Citrus Sinensis ID: 040261

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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---
Protein Sequence
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT
Secondary Structure (PSIPRED)
ccHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHcHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEEcc
Coil and Loop (DISEMBL)
fcifdymlrmhpspppvcsfnilfgclaknkhYDTVLSLFKRLnsiglfpdlytYNILINCFckmgrvspgFVVLGRILrscftpdavTFTSLIKGLCAESRIMEAAALFTKLrafgckpdvftYTTLINGLCRTGHTIVALNLFEEmangngefgvvckpdaitystitdglckEGFVDKAKELFLKMkdeninpdvvtYTSLIRGFCYANDWNEAKCLFIEMmdqgvqpnvVTFNVIMNELCKNGKMDEASRLLELMIQIgvrpdasvyntlMDGFCLTGRVNRAKELFVSMesngcmrdvfSYGILINGYCKNKEIEGALSLYSEMLskgirptvvtynt
Flexible Loop (DISEMBL)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFlkmkdeninpdVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYsemlskgirptvvtynt
Low Complexity Region (SEG)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT
Disordered region (IsUnstruct)
*****************CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVV****
Disordered Region (DISOPRED)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYN*
Disordered Region (DISEMBL)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT
Disordered Region (DISPRO)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT
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	343	2.2.26 [Sep-21-2011]
P0C7Q7	602	Putative pentatricopeptid	no	no	0.970	0.553	0.382	1e-70
Q9LPX2	644	Pentatricopeptide repeat-	no	no	0.973	0.518	0.372	2e-69
Q9LQ14	629	Pentatricopeptide repeat-	no	no	0.973	0.531	0.361	2e-67
Q9CAN5	614	Pentatricopeptide repeat-	no	no	0.973	0.543	0.351	6e-67
Q0WKV3	637	Pentatricopeptide repeat-	no	no	0.962	0.518	0.372	6e-67
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.973	0.539	0.359	1e-66
Q9CAM8	629	Pentatricopeptide repeat-	no	no	0.973	0.531	0.356	3e-66
Q9ASZ8	621	Pentatricopeptide repeat-	no	no	0.991	0.547	0.364	4e-66
Q9LQ16	632	Pentatricopeptide repeat-	no	no	0.973	0.528	0.356	4e-66
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.973	0.526	0.359	5e-66

>sp|P0C7Q7|PPR38_ARATH Putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial OS=Arabidopsis thaliana GN=At1g12700 PE=3 SV=1

 Score =  266 bits (681), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/340 (38%), Positives = 202/340 (59%), Gaps = 7/340 (2%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M+R  P P  V  F+  F  +A+ K ++ VL   K+L   G+  ++YT NI+INCF
Sbjct: 75  LFQEMIRSRPLPSLV-DFSRFFSAIARTKQFNLVLDFCKQLELNGIAHNIYTLNIMINCF 133

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  +    + VLG++++  + PD  TF +LIKGL  E ++ EA  L  ++   GC+PDV
Sbjct: 134 CRCCKTCFAYSVLGKVMKLGYEPDTTTFNTLIKGLFLEGKVSEAVVLVDRMVENGCQPDV 193

Query: 123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
            TY +++NG+CR+G T +AL+L  +M   N       K D  TYSTI D LC++G +D A
Sbjct: 194 VTYNSIVNGICRSGDTSLALDLLRKMEERN------VKADVFTYSTIIDSLCRDGCIDAA 247

Query: 183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
             LF +M+ + I   VVTY SL+RG C A  WN+   L  +M+ + + PNV+TFNV+++ 
Sbjct: 248 ISLFKEMETKGIKSSVVTYNSLVRGLCKAGKWNDGALLLKDMVSREIVPNVITFNVLLDV 307

Query: 243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             K GK+ EA+ L + MI  G+ P+   YNTLMDG+C+  R++ A  +   M  N C  D
Sbjct: 308 FVKEGKLQEANELYKEMITRGISPNIITYNTLMDGYCMQNRLSEANNMLDLMVRNKCSPD 367

Query: 303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYN 342
           + ++  LI GYC  K ++  + ++  +  +G+    VTY+
Sbjct: 368 IVTFTSLIKGYCMVKRVDDGMKVFRNISKRGLVANAVTYS 407

