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d--~~~~~~  209 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAK-IDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGD--WERRNR  209 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSH-HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCC--THHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHH-HHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCC--HHHHHH
Confidence            44558889999999999999999998754443333 446778899999999988888888888777665532  221   


Q ss_pred             -hHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          190 -QALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       190 -~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                       ..|..++  +...+++.+|.+.|-+....
T Consensus       210 lk~~~gl~--~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          210 YKTYYGIH--CLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             HHHHHHHG--GGGTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HHHhChHHHHHHHHHHHhcc
Confidence             1233332  33468899999988887654

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=82.79  E-value=11  Score=28.66  Aligned_cols=96  Identities=8%  Similarity=0.027  Sum_probs=61.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHH---HHHHHHHHHHCCCCc--CHHhHHHHHHHH
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLED---MERIVNQMESDGTRV--DTVCSNMVLSSY  269 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~---a~~~~~~m~~~g~~~--~~~~yn~li~~~  269 (425)
                      ++........+..+.+-|.+....|- |+..+--.+--++++.....+   +..++++....+ .|  .....-.|--++
T Consensus         7 ~l~~~~~~~~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~   84 (126)
T 1nzn_A            7 VLNELVSVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGN   84 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHH
T ss_pred             HHhccCCHHHHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHH
Confidence            33344444455666666666665554 555555555557777765444   888888877754 13  334444555678


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCH
Q 042756          270 GDHNELSRMVLWLQKMKDSGIPFSV  294 (425)
Q Consensus       270 ~~~g~~~~A~~l~~~M~~~g~~pd~  294 (425)
                      .+.|++++|.+.++.+.+.  .|+-
T Consensus        85 yklg~Y~~A~~~~~~lL~~--eP~n  107 (126)
T 1nzn_A           85 YRLKEYEKALKYVRGLLQT--EPQN  107 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHhhhHHHHHHHHHHHHHh--CCCC
Confidence            8899999999999888764  5644

>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=82.10  E-value=12  Score=27.09  Aligned_cols=70  Identities=13%  Similarity=0.119  Sum_probs=57.5

Q ss_pred             HHcCC-CHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Q 042756          234 YGRLG-LLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLNSC  304 (425)
Q Consensus       234 ~~~~g-~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~  304 (425)
                      |-+.. |.-+..+-++.+....+.|+.....+.+.+|-+.+++..|+++|+-.+.. +.+...+|..+++-+
T Consensus        19 F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lqEl   89 (109)
T 1v54_E           19 FNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQEL   89 (109)
T ss_dssp             HTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHHH
T ss_pred             cCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHHHH
Confidence            33444 67778999999999999999999999999999999999999999987643 344456798888754

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.95  E-value=35  Score=32.20  Aligned_cols=256  Identities=6%  Similarity=0.018  Sum_probs=152.0

Q ss_pred             HHHHhhHHHHHHHHHHhHHh------cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc----hhhhHHHHHH
Q 042756           30 CLTARLTKQGQRFLSSLALA------VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR----LSSLAFPLYM   99 (425)
Q Consensus        30 ~l~~~~~~~a~~~~~~m~~~------~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~----~~~~a~~lf~   99 (425)
                      .+.++.++.|.+-+..+.+.      ..-+......++..|...++++...+.+.-+..+.+....    .+..+...++
T Consensus        26 ~l~~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai~~~V~~~~~~l~  105 (445)
T 4b4t_P           26 SLAQNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLK  105 (445)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence            35578888898877776654      3445777888999999999998887766655544443222    2333333333


Q ss_pred             Hhhhc-----------------CCCcc---CHHHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHH
Q 042756          100 RITEE-----------------SWFQW---NPKLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLID  157 (425)
Q Consensus       100 ~m~~~-----------------~~~~~---~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~  157 (425)
                      ..+..                 +.+-.   .......|...+-..|++.+|..++.++...  +......-...|...+.
T Consensus       106 ~~~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~r  185 (445)
T 4b4t_P          106 SSKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQME  185 (445)
T ss_dssp             HHCTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHH
T ss_pred             cCCchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            33211                 11111   2234456788888999999999999998653  22222333456777888


Q ss_pred             HHHhcCCcccHHHHHHHHHHHhhcCCCCccC--hhHHHHHHHHHHhcCChhHHHHHHHHHHHc-CCCCCHHHHHHHHH--
Q 042756          158 SFCKHDSKRGFDDTYARLNQLVNSSSSVYVK--RQALKSMISGLCEMGQPHEAENLIEEMRVK-GLEPSGFEYKCIIY--  232 (425)
Q Consensus       158 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~ty~~ll~--  232 (425)
                      .|...+++..+............... ..|+  ..-|..++..+...+++.+|.+.|.+.... .+.-|...+..++.  
T Consensus       186 l~l~~~d~~~a~~~~~ki~~~~~~~~-~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~  264 (445)
T 4b4t_P          186 LSILKGDYSQATVLSRKILKKTFKNP-KYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHI  264 (445)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHSS-CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhhcccC-CcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHH
Confidence            99999998777777666544332221 2233  346777888888899999999988888653 12223332222211  


Q ss_pred             --HHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc--CCHHHHHHHHHHHH
Q 042756          233 --GYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH--NELSRMVLWLQKMK  286 (425)
Q Consensus       233 --~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~--g~~~~A~~l~~~M~  286 (425)
                        +..-.+....-..+........-.++...|..++.+|...  .+++.+.+.|....
T Consensus       265 v~~~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L  322 (445)
T 4b4t_P          265 VYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVL  322 (445)
T ss_dssp             HHHHHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSST
T ss_pred             HHHHHhCCCCchHHHHHHHHhhcccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHh
Confidence              1111221122222222222222235778899999999764  35677777666543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=81.68  E-value=13  Score=37.78  Aligned_cols=129  Identities=12%  Similarity=0.012  Sum_probs=79.1

Q ss_pred             HHHHHHHHhcCC-hhHHHHHHHHHHHhcCCCchhHHHHH-HHHHHHHHhcCCcccHHHHHHHHHHHhhc-------CCCC
Q 042756          115 AEIIAFLDKQGQ-REEAETLILETLSKLGSRERELVLFY-CNLIDSFCKHDSKRGFDDTYARLNQLVNS-------SSSV  185 (425)
Q Consensus       115 ~~ll~~~~~~g~-~~~A~~l~~~m~~~~~~~~~~~~~~y-~~li~~~~~~g~~~~~~~~~~~~~~~~~~-------~~~~  185 (425)
                      ..++..+...|+ .+.|..+|+++.+.    .+.....| .++|..+.+.++  .-.++..++.+....       -...
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~----~p~~~~~~~~~~i~~~~~~~~--~Ev~av~ll~~~l~~~~~~~~~l~~~  325 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKK----DPIHDIYYKTAMITILDHIET--KELDMITILNETLDPLLSLLNDLPPR  325 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHH----CGGGHHHHHHHHHHHHTTCGG--GHHHHHHHHHHHHHHHHHHHHTCSSC
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhh----CCchhHHHHHHHHHHHHHhhh--hhHHHHHHHHHHHHHhhhhhhhhccc
Confidence            345555555566 58899999998875    22211122 233433333332  133445555444321       1000


Q ss_pred             ccC--------hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          186 YVK--------RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       186 ~p~--------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      ..+        ....+.=.+.+...|+++-|+.+-++...  +.|+ -.||-.|..+|.+.|+++.|.-.++.+.
T Consensus       326 ~~~~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~--~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          326 DADSARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE--LALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccccccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh--cCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            000        01122224556778999999999999876  5676 5599999999999999999999999883

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	425
d2d9ia1	83	d.68.8.1 (A:8-90) Nedd4-binding protein 2 {Human (	1e-07

>d2d9ia1 d.68.8.1 (A:8-90) Nedd4-binding protein 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: SMR domain-like
family: Smr domain
domain: Nedd4-binding protein 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 357 ETKLDLHGMHLGSAYFIILQWMDEMRNRFNNEKHVIPAEITVVCGSGKHSTVRGESSVKA 416
           +  LDLHG+H+  A   +++ +++    F          ++V+ G G HS   G + +K 
Sbjct: 1   QNVLDLHGLHVDEALEHLMRVLEKKTEEFKQNGGKP--YLSVITGRGNHSQ-GGVARIKP 57

Query: 417 MVKKMMVR 424
            V K ++ 
Sbjct: 58  AVIKYLIS 65

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	425
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.52
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.39
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.09
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.93
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.8
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.69
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.45
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.45
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.38
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.36
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.34
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.33
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.24
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.13
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.98
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.88
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.87
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.79
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.66
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.65
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.64
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.63
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.58
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.36
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.36
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.36
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.35
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.34
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.14
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.12
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.1
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.03
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.93
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.87
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.82
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.54
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.47
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.27
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.2
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.18
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.11
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.85
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.8
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.49
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.15
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	94.99
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	94.53
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	94.27
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	93.91
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	93.85
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.78
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.32
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.0
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	92.83
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	85.16
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	84.91
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	84.0

>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=99.52  E-value=1e-11  Score=114.65  Aligned_cols=316  Identities=10%  Similarity=-0.040  Sum_probs=173.2

Q ss_pred             HHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCc
Q 042756           29 QCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQ  108 (425)
Q Consensus        29 ~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~  108 (425)
                      .....|++++|.+.|+.+.+..+-+..++..+...+.+.|+++.|...+.+.+....                       
T Consensus         8 ~~~~~G~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-----------------------   64 (388)
T d1w3ba_           8 REYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNP-----------------------   64 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-----------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-----------------------
Confidence            345678999999999999877555788899999999999988777777777643221                       


Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHH------------------------------HHHHHHHHH
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELV------------------------------LFYCNLIDS  158 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~------------------------------~~y~~li~~  158 (425)
                      -++.++..+...|.+.|++++|.+.+....+..........                              .........
T Consensus        65 ~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (388)
T d1w3ba_          65 LLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNL  144 (388)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhhhcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            14455666666666677777777666665543221111000                              000111111


Q ss_pred             HHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcC
Q 042756          159 FCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRL  237 (425)
Q Consensus       159 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~  237 (425)
                      ....+.   .........+.....+   -+...+..+...+...|++++|...+++..+.  .| +..+|..+...+...
T Consensus       145 ~~~~~~---~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~  216 (388)
T d1w3ba_         145 LKALGR---LEEAKACYLKAIETQP---NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL--DPNFLDAYINLGNVLKEA  216 (388)
T ss_dssp             HHTTSC---HHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTT
T ss_pred             ccccch---hhhhHHHHHHhhccCc---chhHHHHhhcccccccCcHHHHHHHHHHHHHh--CcccHHHHHHHhhhhhcc
Confidence            111111   1122222222222211   11235555556666666666666666655543  23 244555566666666


Q ss_pred             CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHhhc-
Q 042756          238 GLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQDLN-  315 (425)
Q Consensus       238 g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~~~-  315 (425)
                      |++++|...++...+.+. .+...+..+...|.+.|++++|+..|++..+.  .| +..++..+...+...|+..++.. 
T Consensus       217 ~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~  293 (388)
T d1w3ba_         217 RIFDRAVAAYLRALSLSP-NHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDC  293 (388)
T ss_dssp             TCTTHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             ccHHHHHHHHHHhHHHhh-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            666666666665554432 24455555566666666666666666665543  23 23455555555555555444422 


Q ss_pred             --------cCCch---hhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          316 --------SNDFP---LSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       316 --------~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                              +....   .+...+...+..+++....+-.-.....+..+|..+-..|.+.|++++|     .+.|++..+
T Consensus       294 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A-----~~~~~~al~  367 (388)
T d1w3ba_         294 YNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEA-----LMHYKEAIR  367 (388)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHH-----HHHHHHHHT
T ss_pred             HHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHH
Confidence                    01000   1111233334444444333322222223456788888999999999999     999999886

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=5.2e-10  Score=102.78  Aligned_cols=263  Identities=12%  Similarity=0.008  Sum_probs=189.6