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LPX2|PPR39_ARATH Pentatricopeptide repeat-containing protein At1g12775, mitochondrial OS=Arabidopsis thaliana GN=At1g12775 PE=2 SV=1

 Score =  263 bits (671), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 140/376 (37%), Positives = 209/376 (55%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P  P V  FN LF  +AK K Y+ VL+L K++ S G+   +YT +I+INCF
Sbjct: 75  LFRDMIQSRP-LPTVIDFNRLFSAIAKTKQYELVLALCKQMESKGIAHSIYTLSIMINCF 133

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++S  F  +G+I++  + PD V F +L+ GLC E R+ EA  L  ++   G KP +
Sbjct: 134 CRCRKLSYAFSTMGKIMKLGYEPDTVIFNTLLNGLCLECRVSEALELVDRMVEMGHKPTL 193

Query: 123 FTYTTLINGL-----------------------------------CRTGHTIVALNLFEE 147
            T  TL+NGL                                   C++G T +A+ L  +
Sbjct: 194 ITLNTLVNGLCLNGKVSDAVVLIDRMVETGFQPNEVTYGPVLNVMCKSGQTALAMELLRK 253

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M   N       K DA+ YS I DGLCK+G +D A  LF +M+ +    D++TY +LI G
Sbjct: 254 MEERN------IKLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIITYNTLIGG 307

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
           FC A  W++   L  +M+ + + PNVVTF+V+++   K GK+ EA +LL+ M+Q G+ P+
Sbjct: 308 FCNAGRWDDGAKLLRDMIKRKISPNVVTFSVLIDSFVKEGKLREADQLLKEMMQRGIAPN 367

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              YN+L+DGFC   R+  A ++   M S GC  D+ ++ ILINGYCK   I+  L L+ 
Sbjct: 368 TITYNSLIDGFCKENRLEEAIQMVDLMISKGCDPDIMTFNILINGYCKANRIDDGLELFR 427

Query: 328 EMLSKGIRPTVVTYNT 343
           EM  +G+    VTYNT
Sbjct: 428 EMSLRGVIANTVTYNT 443

Arabidopsis thaliana (taxid: 3702)

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

 Score =  256 bits (654), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 136/376 (36%), Positives = 209/376 (55%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P  P +  FN L   +AK   +D V+SL +R+ ++ +  DLY+YNILINCF
Sbjct: 67  LFGEMVQSRP-LPSIVEFNKLLSAIAKMNKFDLVISLGERMQNLRISYDLYSYNILINCF 125

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI------------------- 103
           C+  ++     VLG++++  + PD VT +SL+ G C   RI                   
Sbjct: 126 CRRSQLPLALAVLGKMMKLGYEPDIVTLSSLLNGYCHGKRISEAVALVDQMFVMEYQPNT 185

Query: 104 ----------------MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEE 147
                            EA AL  ++ A GC+PD+FTY T++NGLC+ G   +AL+L ++
Sbjct: 186 VTFNTLIHGLFLHNKASEAVALIDRMVARGCQPDLFTYGTVVNGLCKRGDIDLALSLLKK 245

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M  G  E       D + Y+TI D LC    V+ A  LF +M ++ I P+VVTY SLIR 
Sbjct: 246 MEKGKIE------ADVVIYTTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRC 299

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++A  L  +M+++ + PNVVTF+ +++   K GK+ EA +L + MI+  + PD
Sbjct: 300 LCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPD 359

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              Y++L++GFC+  R++ AK +F  M S  C  +V +Y  LI G+CK K +E  + L+ 
Sbjct: 360 IFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFR 419

Query: 328 EMLSKGIRPTVVTYNT 343
           EM  +G+    VTYNT
Sbjct: 420 EMSQRGLVGNTVTYNT 435

Arabidopsis thaliana (taxid: 3702)

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

 Score =  254 bits (649), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 132/376 (35%), Positives = 208/376 (55%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P P  +  F+ L   +AK K +D V+S  +++  +G+  +LYTYNI+INC 
Sbjct: 52  LFGEMVKSRPFPS-IVEFSKLLSAIAKMKKFDLVISFGEKMEILGVSHNLYTYNIMINCL 110

Query: 63  CKMGRVSPGFVVLGRILR-----------------------------------SCFTPDA 87
           C+  ++S    +LG++++                                     + PD 
Sbjct: 111 CRRSQLSFALAILGKMMKLGYGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDT 170

Query: 88  VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEE 147
           VTFT+L+ GL   ++  EA AL  ++   GC+PD+ TY  +INGLC+ G   +ALNL  +
Sbjct: 171 VTFTTLVHGLFQHNKASEAVALVERMVVKGCQPDLVTYGAVINGLCKRGEPDLALNLLNK 230

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M  G  E       D + YST+ D LCK   VD A  LF +M ++ I PDV TY+SLI  
Sbjct: 231 MEKGKIE------ADVVIYSTVIDSLCKYRHVDDALNLFTEMDNKGIRPDVFTYSSLISC 284

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++A  L  +M+++ + PNVVTFN +++   K GK+ EA +L + MIQ  + P+
Sbjct: 285 LCNYGRWSDASRLLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPN 344

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              YN+L++GFC+  R++ A+++F  M S  C+ DV +Y  LING+CK K++   + L+ 
Sbjct: 345 IVTYNSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFR 404

Query: 328 EMLSKGIRPTVVTYNT 343
           +M  +G+    VTY T
Sbjct: 405 DMSRRGLVGNTVTYTT 420

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WKV3|PPR36_ARATH Pentatricopeptide repeat-containing protein At1g12300, mitochondrial OS=Arabidopsis thaliana GN=At1g12300 PE=2 SV=1

 Score =  254 bits (649), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 137/368 (37%), Positives = 207/368 (56%), Gaps = 38/368 (10%)

Query: 10  MHPSP-PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRV 68
           +H  P P V  F+ LF  +AK K YD VL+L K++   G+  +LYT +I+INCFC+  ++
Sbjct: 80  IHSRPLPTVIDFSRLFSAIAKTKQYDLVLALCKQMELKGIAHNLYTLSIMINCFCRCRKL 139

Query: 69  SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL 128
              F  +G+I++  + P+ +TF++LI GLC E R+ EA  L  ++   G KPD+ T  TL
Sbjct: 140 CLAFSAMGKIIKLGYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMGHKPDLITINTL 199

Query: 129 INGLCRTGHTIVALNLFEEMANGNGEFG-------------VVCKP-------------- 161
           +NGLC +G    A+ L ++M     E+G             V+CK               
Sbjct: 200 VNGLCLSGKEAEAMLLIDKMV----EYGCQPNAVTYGPVLNVMCKSGQTALAMELLRKME 255

Query: 162 ------DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWN 215
                 DA+ YS I DGLCK G +D A  LF +M+ + I  +++TY  LI GFC A  W+
Sbjct: 256 ERNIKLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGFCNAGRWD 315

Query: 216 EAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM 275
           +   L  +M+ + + PNVVTF+V+++   K GK+ EA  L + MI  G+ PD   Y +L+
Sbjct: 316 DGAKLLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDTITYTSLI 375

Query: 276 DGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIR 335
           DGFC    +++A ++   M S GC  ++ ++ ILINGYCK   I+  L L+ +M  +G+ 
Sbjct: 376 DGFCKENHLDKANQMVDLMVSKGCDPNIRTFNILINGYCKANRIDDGLELFRKMSLRGVV 435

Query: 336 PTVVTYNT 343
              VTYNT
Sbjct: 436 ADTVTYNT 443

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQ83|PP247_ARATH Pentatricopeptide repeat-containing protein At3g22470, mitochondrial OS=Arabidopsis thaliana GN=At3g22470 PE=2 SV=1

 Score =  253 bits (646), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 135/376 (35%), Positives = 204/376 (54%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F+ M++  P P P+  FN L   +A+ K YD VL   K +   G+  D+YT  I+INC+
Sbjct: 57  LFESMIQSRPLPTPI-DFNRLCSAVARTKQYDLVLGFCKGMELNGIEHDMYTMTIMINCY 115