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCc---------------------
Q 042756           31 LTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPR---------------------   89 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~---------------------   89 (425)
                      ...|++++|.+.|+...+.-+-+..+|..+...|.+.|+++.|...+............                     
T Consensus        44 ~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (388)
T d1w3ba_          44 FQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQA  123 (388)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHhhhhccccccccccccccccccccccccccccccccccccccccccc
Confidence            45679999999999988765557889999999999999999999999887654332111                     


Q ss_pred             --------------------------hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCC
Q 042756           90 --------------------------LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGS  143 (425)
Q Consensus        90 --------------------------~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~  143 (425)
                                                ....+...+.......  +-+...+..+...+...|++++|.+.+++..+.   
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~---  198 (388)
T d1w3ba_         124 YVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ--PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL---  198 (388)
T ss_dssp             HHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH---
T ss_pred             cccccccccccccccccccccccccchhhhhHHHHHHhhccC--cchhHHHHhhcccccccCcHHHHHHHHHHHHHh---
Confidence                                      0112233333332222  124566777778888889999999999887764   


Q ss_pred             CchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-
Q 042756          144 RERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-  222 (425)
Q Consensus       144 ~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-  222 (425)
                       .|.....|..+...+...|+++++.+.+....+...      .+...+..+...+.+.|++++|.+.|++..+.  .| 
T Consensus       199 -~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~------~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~  269 (388)
T d1w3ba_         199 -DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP------NHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPH  269 (388)
T ss_dssp             -CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSS
T ss_pred             -CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh------hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCC
Confidence             222234677888888899997665555555444321      23447888888999999999999999988774  44 


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH
Q 042756          223 SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS-VRTYNSVL  301 (425)
Q Consensus       223 ~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd-~~t~~~ll  301 (425)
                      +..++..+...+.+.|++++|.+.++...... +.+...+..+...|...|++++|++.|++..+.  .|+ ..++..+-
T Consensus       270 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la  346 (388)
T d1w3ba_         270 FPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLA  346 (388)
T ss_dssp             CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            46688888899999999999999998877643 346788888889999999999999999988754  564 34555555


Q ss_pred             HHHHHHHHH
Q 042756          302 NSCSTIMSM  310 (425)
Q Consensus       302 ~~~~~~~~~  310 (425)
                      ..|.+.|++
T Consensus       347 ~~~~~~g~~  355 (388)
T d1w3ba_         347 SVLQQQGKL  355 (388)
T ss_dssp             HHHHTTTCC
T ss_pred             HHHHHcCCH
Confidence            555554444

>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=99.09  E-value=2.5e-08  Score=89.70  Aligned_cols=230  Identities=9%  Similarity=-0.036  Sum_probs=166.7

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWF  107 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~  107 (425)
                      ...+..|++++|.+.|+...+.-+-+..+|..+...+...|+++.|...+.+.+.                     .+  
T Consensus        27 ~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~---------------------~~--   83 (323)
T d1fcha_          27 LRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLE---------------------LK--   83 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------------HC--
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhc---------------------cc--
Confidence            4567788999999999999876555788999999999999987777777766542                     11  


Q ss_pred             ccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCch-----hHHH------HHHHHHHHHHhcCCcccHHHHHHHHH
Q 042756          108 QWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRER-----ELVL------FYCNLIDSFCKHDSKRGFDDTYARLN  176 (425)
Q Consensus       108 ~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~-----~~~~------~y~~li~~~~~~g~~~~~~~~~~~~~  176 (425)
                      +-+...+..+...|...|++++|.+.+++..........     ....      .....+..+.+.+.   ..++...+.
T Consensus        84 p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~a~~~~~  160 (323)
T d1fcha_          84 PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSL---FLEVKELFL  160 (323)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHH---HHHHHHHHH
T ss_pred             cccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhH---HHHHHHHHH
Confidence            125667888889999999999999999998753211000     0000      00111112222233   334444444


Q ss_pred             HHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          177 QLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       177 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      +.....+ -.++...|..+...+...|++++|...|++....  .| +..+|..+-.+|.+.|++++|.+.|+...+.. 
T Consensus       161 ~al~~~p-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-  236 (323)
T d1fcha_         161 AAVRLDP-TSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-  236 (323)
T ss_dssp             HHHHHST-TSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHhh-cccccccchhhHHHHHHHHHHhhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHHh-
Confidence            4433222 1245568889999999999999999999998875  34 46789999999999999999999999988753 


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      +-+..+|..+..+|.+.|++++|++.|++.++
T Consensus       237 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         237 PGYIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            12577899999999999999999999999765

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=7.1e-08  Score=86.61  Aligned_cols=216  Identities=10%  Similarity=-0.055  Sum_probs=153.2

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+++|++.|+...+.+.  -++.+|..+...+...|++++|...|++..+..    |.....|..+...|...|+++.+.
T Consensus        34 ~~~~A~~~~~~al~~~P--~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~~~~~~A~  107 (323)
T d1fcha_          34 DLPNAVLLFEAAVQQDP--KHMEAWQYLGTTQAENEQELLAISALRRCLELK----PDNQTALMALAVSFTNESLQRQAC  107 (323)
T ss_dssp             CHHHHHHHHHHHHHSCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc----cccccccccccccccccccccccc
Confidence            56777777777666541  267789999999999999999999999987652    222346778889999999955444


Q ss_pred             HHHHHHHHHhhcCCCCc-c--------ChhHHHHHHHHHHhcCChhHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCC
Q 042756          170 DTYARLNQLVNSSSSVY-V--------KRQALKSMISGLCEMGQPHEAENLIEEMRVKG-LEPSGFEYKCIIYGYGRLGL  239 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~-p--------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~g~  239 (425)
                      +.+.......+...... +        +.......+..+...+.+++|.+.|.+..... -.++..++..+-..+...|+
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~  187 (323)
T d1fcha_         108 EILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGE  187 (323)
T ss_dssp             HHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTC
T ss_pred             cchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHH
Confidence            44444333222110000 0        00112223344455677888999998877643 33467788889999999999


Q ss_pred             HHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHHHHHHHHHhh
Q 042756          240 LEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPF-SVRTYNSVLNSCSTIMSMLQDL  314 (425)
Q Consensus       240 ~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~p-d~~t~~~ll~~~~~~~~~~~~~  314 (425)
                      +++|...|+......- -+...|..+...|...|++++|.+.|++..+.  .| +...|..+-.+|.+.|+.++++
T Consensus       188 ~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~  260 (323)
T d1fcha_         188 YDKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGAHREAV  260 (323)
T ss_dssp             HHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             Hhhhhccccccccccc-ccccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCCHHHHH
Confidence            9999999999876532 25788999999999999999999999998764  35 4567778888888888776663

>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=98.80  E-value=7.2e-07  Score=79.62  Aligned_cols=234  Identities=10%  Similarity=-0.008  Sum_probs=157.3

Q ss_pred             HHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHH
Q 042756           36 TKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVA  115 (425)
Q Consensus        36 ~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~  115 (425)
                      .+.+..+|++.....+.+...|-.-+.-+-..+.....       ...........++|..+|++..... .+.+...+.
T Consensus        32 ~~Rv~~vyerAl~~~~~~~~lW~~y~~~~~~~~~~~~~-------~~~~~~~~~~~~~a~~i~~ral~~~-~p~~~~l~~  103 (308)
T d2onda1          32 TKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAE-------KGDMNNAKLFSDEAANIYERAISTL-LKKNMLLYF  103 (308)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHH-------TSCCHHHHHHHHHHHHHHHHHHTTT-TTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCchHHH-------HHHHhhcccchHHHHHHHHHHHHHc-CCCCHHHHH
Confidence            34466677777766556666666555443332211000       0000001124577888888866532 334666777


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHH
Q 042756          116 EIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSM  195 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~l  195 (425)
                      ..+....+.|+++.|..+|+++.+....   +...+|...+..+.+.|..+.+.+++   .+.....+.   +...|-..
T Consensus       104 ~ya~~~~~~~~~~~a~~i~~~~l~~~~~---~~~~~w~~~~~~~~~~~~~~~ar~i~---~~al~~~~~---~~~~~~~~  174 (308)
T d2onda1         104 AYADYEESRMKYEKVHSIYNRLLAIEDI---DPTLVYIQYMKFARRAEGIKSGRMIF---KKAREDART---RHHVYVTA  174 (308)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTSSSS---CTHHHHHHHHHHHHHHHCHHHHHHHH---HHHHTSTTC---CTHHHHHH
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHHhcC---ChHHHHHHHHHHHHHcCChHHHHHHH---HHHHHhCCC---cHHHHHHH
Confidence            7888889999999999999998764222   11336788889998888855544444   444333211   12233333


Q ss_pred             HHH-HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCcC--HHhHHHHHHHHHh
Q 042756          196 ISG-LCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG-TRVD--TVCSNMVLSSYGD  271 (425)
Q Consensus       196 i~~-~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g-~~~~--~~~yn~li~~~~~  271 (425)
                      ... +...|+.+.|..+|+++... .+-+...|...++.+.+.|+++.|..+|+...+.. ..|+  ...|...+.--..
T Consensus       175 a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~  253 (308)
T d2onda1         175 ALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESN  253 (308)
T ss_dssp             HHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHH
Confidence            322 33468999999999999986 33457789999999999999999999999987653 4443  5689999998899


Q ss_pred             cCCHHHHHHHHHHHHh
Q 042756          272 HNELSRMVLWLQKMKD  287 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~~  287 (425)
                      .|+.+.+.++++++.+
T Consensus       254 ~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         254 IGDLASILKVEKRRFT  269 (308)
T ss_dssp             HSCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            9999999999999865

>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=98.69  E-value=3.8e-06  Score=75.11  Aligned_cols=257  Identities=13%  Similarity=0.027  Sum_probs=173.8

Q ss_pred             HHHhhHHHHHHHHHHhHHhcCCC-----HHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCC-----------------
Q 042756           31 LTARLTKQGQRFLSSLALAVTRD-----SKAASRLISKFVASSPQFIALNALSHLLSPDTTHP-----------------   88 (425)
Q Consensus        31 l~~~~~~~a~~~~~~m~~~~~~d-----~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~-----------------   88 (425)
                      +..|++++|.++++......+.+     ..+++.+-..+...|+++.|...+.+.+......+                 
T Consensus        23 ~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  102 (366)
T d1hz4a_          23 INDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILF  102 (366)
T ss_dssp             HHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHH
Confidence            56789999999999987762222     35677788899999999999999988754211111                 


Q ss_pred             --chhhhHHHHHHHhhh----cC-C-CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-CchhHHHHHHHHHHHH
Q 042756           89 --RLSSLAFPLYMRITE----ES-W-FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGS-RERELVLFYCNLIDSF  159 (425)
Q Consensus        89 --~~~~~a~~lf~~m~~----~~-~-~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~-~~~~~~~~y~~li~~~  159 (425)
                        +.+..+...+.....    .. . .......+..+-..+...|+++.+...+......... ........+..+...+
T Consensus       103 ~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (366)
T d1hz4a_         103 AQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCS  182 (366)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHH
Confidence              124445555544321    11 1 1112335566777888999999999999988764322 1222233455666677


Q ss_pred             HhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCC---CCHHHHHHHHHHHH
Q 042756          160 CKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVKGLE---PSGFEYKCIIYGYG  235 (425)
Q Consensus       160 ~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~---p~~~ty~~ll~~~~  235 (425)
                      ...++.......+..............+. ...+......+...|++++|...+.+.......   .....+..+..++.
T Consensus       183 ~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  262 (366)
T d1hz4a_         183 LARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQI  262 (366)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHH
Confidence            77888655555555544444443222222 245677778888999999999999887654322   23456677888999


Q ss_pred             cCCCHHHHHHHHHHHHH----CCCCcC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 042756          236 RLGLLEDMERIVNQMES----DGTRVD-TVCSNMVLSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       236 ~~g~~~~a~~~~~~m~~----~g~~~~-~~~yn~li~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      ..|++++|.+.++....    .+..|+ ..++..+-..|.+.|++++|.+.|++..+
T Consensus       263 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         263 LLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999998753    354444 46788888999999999999999998654

>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=98.45  E-value=6.3e-05  Score=64.22  Aligned_cols=191  Identities=10%  Similarity=0.015  Sum_probs=104.6

Q ss_pred             hhhHHHHHHHhhhcCCCcc--CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           91 SSLAFPLYMRITEESWFQW--NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        91 ~~~a~~lf~~m~~~~~~~~--~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      .+.++.-+++........+  .+.+|..+-..|.+.|++++|.+.|++..+.    .|+...+|..+-.+|.+.|+++.+
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l----~p~~~~a~~~lg~~~~~~g~~~~A   90 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAI----RPDMPEVFNYLGIYLTQAGNFDAA   90 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhcc----CCCCHHHHhhhchHHHHHHHHHHh
Confidence            4445555555443322211  2234555666777778888888877777654    122234667777777777774444


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVN  248 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~  248 (425)
                      .+.++...+..+.      +..+|..+..+|...|++++|...|++..+.. +.+......+..++.+.+..+.+..+..
T Consensus        91 ~~~~~~al~~~p~------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (259)
T d1xnfa_          91 YEAFDSVLELDPT------YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQ  163 (259)
T ss_dssp             HHHHHHHHHHCTT------CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             hhhhhHHHHHHhh------hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            4444433333211      12367777777777788888888777776642 1123333222233333333222222222


Q ss_pred             HHHHCC----------------------------------CCc-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC
Q 042756          249 QMESDG----------------------------------TRV-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS  293 (425)
Q Consensus       249 ~m~~~g----------------------------------~~~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd  293 (425)
                      ......                                  ..| ...+|..+-..|...|++++|.+.|++..+.  .|+
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~  241 (259)
T d1xnfa_         164 HFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVH  241 (259)
T ss_dssp             HHHHSCCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCT
T ss_pred             HhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCC
Confidence            222110                                  011 2346667778888899999999999988764  454


Q ss_pred             H
Q 042756          294 V  294 (425)
Q Consensus       294 ~  294 (425)
                      .
T Consensus       242 ~  242 (259)
T d1xnfa_         242 N  242 (259)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=4e-05  Score=68.16  Aligned_cols=201  Identities=11%  Similarity=-0.054  Sum_probs=142.4

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQG-QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGF  168 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g-~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~  168 (425)
                      ..++|+++++...+-+.  -+...|+..-..+...| ++++|.+.++...+.    .|....+|..+-..+.+.|+++++
T Consensus        58 ~~~~Al~~~~~ai~lnP--~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~----~p~~~~a~~~~~~~~~~l~~~~eA  131 (315)
T d2h6fa1          58 RSERAFKLTRDAIELNA--ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE----QPKNYQVWHHRRVLVEWLRDPSQE  131 (315)
T ss_dssp             CCHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHHTCCTTH
T ss_pred             chHHHHHHHHHHHHHCC--CChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH----HHhhhhHHHHHhHHHHhhccHHHH
Confidence            44556666666555441  25667888888888876 589999999998765    233345788888899999998777


Q ss_pred             HHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCC------HH
Q 042756          169 DDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGL------LE  241 (425)
Q Consensus       169 ~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~------~~  241 (425)
                      .+.+....+.-+.      +...|+.+...+.+.|++++|++.|++..+.  .| +...|+.+-..+.+.+.      ++
T Consensus       132 l~~~~kal~~dp~------n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~--~p~n~~a~~~r~~~l~~~~~~~~~~~~~  203 (315)
T d2h6fa1         132 LEFIADILNQDAK------NYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYNDRAVLE  203 (315)
T ss_dssp             HHHHHHHHHHCTT------CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSCSHHHHH
T ss_pred             HHHHhhhhhhhhc------chHHHHHHHHHHHHHHhhHHHHHHHHHHHHH--CCccHHHHHHHHHHHHHccccchhhhhH
Confidence            6666666554222      3459999999999999999999999999985  34 56678777666666554      67


Q ss_pred             HHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHHH
Q 042756          242 DMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIP-FSVRTYNSVLNSCST  306 (425)
Q Consensus       242 ~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~-pd~~t~~~ll~~~~~  306 (425)
                      +|.+.+....+.. +-+...|+.+...+...| .+++.+.++...+..-. .+...+..+...|..
T Consensus       204 ~ai~~~~~al~~~-P~~~~~~~~l~~ll~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~  267 (315)
T d2h6fa1         204 REVQYTLEMIKLV-PHNESAWNYLKGILQDRG-LSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYED  267 (315)
T ss_dssp             HHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTC-GGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHhC-CCchHHHHHHHHHHHhcC-hHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHH
Confidence            8888888777653 236788888766655444 67888888877653222 245566667666654

>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=98.38  E-value=4.5e-05  Score=67.46  Aligned_cols=187  Identities=8%  Similarity=0.028  Sum_probs=129.1

Q ss_pred             hHHHHHHHHHHhHHh-cCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHH
Q 042756           35 LTKQGQRFLSSLALA-VTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKL  113 (425)
Q Consensus        35 ~~~~a~~~~~~m~~~-~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~  113 (425)
                      ..++|..+|++.... .+.+...|...+..+-+.|+.+.+..++.+++..                     . ......+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~---------------------~-~~~~~~~  136 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI---------------------E-DIDPTLV  136 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS---------------------S-SSCTHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH---------------------h-cCChHHH
Confidence            456777888887765 4556677777777777777666666666665432                     2 1113446


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHH-HHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLID-SFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      |...+..+.+.|+++.|+++|+...+.... ...   .|..... -+...|+.+.+..   .+.......   .-+...|
T Consensus       137 w~~~~~~~~~~~~~~~ar~i~~~al~~~~~-~~~---~~~~~a~~e~~~~~~~~~a~~---i~e~~l~~~---p~~~~~w  206 (308)
T d2onda1         137 YIQYMKFARRAEGIKSGRMIFKKAREDART-RHH---VYVTAALMEYYCSKDKSVAFK---IFELGLKKY---GDIPEYV  206 (308)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHHTSTTC-CTH---HHHHHHHHHHHTSCCHHHHHH---HHHHHHHHH---TTCHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHhCCC-cHH---HHHHHHHHHHHhccCHHHHHH---HHHHHHHhh---hhhHHHH
Confidence            788889999999999999999998765332 222   2322222 2334567444444   444444321   1124589


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcC-CCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKG-LEPS--GFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      ...+..+.+.|+++.|..+|++..... ..|+  ...|...+..-...|+++.+.++++++.+.
T Consensus       207 ~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         207 LAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999999988764 4553  457888888888999999999999988653

>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=98.36  E-value=5.5e-05  Score=67.19  Aligned_cols=249  Identities=8%  Similarity=-0.040  Sum_probs=159.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCC-CccC
Q 042756          112 KLVAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSS-VYVK  188 (425)
Q Consensus       112 ~~~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~-~~p~  188 (425)
                      ..+..+-..|...|++++|.+.|++..+.  .....+.....+..+...+...|++..+.+.+............ ..+.
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            45667788899999999999999987652  22223333445666777888889966555555444443332211 1122


Q ss_pred             -hhHHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCc--
Q 042756          189 -RQALKSMISGLCEMGQPHEAENLIEEMRVKG----LEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESD----GTRV--  257 (425)
Q Consensus       189 -~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----g~~~--  257 (425)
                       ...+..+-..+...|+++.+...+.......    ......++......+...++...+...+......    +-.+  
T Consensus       132 ~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~  211 (366)
T d1hz4a_         132 HEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDW  211 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHH
T ss_pred             HHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCch
Confidence             2356667788899999999999999987642    2234556777778888999999998888766542    2111  


Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhh
Q 042756          258 DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFS---VRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEE  334 (425)
Q Consensus       258 ~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd---~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  334 (425)
                      ....++.+...+...|++++|...+.+..+..-..+   ...+..+...+...|+...+..                  .
T Consensus       212 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~------------------~  273 (366)
T d1hz4a_         212 ISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEI------------------V  273 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHH------------------H
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHH------------------H
Confidence            234567777788899999999999998765332222   2334445555555555544422                  1


Q ss_pred             HHHHHHHH-hCCCCcc-cceeeccccchhcccCcchhHHHHHHHHHHHHHh
Q 042756          335 VSVVKELE-DSSVLDE-AMKWDSGETKLDLHGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       335 ~~~~~~~~-~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      ...+.... ..+..|+ ..+|..+-..|...|++++|     .+.|++..+
T Consensus       274 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A-----~~~l~~Al~  319 (366)
T d1hz4a_         274 LEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDA-----QRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH-----HHHHHHHHH
T ss_pred             HHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHH-----HHHHHHHHH
Confidence            11111111 2233333 34577777889999999999     888887654

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.34  E-value=2.6e-05  Score=68.49  Aligned_cols=175  Identities=9%  Similarity=-0.114  Sum_probs=126.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          114 VAEIIAFLDKQGQREEAETLILETLSK--LGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       114 ~~~ll~~~~~~g~~~~A~~l~~~m~~~--~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      |...-..|-..|++++|.+.|.+..+-  .....++...+|..+-..|.+.|+++.+.+.++...+.............+
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  119 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHH
Confidence            444566788999999999999987652  222234445678899999999999887777777666665554333334457


Q ss_pred             HHHHHHHHHh-cCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-----CH-
Q 042756          192 LKSMISGLCE-MGQPHEAENLIEEMRVK----GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-----DT-  259 (425)
Q Consensus       192 ~~~li~~~~~-~g~~~~a~~~~~~m~~~----g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-----~~-  259 (425)
                      +..+...|-. .|++++|++.|.+..+.    +-.+. ..+|..+...+.+.|++++|.+.|+......-..     .. 
T Consensus       120 ~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~  199 (290)
T d1qqea_         120 KFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLK  199 (290)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHH
T ss_pred             HHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHH
Confidence            7777777754 69999999999987642    22222 3468889999999999999999999987642211     11 


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          260 VCSNMVLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       260 ~~yn~li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      ..|...+..+...|+++.|.+.|++..+.
T Consensus       200 ~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         200 DYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            22344555677899999999999998765

>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=98.33  E-value=8.7e-05  Score=64.95  Aligned_cols=212  Identities=10%  Similarity=-0.007  Sum_probs=133.2

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 042756           58 SRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILET  137 (425)
Q Consensus        58 ~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m  137 (425)
                      ...-..|...++++.|...+.+.              .+++......   .....+|..+-.+|.+.|++++|.+.+++.
T Consensus        41 ~~aa~~y~~~~~~~~A~~~y~kA--------------~~~~~~~~~~---~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a  103 (290)
T d1qqea_          41 VQAATIYRLRKELNLAGDSFLKA--------------ADYQKKAGNE---DEAGNTYVEAYKCFKSGGNSVNAVDSLENA  103 (290)
T ss_dssp             HHHHHHHHHTTCTHHHHHHHHHH--------------HHHHHHTTCH---HHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHH--------------HHHHHHcCCC---HHHHHHHHHHHHHHHHhCCcHHHHHHHHHh
Confidence            33445566666666666655553              3333332221   123568888999999999999999999976


Q ss_pred             HHh--cCCCchhHHHHHHHHHHHHH-hcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHH
Q 042756          138 LSK--LGSRERELVLFYCNLIDSFC-KHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEE  214 (425)
Q Consensus       138 ~~~--~~~~~~~~~~~y~~li~~~~-~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  214 (425)
                      .+.  ..........++..+...|- ..|+++.+.+.+....++....+...--..+|..+...|.+.|++++|...|++
T Consensus       104 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~  183 (290)
T d1qqea_         104 IQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSK  183 (290)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHH
Confidence            542  11112222335556666664 468866666666555554333322111234788899999999999999999999


Q ss_pred             HHHcCCC-----CCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-cC---HHhHHHHHHHHHh--cCCHHHHHHHH
Q 042756          215 MRVKGLE-----PSG-FEYKCIIYGYGRLGLLEDMERIVNQMESDGTR-VD---TVCSNMVLSSYGD--HNELSRMVLWL  282 (425)
Q Consensus       215 m~~~g~~-----p~~-~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~-~~---~~~yn~li~~~~~--~g~~~~A~~l~  282 (425)
                      .......     ... ..|..+...+...|+++.|.+.++...+.... ++   ......++.++-.  .+.+++|+.-|
T Consensus       184 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y  263 (290)
T d1qqea_         184 LIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEF  263 (290)
T ss_dssp             HHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHH
T ss_pred             HHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            8775311     121 23345555777899999999999988765211 12   2345667777765  34588999888