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++   F VLGR  +  + PD +TF++L+ G C E R+ EA AL  ++     +PD+
Sbjct: 116 CRKKKLLFAFSVLGRAWKLGYEPDTITFSTLVNGFCLEGRVSEAVALVDRMVEMKQRPDL 175

Query: 123 FTYTTLINGLC-----------------------------------RTGHTIVALNLFEE 147
            T +TLINGLC                                   ++G++ +AL+LF +
Sbjct: 176 VTVSTLINGLCLKGRVSEALVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNSALALDLFRK 235

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M   N       K   + YS + D LCK+G  D A  LF +M+ + I  DVVTY+SLI G
Sbjct: 236 MEERN------IKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGG 289

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++   +  EM+ + + P+VVTF+ +++   K GK+ EA  L   MI  G+ PD
Sbjct: 290 LCNDGKWDDGAKMLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNEMITRGIAPD 349

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              YN+L+DGFC    ++ A ++F  M S GC  D+ +Y ILIN YCK K ++  + L+ 
Sbjct: 350 TITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFR 409

Query: 328 EMLSKGIRPTVVTYNT 343
           E+ SKG+ P  +TYNT
Sbjct: 410 EISSKGLIPNTITYNT 425

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAM8|PP100_ARATH Pentatricopeptide repeat-containing protein At1g63150 OS=Arabidopsis thaliana GN=At1g63150 PE=2 SV=1

 Score =  252 bits (644), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 134/376 (35%), Positives = 206/376 (54%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P P  +  FN L   +AK   ++ V+SL +++ ++G+  DLYTY+I INCF
Sbjct: 70  LFGDMVKSRPFPS-IVEFNKLLSAVAKMNKFELVISLGEQMQTLGISHDLYTYSIFINCF 128

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++S    VL ++++  + PD VT +SL+ G C   RI +A AL  ++   G KPD 
Sbjct: 129 CRRSQLSLALAVLAKMMKLGYEPDIVTLSSLLNGYCHSKRISDAVALVDQMVEMGYKPDT 188

Query: 123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD-- 180
           FT+TTLI+GL        A+ L ++M          C+PD +TY T+ +GLCK G +D  
Sbjct: 189 FTFTTLIHGLFLHNKASEAVALVDQMVQRG------CQPDLVTYGTVVNGLCKRGDIDLA 242

Query: 181 ---------------------------------KAKELFLKMKDENINPDVVTYTSLIRG 207
                                             A +LF +M+ + I P+VVTY SLI  
Sbjct: 243 LNLLNKMEAARIKANVVIFNTIIDSLCKYRHVEVAVDLFTEMETKGIRPNVVTYNSLINC 302

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++A  L   M+++ + PNVVTFN +++   K GK+ EA +L E MIQ  + PD
Sbjct: 303 LCNYGRWSDASRLLSNMLEKKINPNVVTFNALIDAFFKEGKLVEAEKLHEEMIQRSIDPD 362

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              YN L++GFC+  R++ AK++F  M S  C+ ++ +Y  LING+CK K +E  + L+ 
Sbjct: 363 TITYNLLINGFCMHNRLDEAKQMFKFMVSKDCLPNIQTYNTLINGFCKCKRVEDGVELFR 422

Query: 328 EMLSKGIRPTVVTYNT 343
           EM  +G+    VTY T
Sbjct: 423 EMSQRGLVGNTVTYTT 438

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ASZ8|PPR37_ARATH Pentatricopeptide repeat-containing protein At1g12620 OS=Arabidopsis thaliana GN=At1g12620 PE=2 SV=1

 Score =  252 bits (643), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 135/370 (36%), Positives = 204/370 (55%), Gaps = 30/370 (8%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M R  P P  +  F+ LF  +A+ K YD VL L K++   G+  +LYT +I+INC 
Sbjct: 59  LFQEMTRSRPRPRLI-DFSRLFSVVARTKQYDLVLDLCKQMELKGIAHNLYTLSIMINCC 117

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++S  F  +G+I++  + PD VTF++LI GLC E R+ EA  L  ++   G KP +
Sbjct: 118 CRCRKLSLAFSAMGKIIKLGYEPDTVTFSTLINGLCLEGRVSEALELVDRMVEMGHKPTL 177

Query: 123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGE---------FGVVCKP------------ 161
            T   L+NGLC  G    A+ L + M     +           V+CK             
Sbjct: 178 ITLNALVNGLCLNGKVSDAVLLIDRMVETGFQPNEVTYGPVLKVMCKSGQTALAMELLRK 237

Query: 162 --------DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND 213
                   DA+ YS I DGLCK+G +D A  LF +M+ +    D++ YT+LIRGFCYA  
Sbjct: 238 MEERKIKLDAVKYSIIIDGLCKDGSLDNAFNLFNEMEIKGFKADIIIYTTLIRGFCYAGR 297

Query: 214 WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNT 273
           W++   L  +M+ + + P+VV F+ +++   K GK+ EA  L + MIQ G+ PD   Y +
Sbjct: 298 WDDGAKLLRDMIKRKITPDVVAFSALIDCFVKEGKLREAEELHKEMIQRGISPDTVTYTS 357

Query: 274 LMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG 333
           L+DGFC   ++++A  +   M S GC  ++ ++ ILINGYCK   I+  L L+ +M  +G
Sbjct: 358 LIDGFCKENQLDKANHMLDLMVSKGCGPNIRTFNILINGYCKANLIDDGLELFRKMSLRG 417

Query: 334 IRPTVVTYNT 343
           +    VTYNT
Sbjct: 418 VVADTVTYNT 427

Arabidopsis thaliana (taxid: 3702)

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

 Score =  251 bits (642), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 134/376 (35%), Positives = 207/376 (55%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P P  +  FN L   +AK   ++ V+SL +++ ++G+  DLYTY+I INCF
Sbjct: 70  LFGDMVKSRPFPS-IVEFNKLLSAVAKMNKFELVISLGEQMQTLGISHDLYTYSIFINCF 128

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++S    VL ++++  + PD VT +SL+ G C   RI +A AL  ++   G KPD 
Sbjct: 129 CRRSQLSLALAVLAKMMKLGYEPDIVTLSSLLNGYCHSKRISDAVALVDQMVEMGYKPDT 188

Query: 123 FTYTTLI-----------------------------------NGLCRTGHTIVALNLFEE 147
           FT+TTLI                                   NGLC+ G   +AL+L ++
Sbjct: 189 FTFTTLIHGLFLHNKASEAVALVDQMVQRGCQPDLVTYGTVVNGLCKRGDIDLALSLLKK 248

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M  G  E       D + Y+TI DGLCK   +D A  LF +M ++ I PDV TY+SLI  
Sbjct: 249 MEKGKIE------ADVVIYNTIIDGLCKYKHMDDALNLFTEMDNKGIRPDVFTYSSLISC 302

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++A  L  +M+++ + PNVVTF+ +++   K GK+ EA +L + MI+  + PD
Sbjct: 303 LCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPD 362

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              Y++L++GFC+  R++ AK +F  M S  C  +V +Y  LI G+CK K +E  + L+ 
Sbjct: 363 IFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYSTLIKGFCKAKRVEEGMELFR 422

Query: 328 EMLSKGIRPTVVTYNT 343
           EM  +G+    VTY T
Sbjct: 423 EMSQRGLVGNTVTYTT 438

Arabidopsis thaliana (taxid: 3702)

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

 Score =  251 bits (641), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 135/376 (35%), Positives = 205/376 (54%), Gaps = 42/376 (11%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +F  M++  P  P +  FN L   +AK K +D V+SL +++  + +   LYTYNILINCF
Sbjct: 72  LFGGMVKSRP-LPSIVEFNKLLSAIAKMKKFDVVISLGEKMQRLEIVHGLYTYNILINCF 130

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           C+  ++S    +LG++++  + P  VT +SL+ G C   RI +A AL  ++   G +PD 
Sbjct: 131 CRRSQISLALALLGKMMKLGYEPSIVTLSSLLNGYCHGKRISDAVALVDQMVEMGYRPDT 190

Query: 123 FTYTTLI-----------------------------------NGLCRTGHTIVALNLFEE 147
            T+TTLI                                   NGLC+ G T +ALNL  +
Sbjct: 191 ITFTTLIHGLFLHNKASEAVALVDRMVQRGCQPNLVTYGVVVNGLCKRGDTDLALNLLNK 250