Q ss_pred             HHHH
Q 042756          283 QKMK  286 (425)
Q Consensus       283 ~~M~  286 (425)
                      +++.
T Consensus       264 ~~~~  267 (290)
T d1qqea_         264 DNFM  267 (290)
T ss_dssp             TTSS
T ss_pred             HHHh
Confidence            7655

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=5e-05  Score=67.52  Aligned_cols=178  Identities=10%  Similarity=0.076  Sum_probs=133.8

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQ  190 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~  190 (425)
                      ...|+.+-..+.+.+..++|++++++..+.    .|.....|+..-..+...|..  .+++...+.+.....+.   +..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~l----nP~~~~a~~~r~~~l~~l~~~--~~eal~~~~~al~~~p~---~~~  113 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIEL----NAANYTVWHFRRVLLKSLQKD--LHEEMNYITAIIEEQPK---NYQ  113 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCC--HHHHHHHHHHHHHHCTT---CHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHH----CCCChHHHHHHHHHHHHhCcC--HHHHHHHHHHHHHHHHh---hhh
Confidence            346777777788889999999999999875    333345778888787776531  44555555555433321   245


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      +|+.+-..+.+.|++++|++.|+++.+.  .| +...|..+...+.+.|++++|.+.|+...+... -+...|+.+-..+
T Consensus       114 a~~~~~~~~~~l~~~~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l  190 (315)
T d2h6fa1         114 VWHHRRVLVEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVI  190 (315)
T ss_dssp             HHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHhHHHHhhccHHHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHH
Confidence            9999999999999999999999999985  44 578999999999999999999999999998653 2677888877777


Q ss_pred             HhcCC------HHHHHHHHHHHHhCCCCC-CHHHHHHHHH
Q 042756          270 GDHNE------LSRMVLWLQKMKDSGIPF-SVRTYNSVLN  302 (425)
Q Consensus       270 ~~~g~------~~~A~~l~~~M~~~g~~p-d~~t~~~ll~  302 (425)
                      .+.|.      .++|++.+.+..+.  .| +...|..+..
T Consensus       191 ~~~~~~~~~~~~~~ai~~~~~al~~--~P~~~~~~~~l~~  228 (315)
T d2h6fa1         191 SNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKG  228 (315)
T ss_dssp             HHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHH
T ss_pred             HHccccchhhhhHHhHHHHHHHHHh--CCCchHHHHHHHH
Confidence            66655      57899999888765  34 4555555433

>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=98.13  E-value=9.1e-05  Score=63.17  Aligned_cols=154  Identities=10%  Similarity=-0.031  Sum_probs=102.7

Q ss_pred             ChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCCh
Q 042756          126 QREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQP  205 (425)
Q Consensus       126 ~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~  205 (425)
                      +.+.+..-+++...+....++....+|..+-..|.+.|+++.+.+.++...+..+.      +..+|+.+-.+|.+.|++
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~------~~~a~~~lg~~~~~~g~~   87 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD------MPEVFNYLGIYLTQAGNF   87 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC------CHHHHhhhchHHHHHHHH
Confidence            45566666677665544334444456667778888899965555555555443222      234899999999999999


Q ss_pred             hHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 042756          206 HEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQK  284 (425)
Q Consensus       206 ~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~  284 (425)
                      ++|++.|++..+.  .| +..++..+-.+|...|++++|.+.|+...+... .+......+..++.+.+..+.+..+...
T Consensus        88 ~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (259)
T d1xnfa_          88 DAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP-NDPFRSLWLYLAEQKLDEKQAKEVLKQH  164 (259)
T ss_dssp             HHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-ccHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            9999999998874  34 355788888889999999999999998876532 2344444444455556655555555555


Q ss_pred             HHhC
Q 042756          285 MKDS  288 (425)
Q Consensus       285 M~~~  288 (425)
                      ....
T Consensus       165 ~~~~  168 (259)
T d1xnfa_         165 FEKS  168 (259)
T ss_dssp             HHHS
T ss_pred             hhcc
Confidence            5543

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.98  E-value=3.5e-05  Score=68.97  Aligned_cols=234  Identities=6%  Similarity=-0.075  Sum_probs=160.9

Q ss_pred             HhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHH
Q 042756           33 ARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPK  112 (425)
Q Consensus        33 ~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~  112 (425)
                      .+.+++|+.+++...+..+-+...|..+..++...+.                   ...++|...+....+.+ . .+..
T Consensus        86 ~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~-------------------~~~~~a~~~~~~al~~~-~-~~~~  144 (334)
T d1dcea1          86 AALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPE-------------------PNWARELELCARFLEAD-E-RNFH  144 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSS-------------------CCHHHHHHHHHHHHHHC-T-TCHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhcc-------------------ccHHHHHHHHHHHHhhC-c-hhhh
Confidence            4467788888888877655577788877777777653                   13455666666655544 1 3455


Q ss_pred             HHHHH-HHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhH
Q 042756          113 LVAEI-IAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQA  191 (425)
Q Consensus       113 ~~~~l-l~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~  191 (425)
                      .+... -..+...|..++|.+.+++..+.    .|.....|..+-..+.+.|+++++...+....+..       |   .
T Consensus       145 ~~~~~~~~~~~~~~~~~~Al~~~~~~i~~----~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------~---~  210 (334)
T d1dcea1         145 CWDYRRFVAAQAAVAPAEELAFTDSLITR----NFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVL-------L---K  210 (334)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHTTTTT----TCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHH-------H---H
T ss_pred             hhhhHHHHHHHhccccHHHHHHHHHHHHc----CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhH-------H---H
Confidence            54433 45666789999999999887654    23334578888888999998765544333322221       1   1


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHh
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGD  271 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~  271 (425)
                      .......+...+..+++...+....... .++...+..+...+...|+.++|.+.+....+... .+...|..+...|.+
T Consensus       211 ~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p-~~~~~~~~l~~~~~~  288 (334)
T d1dcea1         211 ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQELEPENK-WCLLTIILLMRALDP  288 (334)
T ss_dssp             HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCH-HHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCc-hHHHHHHHHHHHHHH
Confidence            1223444566788888999888887753 34456677778888888999999999998876542 267888889999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHH
Q 042756          272 HNELSRMVLWLQKMKDSGIPFSV-RTYNSVLNSCS  305 (425)
Q Consensus       272 ~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~~~~  305 (425)
                      .|+.++|.+.|++..+.  .|+. .-|..|-..+.
T Consensus       289 ~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         289 LLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             GGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            99999999999998864  6754 35555554444

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.88  E-value=0.00019  Score=53.30  Aligned_cols=100  Identities=7%  Similarity=-0.143  Sum_probs=82.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCC
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNE  274 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~  274 (425)
                      --+.+.+.|++++|+.+|++..+.. +-+...|..+-.+|.+.|++++|...++...+..- .+...|..+..+|...|+
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHHHHHccC
Confidence            3456788899999999999998752 33577899999999999999999999999887653 478899999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHH
Q 042756          275 LSRMVLWLQKMKDSGIPFSVRTYN  298 (425)
Q Consensus       275 ~~~A~~l~~~M~~~g~~pd~~t~~  298 (425)
                      +++|+..|++..+.  .|+...+.
T Consensus        87 ~~~A~~~~~~a~~~--~p~~~~~~  108 (117)
T d1elwa_          87 FEEAKRTYEEGLKH--EANNPQLK  108 (117)
T ss_dssp             HHHHHHHHHHHHTT--CTTCHHHH
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHH
Confidence            99999999998864  56654443

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.87  E-value=0.00013  Score=59.56  Aligned_cols=98  Identities=11%  Similarity=-0.054  Sum_probs=83.2

Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-CHHhHHHH
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-DTVCSNMV  265 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~yn~l  265 (425)
                      |+...+...-..|.+.|++++|+..|.+..... +-+...|..+-.+|.+.|++++|.+.|+...+.  .| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            566677777888999999999999999988753 336778999999999999999999999998765  34 57789999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh
Q 042756          266 LSSYGDHNELSRMVLWLQKMKD  287 (425)
Q Consensus       266 i~~~~~~g~~~~A~~l~~~M~~  287 (425)
                      -.+|...|++++|+..|++..+
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999998754

>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=97.79  E-value=0.00092  Score=54.28  Aligned_cols=131  Identities=7%  Similarity=-0.065  Sum_probs=98.8

Q ss_pred             HHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 042756          157 DSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR  236 (425)
Q Consensus       157 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~  236 (425)
                      ..+...|+   .+++.+.+.+.      ..|+..+|..+-.+|.+.|++++|++.|++..+.. +-+...|..+-.+|.+
T Consensus        13 ~~~~~~~d---~~~Al~~~~~i------~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~   82 (192)
T d1hh8a_          13 VLAADKKD---WKGALDAFSAV------QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQ   82 (192)
T ss_dssp             HHHHHTTC---HHHHHHHHHTS------SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCC---HHHHHHHHHhc------CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHh
Confidence            34556778   55666666553      33566789999999999999999999999998853 2257799999999999


Q ss_pred             CCCHHHHHHHHHHHHHC------------CCC--c-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 042756          237 LGLLEDMERIVNQMESD------------GTR--V-DTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTY  297 (425)
Q Consensus       237 ~g~~~~a~~~~~~m~~~------------g~~--~-~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~  297 (425)
                      .|++++|.+.|+.....            |..  + ...++..+-.+|.+.|++++|.+.|.+..+....|+....
T Consensus        83 ~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~  158 (192)
T d1hh8a_          83 TEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKI  158 (192)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHH
T ss_pred             hccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHH
Confidence            99999999999987642            111  1 1355667778899999999999999998866544433333

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=0.00087  Score=52.46  Aligned_cols=99  Identities=6%  Similarity=-0.126  Sum_probs=82.7

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                      ...-..|.+.|++++|+..|++..+.. +-+...|..+-.+|...|++++|.+.|+...+.. +-+...|..+..+|...
T Consensus        14 ~~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~   91 (159)
T d1a17a_          14 KTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMAL   91 (159)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHc
Confidence            334456789999999999999999863 3357789999999999999999999999998764 23678999999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHH
Q 042756          273 NELSRMVLWLQKMKDSGIPFSVR  295 (425)
Q Consensus       273 g~~~~A~~l~~~M~~~g~~pd~~  295 (425)
                      |++++|...|++..+.  .|+..
T Consensus        92 g~~~eA~~~~~~a~~~--~p~~~  112 (159)
T d1a17a_          92 GKFRAALRDYETVVKV--KPHDK  112 (159)
T ss_dssp             TCHHHHHHHHHHHHHH--STTCH
T ss_pred             CCHHHHHHHHHHHHHc--CCCCH
Confidence            9999999999998875  45543

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=0.00028  Score=52.76  Aligned_cols=108  Identities=6%  Similarity=0.059  Sum_probs=85.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCCCcC-HHhHHHHHH
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGL---LEDMERIVNQMESDGTRVD-TVCSNMVLS  267 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~---~~~a~~~~~~m~~~g~~~~-~~~yn~li~  267 (425)
                      ...+++.+...+++++|.+.|++....+ +.+..++..+-.++.+.++   +++|.++|+......-.|+ ..+|..|-.
T Consensus         2 ~~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           2 MEAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            3567888999999999999999998853 3467788888888887655   5569999999887654444 347888899


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 042756          268 SYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVLN  302 (425)
Q Consensus       268 ~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll~  302 (425)
                      +|.+.|++++|.+.|++..+.  .|+..-...+..
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~~--~P~~~~A~~l~~  113 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQT--EPQNNQAKELER  113 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHHh--CcCCHHHHHHHH
Confidence            999999999999999999874  687665554443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.64  E-value=0.00013  Score=65.10  Aligned_cols=218  Identities=7%  Similarity=-0.042  Sum_probs=113.2

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHH-HHHHHHhc
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKS-MISGLCEM  202 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~-li~~~~~~  202 (425)
                      .|++++|..+++...+.    .|.....|..+..++...+..+ ..++...+.+.....+   ++...|.. .-..+...
T Consensus        86 ~~~~~~al~~~~~~l~~----~pk~~~~~~~~~~~~~~~~~~~-~~~a~~~~~~al~~~~---~~~~~~~~~~~~~~~~~  157 (334)
T d1dcea1          86 AALVKAELGFLESCLRV----NPKSYGTWHHRCWLLSRLPEPN-WARELELCARFLEADE---RNFHCWDYRRFVAAQAA  157 (334)
T ss_dssp             HHHHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHTCSSCC-HHHHHHHHHHHHHHCT---TCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHh----CCCcHHHHHHhhHHHHHhcccc-HHHHHHHHHHHHhhCc---hhhhhhhhHHHHHHHhc
Confidence            34466777777776553    1111224455555555554422 3444444444433221   12234433 33555566


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHH
Q 042756          203 GQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWL  282 (425)
Q Consensus       203 g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~  282 (425)
                      +..++|+..+++.....- -+...|+.+-.++.+.|++++|...+....+.  .|+   ...+...+...+..+++...+
T Consensus       158 ~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~---~~~~~~~~~~l~~~~~a~~~~  231 (334)
T d1dcea1         158 VAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENV--LLK---ELELVQNAFFTDPNDQSAWFY  231 (334)
T ss_dssp             CCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHH---HHHHHHHHHHHCSSCSHHHHH
T ss_pred             cccHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHH---HHHHHHHHHHhcchhHHHHHH
Confidence            777777777776665421 24566777777777777776665544433221  111   112233344556666777777


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHHHHHHHHhhccCCchhhHHHHHhhcchhhHHHHHHHHhCCCCcccceeeccccchhc
Q 042756          283 QKMKDSGIPFSVRTYNSVLNSCSTIMSMLQDLNSNDFPLSILELTEVLNEEEVSVVKELEDSSVLDEAMKWDSGETKLDL  362 (425)
Q Consensus       283 ~~M~~~g~~pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~  362 (425)
                      ....... .++..++..+...+...++...+.                     ..+.+..+ ....+..+|..+...|..
T Consensus       232 ~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~---------------------~~~~~~~~-~~p~~~~~~~~l~~~~~~  288 (334)
T d1dcea1         232 HRWLLGR-AEPLFRCELSVEKSTVLQSELESC---------------------KELQELEP-ENKWCLLTIILLMRALDP  288 (334)
T ss_dssp             HHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHH---------------------HHHHHHCT-TCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHhC-cchhhHHHHHHHHHHHHhhHHHHH---------------------HHHHHHHh-hCchHHHHHHHHHHHHHH
Confidence            7665542 233344444445555545543321                     11111111 111234556667777888


Q ss_pred             ccCcchhHHHHHHHHHHHHHh
Q 042756          363 HGMHLGSAYFIILQWMDEMRN  383 (425)
Q Consensus       363 ~~~~~~a~~~~~~~~~~~m~~  383 (425)
                      .|+.++|     ++.|++..+
T Consensus       289 ~~~~~eA-----~~~~~~ai~  304 (334)
T d1dcea1         289 LLYEKET-----LQYFSTLKA  304 (334)
T ss_dssp             GGGHHHH-----HHHHHHHHH
T ss_pred             CCCHHHH-----HHHHHHHHH
Confidence            8888888     888888876

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=0.00019  Score=53.82  Aligned_cols=103  Identities=9%  Similarity=0.006  Sum_probs=78.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHH
Q 042756          115 AEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALK  193 (425)
Q Consensus       115 ~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~  193 (425)
                      ..+++.+...+++++|++.|+...+.... .   ..++..+-.++.+.++.+...++...+.+.....  ..|+ ..+|.
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~-~---~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~--~~~~~~~~~~   76 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSV-S---KSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG--SKEEQRDYVF   76 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCC-C---HHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS--CHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCC-C---HHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcc--CCchHHHHHH
Confidence            45888899999999999999998875222 2   2356677888888888777788998888876544  2233 24778


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCCCHH
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKGLEPSGF  225 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  225 (425)
                      .+-.+|.+.|++++|.+.|++..+  +.|+..
T Consensus        77 ~Lg~~y~~~g~~~~A~~~~~~aL~--~~P~~~  106 (122)
T d1nzna_          77 YLAVGNYRLKEYEKALKYVRGLLQ--TEPQNN  106 (122)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH--HCTTCH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHH--hCcCCH
Confidence            888999999999999999999988  457543

>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=97.58  E-value=0.003  Score=51.06  Aligned_cols=121  Identities=8%  Similarity=-0.006  Sum_probs=73.6

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .++.|++.|.++     ..+++.+|..+-..|.+.|++++|.+.|++..+.    .|.....|..+-.+|.+.|+++.+.
T Consensus        20 d~~~Al~~~~~i-----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~l----dp~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          20 DWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR----DKHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             CHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHH----hhhhhhhHHHHHHHHHhhccHHHHH
Confidence            455566666543     2356777778888888888888888888887764    2223446777888888888855444


Q ss_pred             HHHHHHHHHhhcCCC---------CccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcC
Q 042756          170 DTYARLNQLVNSSSS---------VYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVKG  219 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~---------~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  219 (425)
                      +.++......+....         ..++ ..++..+-.++.+.|++++|.+.|.......
T Consensus        91 ~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          91 KDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            444433322211110         0011 1345556666777777777777777666543

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.36  E-value=0.00051  Score=55.79  Aligned_cols=98  Identities=13%  Similarity=-0.008  Sum_probs=76.1

Q ss_pred             cCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC
Q 042756          109 WNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK  188 (425)
Q Consensus       109 ~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~  188 (425)
                      |++..+-..-..|.+.|++++|.+.|++..+..    |.....|..+-.+|.+.|+   .++|...+.+...-    .|+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~----p~~~~~~~~lg~~y~~~~~---~~~Ai~~~~~al~l----~p~   70 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN----PLVAVYYTNRALCYLKMQQ---PEQALADCRRALEL----DGQ   70 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----SCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHTTS----CTT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHhHHHHHhhhhh---hhhhhHHHHHHHHh----CCC
Confidence            566666777788999999999999999987752    2234578889999999999   55666666665432    232


Q ss_pred             -hhHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756          189 -RQALKSMISGLCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       189 -~~~~~~li~~~~~~g~~~~a~~~~~~m~~  217 (425)
                       ..+|..+-.+|.+.|++++|+..|++..+
T Consensus        71 ~~~a~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          71 SVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             45899999999999999999999998765

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.0015  Score=50.97  Aligned_cols=88  Identities=11%  Similarity=0.001  Sum_probs=42.6

Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHH
Q 042756          120 FLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGL  199 (425)
Q Consensus       120 ~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~  199 (425)
                      .|.+.|++++|...|++..+.    .|.....|..+-..|...|+++.+.+.++...+..+.      +..+|..+..+|
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~----~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~------~~~a~~~~g~~~   88 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIEL----NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK------YIKGYYRRAASN   88 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHhhhcccc----chhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc------chHHHHHHHHHH
Confidence            345666666666666665543    1122234555555555555533333333333222111      123555555555


Q ss_pred             HhcCChhHHHHHHHHHHH
Q 042756          200 CEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       200 ~~~g~~~~a~~~~~~m~~  217 (425)
                      ...|++++|...|++...
T Consensus        89 ~~~g~~~eA~~~~~~a~~  106 (159)
T d1a17a_          89 MALGKFRAALRDYETVVK  106 (159)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            555555555555555555

>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=97.36  E-value=0.0018  Score=51.74  Aligned_cols=71  Identities=10%  Similarity=-0.014  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHHHH-----hCCCCCCHHH
Q 042756          225 FEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQKMK-----DSGIPFSVRT  296 (425)
Q Consensus       225 ~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~-----~~g~~pd~~t  296 (425)
                      ..+..+..++.+.|++++|...++...+.. .-+...|..++.+|.+.|+..+|++.|++..     +.|+.|...|
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            466778899999999999999999998754 2478999999999999999999999999974     4699998765

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.35  E-value=0.00096  Score=49.24  Aligned_cols=89  Identities=13%  Similarity=0.057  Sum_probs=46.7

Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHH
Q 042756          119 AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISG  198 (425)
Q Consensus       119 ~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~  198 (425)
                      ..+.+.|++++|..+|++..+.    .|.....|..+-.+|.+.|+++.+.+.+....+.   .+   .+...|..+..+
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~----~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~---~p---~~~~~~~~~g~~   80 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKL----DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL---KP---DWGKGYSRKAAA   80 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CT---TCHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc----CCcchhhhhcccccccccccccccchhhhhHHHh---cc---chhhHHHHHHHH
Confidence            3455666777777777666554    1222334555666666666633333333332222   11   123356666666


Q ss_pred             HHhcCChhHHHHHHHHHHH
Q 042756          199 LCEMGQPHEAENLIEEMRV  217 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~  217 (425)
                      +...|++++|+..|++..+
T Consensus        81 ~~~~~~~~~A~~~~~~a~~   99 (117)
T d1elwa_          81 LEFLNRFEEAKRTYEEGLK   99 (117)
T ss_dssp             HHHTTCHHHHHHHHHHHHT
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            6666666666666666654

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.34  E-value=0.00084  Score=49.16  Aligned_cols=90  Identities=11%  Similarity=-0.021  Sum_probs=74.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhc
Q 042756          194 SMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDH  272 (425)
Q Consensus       194 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~  272 (425)
                      .+-..+.+.|++++|...|++....  .| +...|..+-.++.+.|++++|...|+...+.. +-+...|..+...|...
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~   97 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNE   97 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHC
Confidence            4556778899999999999998875  45 47788999999999999999999999887753 23588889999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 042756          273 NELSRMVLWLQKMK  286 (425)
Q Consensus       273 g~~~~A~~l~~~M~  286 (425)
                      |+.++|.+.|++..
T Consensus        98 g~~~~A~~~l~~~l  111 (112)
T d1hxia_          98 HNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999998753

>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=97.14  E-value=0.0061  Score=48.02  Aligned_cols=104  Identities=8%  Similarity=-0.165  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC-----CCC---------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKG-----LEP---------SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g-----~~p---------~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      .+...-..+.+.|++++|+..|.+....-     ...         -..+|+.+-.+|.+.|++++|...++...+.. +
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p   93 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-S   93 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-c
Confidence            44444556677777777777777665431     110         12467778888999999999999999888764 2


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTY  297 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~  297 (425)
                      -+..+|..+..+|...|++++|...|++..+.  .|+....
T Consensus        94 ~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~  132 (170)
T d1p5qa1          94 NNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAA  132 (170)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHH
T ss_pred             cchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHH
Confidence            37889999999999999999999999998764  5654433

>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=97.12  E-value=0.01  Score=45.66  Aligned_cols=108  Identities=7%  Similarity=-0.206  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcC----CCC-----------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKG----LEP-----------SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGT  255 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p-----------~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~  255 (425)
                      .+..--..+.+.|++++|+..|.+....-    -.+           ...+|+.+..+|.+.|++++|.+.++...+.. 
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-   97 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-   97 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-
Confidence            34444455667777777777777766421    011           13477788889999999999999999988764 


Q ss_pred             CcCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 042756          256 RVDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVL  301 (425)
Q Consensus       256 ~~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll  301 (425)
                      +.+..+|..+..+|...|++++|...|++..+.  .|+.......+
T Consensus        98 p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~~~~~l  141 (153)
T d2fbna1          98 KNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSY  141 (153)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHH
T ss_pred             chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            337899999999999999999999999998764  46554443333

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.10  E-value=0.00084  Score=49.16  Aligned_cols=90  Identities=9%  Similarity=-0.135  Sum_probs=68.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHH
Q 042756          117 IIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMI  196 (425)
Q Consensus       117 ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li  196 (425)
                      +-..+.+.|++++|...|++..+..    |.....|..+-.++.+.|+++++...++...+..+.      +..+|..+.
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~----p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~------~~~a~~~la   91 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE----PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK------DIAVHAALA   91 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc----cccchhhhhhhhhhhhhhhHHHhhcccccccccccc------cccchHHHH
Confidence            4556788999999999999988752    223457888999999999965555555554444222      345999999