Query: 148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG 207
           M     E       D + ++TI D LCK   VD A  LF +M+ + I P+VVTY+SLI  
Sbjct: 251 MEAAKIE------ADVVIFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNVVTYSSLISC 304

Query: 208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD 267
            C    W++A  L  +M+++ + PN+VTFN +++   K GK  EA +L + MI+  + PD
Sbjct: 305 LCSYGRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPD 364

Query: 268 ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS 327
              YN+L++GFC+  R+++AK++F  M S  C  DV +Y  LI G+CK+K +E    L+ 
Sbjct: 365 IFTYNSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFR 424

Query: 328 EMLSKGIRPTVVTYNT 343
           EM  +G+    VTY T
Sbjct: 425 EMSHRGLVGDTVTYTT 440

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	343
359479583	627	PREDICTED: pentatricopeptide repeat-cont	0.997	0.545	0.559	1e-107
449529622	618	PREDICTED: pentatricopeptide repeat-cont	0.997	0.553	0.518	2e-99
255559961	628	pentatricopeptide repeat-containing prot	0.985	0.538	0.504	1e-95
449520323	605	PREDICTED: pentatricopeptide repeat-cont	0.991	0.561	0.513	2e-94
449520325	605	PREDICTED: pentatricopeptide repeat-cont	0.988	0.560	0.502	3e-94
449462477	597	PREDICTED: pentatricopeptide repeat-cont	0.967	0.556	0.501	5e-90
449462479	580	PREDICTED: pentatricopeptide repeat-cont	0.915	0.541	0.467	3e-82
359488005	586	PREDICTED: putative pentatricopeptide re	0.970	0.568	0.444	1e-78
225451354	744	PREDICTED: putative pentatricopeptide re	0.970	0.447	0.447	1e-78
224133106	487	predicted protein [Populus trichocarpa]	0.970	0.683	0.429	1e-78

>gi|359479583|ref|XP_002275680.2| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Vitis vinifera] gi|297735515|emb|CBI17955.3| unnamed protein product [Vitis vinifera]

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 192/343 (55%), Positives = 246/343 (71%), Gaps = 1/343 (0%)

Query: 1   FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILIN 60
           F +F++++ M P+PP + SFN L G +AK K Y  V+SL+KR++ IGL PD  T NILIN
Sbjct: 77  FSVFNHLIDMQPTPP-ISSFNTLLGAVAKIKRYFDVISLYKRMSLIGLAPDFITLNILIN 135

Query: 61  CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP 120
           C+C + +V  G  VLG +LR   +P+ VTFTSL+KGLC  SRI EA  L  K+   G +P
Sbjct: 136 CYCNLNKVDFGLAVLGEMLRRGHSPNTVTFTSLVKGLCLGSRISEATGLLRKMVRMGYRP 195

Query: 121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD 180
           +V TY TL+NGLC TG+T++A+ L EEM NGNG FGV  KP+ + Y TI D LCK+G +D
Sbjct: 196 NVVTYGTLLNGLCMTGNTMLAVKLHEEMLNGNGGFGVTIKPNLVCYCTIIDSLCKDGLID 255

Query: 181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM 240
           K KELFL+MK   I+PDVV Y+S+I G C+   W  AK LF EM+D+GV PNVVTFNV++
Sbjct: 256 KGKELFLEMKGRGISPDVVAYSSIIHGMCHTGRWEGAKGLFNEMVDEGVHPNVVTFNVLI 315

Query: 241 NELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM 300
           + LCK GKM+EA+ LL+LMIQ G  PD   YNTL+DGFCL GR++ A++LFVSMES G  
Sbjct: 316 DALCKAGKMEEANHLLKLMIQRGESPDTFTYNTLIDGFCLEGRIDDARDLFVSMESKGIE 375

Query: 301 RDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            D  SY +LINGYCK+  +  A  LY EM+ K I PTV+TYNT
Sbjct: 376 TDAVSYNVLINGYCKSGRMVEAKKLYREMMCKEIMPTVITYNT 418