Q ss_pred             HHHHhcCChhHHHHHHHHHH
Q 042756          197 SGLCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       197 ~~~~~~g~~~~a~~~~~~m~  216 (425)
                      ..|.+.|++++|++.|++..
T Consensus        92 ~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          92 VSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHh
Confidence            99999999999999998753

>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=97.03  E-value=0.0066  Score=45.24  Aligned_cols=97  Identities=8%  Similarity=-0.033  Sum_probs=77.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC---C--CcC-HHhHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG---T--RVD-TVCSNM  264 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g---~--~~~-~~~yn~  264 (425)
                      -+..+-..|.+.|++++|++.|.+..+.+ +.+...|..+-.+|.+.|++++|.+.++...+..   .  .+. ..+|..
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            45566778999999999999999999863 3357899999999999999999999999877531   0  011 356777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC
Q 042756          265 VLSSYGDHNELSRMVLWLQKMKDS  288 (425)
Q Consensus       265 li~~~~~~g~~~~A~~l~~~M~~~  288 (425)
                      +-..+...+++++|++.|.+-...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            888888899999999999887654

>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=96.93  E-value=0.0078  Score=47.89  Aligned_cols=129  Identities=9%  Similarity=-0.010  Sum_probs=89.5

Q ss_pred             CHHHHHHHH---HHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          110 NPKLVAEII---AFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       110 ~~~~~~~ll---~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      |...|..+.   ......|++++|.+.|.+...-...+...          .+ ..+.+  +......+....       
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~----------~~-~~~~w--~~~~r~~l~~~~-------   66 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLD----------DL-RDFQF--VEPFATALVEDK-------   66 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTG----------GG-TTSTT--HHHHHHHHHHHH-------
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccc----------cC-cchHH--HHHHHHHHHHHH-------
Confidence            344444444   46677899999999998877542221111          00 01111  222222332221       


Q ss_pred             cChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCcCHHh
Q 042756          187 VKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMES-----DGTRVDTVC  261 (425)
Q Consensus       187 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~~  261 (425)
                        ...+..+..++.+.|++++|+..+++..... +-+...|..++.+|.+.|+..+|.+.|+.+.+     .|+.|+..+
T Consensus        67 --~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          67 --VLAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             --HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             --HHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence              1278889999999999999999999998852 33788999999999999999999999998743     699998765

>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=96.87  E-value=0.014  Score=43.37  Aligned_cols=99  Identities=7%  Similarity=-0.012  Sum_probs=66.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHH
Q 042756          116 EIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKS  194 (425)
Q Consensus       116 ~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~  194 (425)
                      .+-..|.+.|++++|.+.|++..+..    |.....|..+-.+|.+.|+++.+.+.+....+..+......+. ..+|..
T Consensus         9 ~~G~~~~~~~~y~~Ai~~y~~al~~~----p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           9 ELGNDAYKKKDFDTALKHYDKAKELD----PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC----cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            35566888899999999998887752    2223467888888888888666666555555554443222222 236667


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHc
Q 042756          195 MISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       195 li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      +-..+...+++++|++.|.+-...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            777777788888888888776653

>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=96.82  E-value=0.022  Score=44.46  Aligned_cols=108  Identities=10%  Similarity=-0.074  Sum_probs=79.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc--------------CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVK--------------GLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~--------------g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      +......+.+.|++++|++.|.+..+.              .+.| +...|..+-.++.+.|++++|...++...+.. +
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p  108 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-P  108 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-h
Confidence            344455566778888888877766421              1223 34467778889999999999999999998764 2


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSV-RTYNSVLN  302 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~-~t~~~ll~  302 (425)
                      -+...|..+-.+|.+.|++++|++.|++..+.  .|+. .....+..
T Consensus       109 ~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~  153 (169)
T d1ihga1         109 SNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLK  153 (169)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            36889999999999999999999999998874  4543 34444433

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.54  E-value=0.058  Score=42.03  Aligned_cols=124  Identities=8%  Similarity=-0.120  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      .+...-..+.+.|++++|.+.|.+..+.......                 ..+........+.            ..+|
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~-----------------~~~~~~~~~~~~~------------~~~~   65 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESS-----------------FSNEEAQKAQALR------------LASH   65 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCC-----------------CCSHHHHHHHHHH------------HHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccc-----------------cchHHHhhhchhH------------HHHH
Confidence            3444555778888888888888887653221110                 0000111111111            1278


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCc-CHHhHHHHHHHH
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEP-SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRV-DTVCSNMVLSSY  269 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~-~~~~yn~li~~~  269 (425)
                      +.+-.+|.+.|++++|+..+++....  .| +..+|..+-.+|...|++++|...|+...+..  | |......+-...
T Consensus        66 ~nla~~y~k~~~~~~A~~~~~~al~~--~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~--P~n~~~~~~l~~~~  140 (170)
T d1p5qa1          66 LNLAMCHLKLQAFSAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY--PNNKAAKTQLAVCQ  140 (170)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhhcccccchhhhhhhc--cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC--CCCHHHHHHHHHHH
Confidence            88999999999999999999999985  45 67899999999999999999999999998753  4 444444443433

>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=96.47  E-value=0.034  Score=42.71  Aligned_cols=96  Identities=9%  Similarity=-0.021  Sum_probs=70.2

Q ss_pred             HHHHH--HHHHHhcCChhHHHHHHHHHHHcC-CCC----------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----
Q 042756          191 ALKSM--ISGLCEMGQPHEAENLIEEMRVKG-LEP----------SGFEYKCIIYGYGRLGLLEDMERIVNQMESD----  253 (425)
Q Consensus       191 ~~~~l--i~~~~~~g~~~~a~~~~~~m~~~g-~~p----------~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~----  253 (425)
                      +|+.+  ...+.+.|++++|+..|++..+.. -.|          ....|+.+-.+|.+.|++++|.+-++...+.    
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            55655  445556788999999888887631 112          1457888889999999999998888876542    


Q ss_pred             -CCCcC-----HHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 042756          254 -GTRVD-----TVCSNMVLSSYGDHNELSRMVLWLQKMK  286 (425)
Q Consensus       254 -g~~~~-----~~~yn~li~~~~~~g~~~~A~~l~~~M~  286 (425)
                       ...++     ...|+.+-.+|...|++++|+..|++..
T Consensus        89 ~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          89 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence             11121     3357778899999999999999999875

>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=96.27  E-value=0.032  Score=43.46  Aligned_cols=108  Identities=7%  Similarity=-0.137  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHc---CCCC-----------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVK---GLEP-----------SGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTR  256 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p-----------~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~  256 (425)
                      .+.-.-..+.+.|++++|.+.|.+....   ...+           ....|+.+-.+|.+.|++++|...++...+.. +
T Consensus        17 ~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p   95 (168)
T d1kt1a1          17 IVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-S   95 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-c
Confidence            3444445566677777777777665431   0000           12356667778899999999999999888753 3


Q ss_pred             cCHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH
Q 042756          257 VDTVCSNMVLSSYGDHNELSRMVLWLQKMKDSGIPFSVRTYNSVL  301 (425)
Q Consensus       257 ~~~~~yn~li~~~~~~g~~~~A~~l~~~M~~~g~~pd~~t~~~ll  301 (425)
                      .+..+|..+..+|...|++++|...|.+..+.  .|+.......+
T Consensus        96 ~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l  138 (168)
T d1kt1a1          96 ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQI  138 (168)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            47888888999999999999999999998864  56654443333

>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=96.20  E-value=0.051  Score=41.63  Aligned_cols=105  Identities=11%  Similarity=-0.014  Sum_probs=53.5

Q ss_pred             HHHHHH--HHHHHhcCChhHHHHHHHHHHHhcCCCc--------hhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhc
Q 042756          112 KLVAEI--IAFLDKQGQREEAETLILETLSKLGSRE--------RELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNS  181 (425)
Q Consensus       112 ~~~~~l--l~~~~~~g~~~~A~~l~~~m~~~~~~~~--------~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~  181 (425)
                      .+|..+  ...+.+.|++++|++.|++..+.....+        +.....|+.+-.+|.+.|+++.+.+.++...++.+.
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            345555  4455677999999999998776322111        011234556666666666644443333333332221


Q ss_pred             CCCCccC-----hhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 042756          182 SSSVYVK-----RQALKSMISGLCEMGQPHEAENLIEEMR  216 (425)
Q Consensus       182 ~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~  216 (425)
                      .....++     ...|+.+-.+|.+.|++++|+..|++..
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            1111111     1234445555556666666666655544

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.18  E-value=0.33  Score=42.19  Aligned_cols=223  Identities=13%  Similarity=0.097  Sum_probs=123.5

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHH--------
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYM--------   99 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~--------   99 (425)
                      -.|...|..+.|..++..+..        |..++..+.+.+++..|.+++.+.-.     +..+........        
T Consensus        22 ~~c~~~~lye~A~~lY~~~~d--------~~rl~~~~v~l~~~~~avd~~~k~~~-----~~~~k~~~~~l~~~~e~~la   88 (336)
T d1b89a_          22 DRCYDEKMYDAAKLLYNNVSN--------FGRLASTLVHLGEYQAAVDGARKANS-----TRTWKEVCFACVDGKEFRLA   88 (336)
T ss_dssp             -------CTTTHHHHHHHTTC--------HHHHHHHHHTTTCHHHHHHHHHHHTC-----HHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHCCCHHHHHHHHHhCCC--------HHHHHHHHHhhccHHHHHHHHHHcCC-----HHHHHHHHHHHHhCcHHHHH
Confidence            344456677777777777654        56677777777777777666655411     111111111111        


Q ss_pred             HhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 042756          100 RITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLV  179 (425)
Q Consensus       100 ~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~  179 (425)
                      .+.... ....+.....++..|-..|.+++...+++..... ....   ...++-++..|++.+.    ....+.+....
T Consensus        89 ~i~~~~-~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~---~~~~~~L~~lyak~~~----~kl~e~l~~~s  159 (336)
T d1b89a_          89 QMCGLH-IVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAH---MGMFTELAILYSKFKP----QKMREHLELFW  159 (336)
T ss_dssp             HHTTTT-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCC---HHHHHHHHHHHHTTCH----HHHHHHHHHHS
T ss_pred             HHHHHH-hhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-Cccc---hHHHHHHHHHHHHhCh----HHHHHHHHhcc
Confidence            111111 2235556677899999999999988888876432 1112   2367889999998753    44444444432


Q ss_pred             hcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHc--------CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 042756          180 NSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVK--------GLEPSGFEYKCIIYGYGRLGLLEDMERIVNQME  251 (425)
Q Consensus       180 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--------g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~  251 (425)
                      ..   .     ...-+++.|-+.+.++++.-++.++.+.        .-.|+..-....+..+.+.++.+...++.....
T Consensus       160 ~~---y-----~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL  231 (336)
T d1b89a_         160 SR---V-----NIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL  231 (336)
T ss_dssp             TT---S-----CHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH
T ss_pred             cc---C-----CHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHH
Confidence            11   1     2233444444445444444444443221        023344455666777888888888777777666


Q ss_pred             HCCCCcCHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 042756          252 SDGTRVDTVCSNMVLSSYGDHNELSRMVLWLQK  284 (425)
Q Consensus       252 ~~g~~~~~~~yn~li~~~~~~g~~~~A~~l~~~  284 (425)
                      +.  .|  ..-+.|+......-++.++++.+++
T Consensus       232 ~~--~p--~~i~~lL~~v~~~~d~~r~V~~~~k  260 (336)
T d1b89a_         232 EF--KP--LLLNDLLMVLSPRLDHTRAVNYFSK  260 (336)
T ss_dssp             HH--CG--GGHHHHHHHHGGGCCHHHHHHHHHH
T ss_pred             Hc--CH--HHHHHHHHHhccCCCHHHHHHHHHh
Confidence            53  24  3457777777777777766666543

>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=96.11  E-value=0.17  Score=38.99  Aligned_cols=93  Identities=6%  Similarity=-0.095  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYG  270 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~  270 (425)
                      .|+.+-.+|.+.|++++|+..+++..... +.+..+|..+..++...|++++|.+.|+...+.. +.+......+-....
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~~  143 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQIFMCQK  143 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            77788889999999999999999998852 3467799999999999999999999999998753 124445555444444


Q ss_pred             hcCCHH-HHHHHHHHH
Q 042756          271 DHNELS-RMVLWLQKM  285 (425)
Q Consensus       271 ~~g~~~-~A~~l~~~M  285 (425)
                      ..+... ...++|..|
T Consensus       144 ~~~~~~e~~kk~~~~~  159 (168)
T d1kt1a1         144 KAKEHNERDRRTYANM  159 (168)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHH
Confidence            444332 344555554

>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=95.85  E-value=0.0035  Score=53.46  Aligned_cols=39  Identities=18%  Similarity=0.342  Sum_probs=18.0

Q ss_pred             cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcc
Q 042756          124 QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKR  166 (425)
Q Consensus       124 ~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~  166 (425)
                      .|++++|.+.|++..+.    .|.....+..+...|+..|+++
T Consensus         9 ~G~l~eAl~~l~~al~~----~P~d~~ar~~La~lL~~~G~~e   47 (264)
T d1zbpa1           9 EGQLQQALELLIEAIKA----SPKDASLRSSFIELLCIDGDFE   47 (264)
T ss_dssp             TTCHHHHHHHHHHHHHT----CTTCHHHHHHHHHHHHHHTCHH
T ss_pred             CCCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHCCCHH
Confidence            35555555555554443    1222223445555555555533

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=95.80  E-value=0.13  Score=38.98  Aligned_cols=113  Identities=11%  Similarity=-0.050  Sum_probs=79.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHH
Q 042756          113 LVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQAL  192 (425)
Q Consensus       113 ~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~  192 (425)
                      .+..--..+.+.|++++|...|.+.........                  .... .........         ....+|
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~------------------~~~~-~~~~~~~~~---------~~~~~~   70 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTE------------------EWDD-QILLDKKKN---------IEISCN   70 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCT------------------TCCC-HHHHHHHHH---------HHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchh------------------hhhh-HHHHHhhhh---------HHHHHH
Confidence            444555677788888888888887664321111                  1000 000011111         011388


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 042756          193 KSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDG  254 (425)
Q Consensus       193 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g  254 (425)
                      +.+..+|.+.|++++|++.+.+..+.. +-+..+|-.+..++...|++++|...|+...+..
T Consensus        71 ~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1          71 LNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            889999999999999999999998853 3367899999999999999999999999988763

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.49  E-value=0.053  Score=42.09  Aligned_cols=108  Identities=11%  Similarity=-0.041  Sum_probs=63.9

Q ss_pred             HHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 042756           60 LISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLS  139 (425)
Q Consensus        60 ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~  139 (425)
                      .-..+.+.|++..|...+.+++.-       .+..............-+.+...|..+-.++.+.|++++|+..+++..+
T Consensus        33 ~~~~~~~~~~y~~Ai~~y~~al~~-------~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~  105 (169)
T d1ihga1          33 IGNTFFKSQNWEMAIKKYTKVLRY-------VEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALE  105 (169)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH-------HHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh-------hhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhh
Confidence            444556677777777766665321       0111111000000010112455677788889999999999999999876


Q ss_pred             hcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 042756          140 KLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQL  178 (425)
Q Consensus       140 ~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~  178 (425)
                      .    .|.....|..+-.+|.+.|+++.+.+.++...++
T Consensus       106 ~----~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1         106 I----DPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             T----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             h----hhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            4    2333456788888999999965555555555444

>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=95.15  E-value=0.053  Score=45.78  Aligned_cols=117  Identities=11%  Similarity=-0.007  Sum_probs=70.7

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .+++|+..|++..+.+  +-|...+..+...++..|++++|.+.|+...+.    .|.....+..+...+...+.   -.
T Consensus        11 ~l~eAl~~l~~al~~~--P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l----~P~~~~~~~~l~~ll~a~~~---~~   81 (264)
T d1zbpa1          11 QLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKL----FPEYLPGASQLRHLVKAAQA---RK   81 (264)
T ss_dssp             CHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH----CGGGHHHHHHHHHHHHHHHH---HH
T ss_pred             CHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh----CCCcHHHHHHHHHHHHhccc---cH
Confidence            6777888888776654  248889999999999999999999999998775    23323344444444332222   11


Q ss_pred             HHHHHHHHHhhcCCCCcc-ChhHHHHHHHHHHhcCChhHHHHHHHHHHHc
Q 042756          170 DTYARLNQLVNSSSSVYV-KRQALKSMISGLCEMGQPHEAENLIEEMRVK  218 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  218 (425)
                      +++.....   ......| +...+......+.+.|+.++|.+.+++..+.
T Consensus        82 ~a~~~~~~---~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          82 DFAQGAAT---AKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHTTSCCC---EECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhhh---hhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            11111000   0000112 2234444456677778888888888887664

>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=94.99  E-value=0.065  Score=40.52  Aligned_cols=40  Identities=8%  Similarity=-0.167  Sum_probs=24.9

Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCC
Q 042756          121 LDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDS  164 (425)
Q Consensus       121 ~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~  164 (425)
                      |-+.+.+++|.+.|+...+.    .|.....+..+-.+|...++
T Consensus         7 ~~r~~~fe~A~~~~e~al~~----~P~~~~~~~~~g~~l~~~~~   46 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKS----NPLDADNLTRWGGVLLELSQ   46 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----CTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhh----CCcchHHHHHHHHHHHHhhh
Confidence            44566788999999888765    22223355556666655444

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=94.53  E-value=0.99  Score=37.00  Aligned_cols=221  Identities=6%  Similarity=-0.089  Sum_probs=129.0

Q ss_pred             HHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCCCCCCCchhhhHHHHHHHhhhcCCCccCH
Q 042756           32 TARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSPDTTHPRLSSLAFPLYMRITEESWFQWNP  111 (425)
Q Consensus        32 ~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~a~~lf~~m~~~~~~~~~~  111 (425)
                      .+++..+|.+.|+...+.  -|..++-.|-..|..                 +...+.....|...+..-...+    ++
T Consensus        14 ~~~d~~~A~~~~~kAa~~--g~~~A~~~Lg~~y~~-----------------G~~~~~d~~~a~~~~~~a~~~~----~~   70 (265)
T d1ouva_          14 KEKDFTQAKKYFEKACDL--KENSGCFNLGVLYYQ-----------------GQGVEKNLKKAASFYAKACDLN----YS   70 (265)
T ss_dssp             HTTCHHHHHHHHHHHHHT--TCHHHHHHHHHHHHH-----------------TSSSCCCHHHHHHHHHHHHHTT----CH
T ss_pred             HCCCHHHHHHHHHHHHHC--CCHHHHHHHHHHHHc-----------------CCCcchhHHHHHHhhccccccc----cc
Confidence            455777888888776543  233333333333322                 1222335566666666655554    33


Q ss_pred             HHHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-cCCcccHHHHHHHHHHHhhcCCCCc
Q 042756          112 KLVAEIIAFLDK----QGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK-HDSKRGFDDTYARLNQLVNSSSSVY  186 (425)
Q Consensus       112 ~~~~~ll~~~~~----~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~-~g~~~~~~~~~~~~~~~~~~~~~~~  186 (425)
                      .....+...+..    ..+.+.|...++...+.+.   ..   ....+...+.. .........+...+.......    
T Consensus        71 ~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~---~~---a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~----  140 (265)
T d1ouva_          71 NGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKY---AE---GCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN----  140 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HH---HHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT----
T ss_pred             chhhccccccccccccchhhHHHHHHHhhhhhhhh---hh---HHHhhcccccCCCcccchhHHHHHHhhhhhccc----
Confidence            333334344433    4567888888887665422   11   12223223322 222223555556665554332    


Q ss_pred             cChhHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCcC
Q 042756          187 VKRQALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDMERIVNQMESDGTRVD  258 (425)
Q Consensus       187 p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a~~~~~~m~~~g~~~~  258 (425)
                       +...+..+...|..    ..+...+...++...+.|   +......+-..|..    ..+.+.|...|....+.|   +
T Consensus       141 -~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~  213 (265)
T d1ouva_         141 -DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---N  213 (265)
T ss_dssp             -CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---C
T ss_pred             -ccchhhhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---C
Confidence             33477888888876    456678888888877765   44444444444443    568999999999998887   4


Q ss_pred             HHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCC
Q 042756          259 TVCSNMVLSSYGD----HNELSRMVLWLQKMKDSGIPF  292 (425)
Q Consensus       259 ~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g~~p  292 (425)
                      ...+..|-..|.+    ..+.++|.+.|++..+.|-.+
T Consensus       214 ~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         214 GGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcCHH
Confidence            5566666666654    337889999999998877443

>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=94.27  E-value=0.1  Score=39.32  Aligned_cols=104  Identities=7%  Similarity=-0.084  Sum_probs=65.2

Q ss_pred             HHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC----------CCHHHHHHHHHHHHHCCCCcCHHhHHHHHHH
Q 042756          199 LCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRL----------GLLEDMERIVNQMESDGTRVDTVCSNMVLSS  268 (425)
Q Consensus       199 ~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~----------g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~  268 (425)
                      |-+.+.+++|...|+...+.. +-+..++..+-.+|...          +.+++|.+.|+...+.. +-+..+|+.+-.+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHH
Confidence            344556777777777776642 22455666555555433          34567777777776643 2256777777777


Q ss_pred             HHhcCC-----------HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Q 042756          269 YGDHNE-----------LSRMVLWLQKMKDSGIPFSVRTYNSVLNSCST  306 (425)
Q Consensus       269 ~~~~g~-----------~~~A~~l~~~M~~~g~~pd~~t~~~ll~~~~~  306 (425)
                      |...|+           +++|.+.|++..+.  .|+..+|..-+..+.+
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~~~k  131 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMTAK  131 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHT
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHHHHH
Confidence            765543           57777788777653  6877777766665544

>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=93.91  E-value=1.7  Score=37.38  Aligned_cols=158  Identities=11%  Similarity=0.087  Sum_probs=97.5

Q ss_pred             hhhhHHHHHHHhhhcCCCccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHH
Q 042756           90 LSSLAFPLYMRITEESWFQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFD  169 (425)
Q Consensus        90 ~~~~a~~lf~~m~~~~~~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~  169 (425)
                      .++.|..+|..+..          |..++..+.+.++++.|.+++....      .+.   +|..+..++.+.....   
T Consensus        29 lye~A~~lY~~~~d----------~~rl~~~~v~l~~~~~avd~~~k~~------~~~---~~k~~~~~l~~~~e~~---   86 (336)
T d1b89a_          29 MYDAAKLLYNNVSN----------FGRLASTLVHLGEYQAAVDGARKAN------STR---TWKEVCFACVDGKEFR---   86 (336)
T ss_dssp             CTTTHHHHHHHTTC----------HHHHHHHHHTTTCHHHHHHHHHHHT------CHH---HHHHHHHHHHHTTCHH---
T ss_pred             CHHHHHHHHHhCCC----------HHHHHHHHHhhccHHHHHHHHHHcC------CHH---HHHHHHHHHHhCcHHH---
Confidence            55666666665432          2237788888999999888776542      222   6777788887766521   


Q ss_pred             HHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 042756          170 DTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQ  249 (425)
Q Consensus       170 ~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~  249 (425)
                       .    .+.....  ...+......++..|-..|.+++...+++..... -.++...++-++..|++.+.    .++.+.
T Consensus        87 -l----a~i~~~~--~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~----~kl~e~  154 (336)
T d1b89a_          87 -L----AQMCGLH--IVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP----QKMREH  154 (336)
T ss_dssp             -H----HHHTTTT--TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH----HHHHHH
T ss_pred             -H----HHHHHHH--hhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh----HHHHHH
Confidence             1    1221111  2223335568999999999999999999987543 35677889999999998753    334444


Q ss_pred             HHHC--CCCc--------CHHhHHHHHHHHHhcCCHHHHHHH
Q 042756          250 MESD--GTRV--------DTVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       250 m~~~--g~~~--------~~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      +...  .+.+        ....|.-++-.|.+.|++++|..+
T Consensus       155 l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~  196 (336)
T d1b89a_         155 LELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT  196 (336)
T ss_dssp             HHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHH
Confidence            4331  1111        123355566666666666666544

>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=93.85  E-value=0.15  Score=47.24  Aligned_cols=77  Identities=13%  Similarity=-0.075  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHH
Q 042756          191 ALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSY  269 (425)
Q Consensus       191 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~  269 (425)
                      ++..+-..+...|++++|...|++..+.  .|+ ...|+.+-..+...|+..+|...|.+-.... .|...+++.|...|
T Consensus       154 ~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         154 CLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKAL  230 (497)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH
Confidence            4444555555555555555555555542  332 3455555555555555555555555544432 23455555555444


Q ss_pred             H
Q 042756          270 G  270 (425)
Q Consensus       270 ~  270 (425)
                      .
T Consensus       231 ~  231 (497)
T d1ya0a1         231 S  231 (497)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=93.78  E-value=0.4  Score=32.74  Aligned_cols=62  Identities=8%  Similarity=-0.104  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 042756          192 LKSMISGLCEMGQPHEAENLIEEMRVK-----GLEPS-GFEYKCIIYGYGRLGLLEDMERIVNQMESD  253 (425)
Q Consensus       192 ~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~-~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~  253 (425)
                      +--+-..+.+.|++++|...|++..+.     ...++ ..++..+-.+|.+.|++++|.+.+++..+.
T Consensus         8 c~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           8 SFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            334555566666666666666655432     11122 234555555555555555555555555443

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.32  E-value=0.96  Score=32.60  Aligned_cols=139  Identities=12%  Similarity=0.017  Sum_probs=76.0

Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHh
Q 042756          122 DKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKRQALKSMISGLCE  201 (425)
Q Consensus       122 ~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~  201 (425)
                      .-.|.+++..+++.+......      ..-||=+|.-....-+   .+..+..+.....-.. +.|- .-.-.++.+|.+
T Consensus        13 ildG~ve~Gveii~k~~~ss~------~~E~NW~ICNiidt~d---C~~v~~~Ld~IG~~FD-ls~C-~Nlk~vv~C~~~   81 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKSST------KSEYNWFICNLLESID---CRYMFQVLDKIGSYFD-LDKC-QNLKSVVECGVI   81 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSC------HHHHTHHHHHHHHHCC---HHHHHHHHHHHGGGSC-GGGC-SCTHHHHHHHHH
T ss_pred             HHhhhHHhHHHHHHHHcccCC------ccccceeeeecccccc---hHHHHHHHHHHhhhcC-chhh-hcHHHHHHHHHH
Confidence            445888999999998876421      1234556666666666   6667777766643321 2110 012233334433


Q ss_pred             cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCcCHHhHHHHHHHHHhcCCHHHHHHH
Q 042756          202 MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLGLLEDMERIVNQMESDGTRVDTVCSNMVLSSYGDHNELSRMVLW  281 (425)
Q Consensus       202 ~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~yn~li~~~~~~g~~~~A~~l  281 (425)
                      .+..                  ..-+...++...++|+-+.-.++.+++.+.+ +|++...-.+-.+|-+-|...++-++
T Consensus        82 ~n~~------------------se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nel  142 (161)
T d1wy6a1          82 NNTL------------------NEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTL  142 (161)
T ss_dssp             TTCC------------------CHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcch------------------HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHH
Confidence            3321                  2233444555566666666666666654432 34555555566666666666666666


Q ss_pred             HHHHHhCCC
Q 042756          282 LQKMKDSGI  290 (425)
Q Consensus       282 ~~~M~~~g~  290 (425)
                      +.+.-+.|+
T Consensus       143 l~~ACe~G~  151 (161)
T d1wy6a1         143 LIEACKKGE  151 (161)
T ss_dssp             HHHHHHTTC
T ss_pred             HHHHHHHhH
Confidence            666666654

>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=93.00  E-value=0.22  Score=34.17  Aligned_cols=75  Identities=8%  Similarity=-0.001  Sum_probs=47.0

Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccC-hhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCC-HHHHHHH
Q 042756          154 NLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVK-RQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPS-GFEYKCI  230 (425)
Q Consensus       154 ~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~ty~~l  230 (425)
                      .+-..+.+.|+++.+.+.++...+..+......++ ..+++.+-.+|.+.|++++|+..|++..+.  .|+ ..+++.+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~~~~a~~Nl   86 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEHQRANGNL   86 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcCCHHHHHHH
Confidence            34555566666444444444433333333222233 358889999999999999999999999884  464 4455444

>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=92.83  E-value=0.35  Score=44.56  Aligned_cols=116  Identities=11%  Similarity=-0.068  Sum_probs=65.3

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          110 NPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       110 ~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +...+..+-..+.+.|+.+.|...+......    .  ...++..+-+.+...|+++.+...+....+..+..      .
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~----~--~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~------~  186 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCSY----I--CQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSN------G  186 (497)
T ss_dssp             ------------------------CCHHHHH----H--HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTB------S
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC----C--HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCc------h
Confidence            4455666777778888888888877765432    1  12356678888888899665555555555543322      2


Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC
Q 042756          190 QALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGRLG  238 (425)
Q Consensus       190 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~~g  238 (425)
                      .+||.+-..+...|+..+|...|.+-.... .|-..++.+|...+.+..
T Consensus       187 ~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         187 QPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHhh
Confidence            499999999999999999999999998754 466788888887776543

>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=85.16  E-value=7.9  Score=31.01  Aligned_cols=162  Identities=10%  Similarity=-0.027  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHh-cCCcccHHHHHHHHHHHhhcCCCCccCh
Q 042756          111 PKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCK-HDSKRGFDDTYARLNQLVNSSSSVYVKR  189 (425)
Q Consensus       111 ~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~-~g~~~~~~~~~~~~~~~~~~~~~~~p~~  189 (425)
                      +..+..|-..+-+.|++++|.+.|++..+.+.   ..   .+-.|-..|.. .|.......+...+......+..     
T Consensus         2 p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~---~~---A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~-----   70 (265)
T d1ouva_           2 PKELVGLGAKSYKEKDFTQAKKYFEKACDLKE---NS---GCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYS-----   70 (265)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC---HH---HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH-----
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC---HH---HHHHHHHHHHcCCCcchhHHHHHHhhccccccccc-----
Confidence            44455565666677888889888888765432   11   22234444443 22233356666666665544321     


Q ss_pred             hHHHHHHHHHHh----cCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHH----cCCCHHHHHHHHHHHHHCCCCcCHHh
Q 042756          190 QALKSMISGLCE----MGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYG----RLGLLEDMERIVNQMESDGTRVDTVC  261 (425)
Q Consensus       190 ~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~----~~g~~~~a~~~~~~m~~~g~~~~~~~  261 (425)
                      ..+..+...+..    ..+.+.|...+++....|...   ....+...+.    .......+...+......   .+...
T Consensus        71 ~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~---a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~  144 (265)
T d1ouva_          71 NGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAE---GCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDGDG  144 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHH---HHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCHHH
T ss_pred             chhhccccccccccccchhhHHHHHHHhhhhhhhhhh---HHHhhcccccCCCcccchhHHHHHHhhhhhcc---cccch
Confidence            144444444443    457778888888877765322   2222222222    234566777777776664   35666


Q ss_pred             HHHHHHHHHh----cCCHHHHHHHHHHHHhCC
Q 042756          262 SNMVLSSYGD----HNELSRMVLWLQKMKDSG  289 (425)
Q Consensus       262 yn~li~~~~~----~g~~~~A~~l~~~M~~~g  289 (425)
                      +..|...|..    ..+...+..+++...+.|
T Consensus       145 ~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g  176 (265)
T d1ouva_         145 CTILGSLYDAGRGTPKDLKKALASYDKACDLK  176 (265)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhhhhhhhccCCCcccccccchhhhhcccccc
Confidence            7777777765    345666777777766655

>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=84.91  E-value=5.2  Score=28.66  Aligned_cols=140  Identities=12%  Similarity=0.083  Sum_probs=89.6

Q ss_pred             HHHHHHhhHHHHHHHHHHhHHhcCCCHHHHHHHHHHHHhcCChHHHHHHHHhhhCC-CCCCCchhhhHHHHHHHhhhcCC
Q 042756           28 VQCLTARLTKQGQRFLSSLALAVTRDSKAASRLISKFVASSPQFIALNALSHLLSP-DTTHPRLSSLAFPLYMRITEESW  106 (425)
Q Consensus        28 ~~~l~~~~~~~a~~~~~~m~~~~~~d~~~~~~ll~~~~~~~~~~~a~~~~~~~l~~-~~~~~~~~~~a~~lf~~m~~~~~  106 (425)
                      ...++.|.++++.+++.....+  .+..-||.+|--....-+-+..+.+++.+-+- +......+......|-.+..   
T Consensus        10 Kk~ildG~ve~Gveii~k~~~s--s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n~---   84 (161)
T d1wy6a1          10 KKFLLDGYIDEGVKIVLEITKS--STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNT---   84 (161)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTC---
T ss_pred             HHHHHhhhHHhHHHHHHHHccc--CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhcc---
Confidence            4678899999999999988875  77888999999988888888888887776211 11111234444444444322   


Q ss_pred             CccCHHHHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhcC
Q 042756          107 FQWNPKLVAEIIAFLDKQGQREEAETLILETLSKLGSRERELVLFYCNLIDSFCKHDSKRGFDDTYARLNQLVNSS  182 (425)
Q Consensus       107 ~~~~~~~~~~ll~~~~~~g~~~~A~~l~~~m~~~~~~~~~~~~~~y~~li~~~~~~g~~~~~~~~~~~~~~~~~~~  182 (425)
                         +..-++..+..+.++|.-+.-.+++.++.+.+. ++|+   ..-.+-.+|.+.|.   ..++-+++.+.-..|
T Consensus        85 ---~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~-i~~~---~llkia~A~kkig~---~re~nell~~ACe~G  150 (161)
T d1wy6a1          85 ---LNEHVNKALDILVIQGKRDKLEEIGREILKNNE-VSAS---ILVAIANALRRVGD---ERDATTLLIEACKKG  150 (161)
T ss_dssp             ---CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CC-SCHH---HHHHHHHHHHHTTC---HHHHHHHHHHHHHTT
T ss_pred             ---hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCC-CCHH---HHHHHHHHHHHhcc---hhhHHHHHHHHHHHh
Confidence               333455577777788887777777777655333 2333   23467777888887   555655555554443

>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=84.00  E-value=5.6  Score=28.35  Aligned_cols=110  Identities=8%  Similarity=-0.071  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHHhhcCCCCccChhHHHHHHHHHHhcCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHH
Q 042756          168 FDDTYARLNQLVNSSSSVYVKRQALKSMISGLCEMGQPHEAENLIEEMRVKGLEPSGFEYKCIIYGYGR----LGLLEDM  243 (425)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~g~~~~a  243 (425)
                      ..++...+.+....+...     .+..|.  .....+.++|+++|++..+.|   +......|-..|..    ..|.+.|
T Consensus         9 ~~~A~~~~~kaa~~g~~~-----a~~~l~--~~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A   78 (133)
T d1klxa_           9 LKKAIQYYVKACELNEMF-----GCLSLV--SNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   78 (133)
T ss_dssp             HHHHHHHHHHHHHTTCTT-----HHHHHH--TCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             HHHHHHHHHHHHHCCChh-----hhhhhc--cccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHH
Confidence            455666666655444321     333332  233467889999999988877   33444444444433    4578999


Q ss_pred             HHHHHHHHHCCCCcCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCC
Q 042756          244 ERIVNQMESDGTRVDTVCSNMVLSSYGD----HNELSRMVLWLQKMKDSGI  290 (425)
Q Consensus       244 ~~~~~~m~~~g~~~~~~~yn~li~~~~~----~g~~~~A~~l~~~M~~~g~  290 (425)
                      .++|+.-.+.|   +......|-..|..    ..+.++|.++|++..+.|.
T Consensus        79 ~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          79 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            99999998877   34445555555554    4578999999999888774