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449529622|ref|XP_004171797.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 178/343 (51%), Positives = 236/343 (68%), Gaps = 1/343 (0%)

Query: 1   FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILIN 60
           F  FD M+R HP PP + SFN L G LAK  HY  + SL+  +   GL PDL+T +IL N
Sbjct: 76  FHFFDLMMRSHPIPP-ISSFNRLLGGLAKINHYSQLFSLYNEMRLAGLSPDLFTLSILAN 134

Query: 61  CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP 120
           C C + RVS     +  ILR  + P+ VT+T+LIKGLC E RI EA  LF +++  GC P
Sbjct: 135 CLCNVNRVSEALAAMAGILRRGYIPNVVTYTTLIKGLCMEHRISEATRLFLRMQKLGCTP 194

Query: 121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD 180
           +  TY TLI GLC+TG+  +AL L +EM N   ++GV CKP  ITYS I DGLCK G  D
Sbjct: 195 NAVTYGTLIKGLCQTGNVNIALKLHKEMLNDASQYGVNCKPGVITYSIIIDGLCKVGRED 254

Query: 181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM 240
           +AKELF +MK + + PDV++Y++LI GFC A  W+++K LF EM+DQGVQP++VTF+V++
Sbjct: 255 EAKELFEEMKAQGMIPDVISYSTLIHGFCCAGKWDQSKHLFDEMVDQGVQPDMVTFSVLI 314

Query: 241 NELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM 300
           + LCK GK+ EA +LLE+MIQ G+ P+   YN+L+DGFC+ G +N A+ELF+SM S G  
Sbjct: 315 DTLCKEGKVTEAKKLLEVMIQRGIVPNLITYNSLIDGFCMVGDLNSARELFLSMPSKGLE 374

Query: 301 RDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            D  SY  LINGYCK  +++ A++LY+EML  G  P V TY T
Sbjct: 375 PDEISYTTLINGYCKTWKVKEAMNLYNEMLQVGKSPNVTTYGT 417

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559961|ref|XP_002520999.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223539836|gb|EEF41416.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  356 bits (913), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 171/339 (50%), Positives = 233/339 (68%), Gaps = 1/339 (0%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F+ M+ M  +P  +  FN LFG LAK K Y  V+S+  R+NSIGL  +  + NIL+NC C
Sbjct: 95  FNQMIHMQTTPA-LSRFNNLFGALAKKKQYLHVISMCGRMNSIGLLKNFISLNILLNCLC 153

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
            + RV  GFVV G ILR  + P+  TFT+L+KGLC E +I EA  +F  +  F C+P   
Sbjct: 154 SVKRVFEGFVVFGMILRKGYRPNTRTFTNLVKGLCLEGKIGEAVRVFKIMGVFDCRPSAI 213

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           T   LI+GLCRTG+T  AL L E M NGN +FG+ CKP  ++YS I D LCK+G V++AK
Sbjct: 214 TCGVLISGLCRTGNTCNALKLHEAMINGNSDFGINCKPTVVSYSCIIDSLCKDGLVERAK 273

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
           E F++MK++ I P+VVTYTSL+ G C A++W EAK LFIEM+D G+ P+VVTF+V++  L
Sbjct: 274 EFFVEMKEKGIFPNVVTYTSLLHGLCSASEWEEAKRLFIEMVDHGLLPDVVTFSVLIGAL 333

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK GK+ EAS L +LM+Q  V P    YN L++G+CL G V+  K++F+SM +  C  D 
Sbjct: 334 CKVGKVKEASGLFDLMVQRYVEPSTRTYNILIEGYCLAGMVDEGKKIFLSMVNKRCQHDA 393

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYN 342
            SY IL+  YCK+ E+ GA+ LY EM+ +GI+PTV+TY+
Sbjct: 394 GSYSILMKAYCKDSEVHGAMILYREMMDRGIQPTVITYS 432

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520323|ref|XP_004167183.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  352 bits (902), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 175/341 (51%), Positives = 230/341 (67%), Gaps = 1/341 (0%)

Query: 1   FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILIN 60
           F  F  M+  +P+PP + SF  L   LAK KHY  V  L+ ++   G+ PD  T NIL+N
Sbjct: 81  FQFFHLMMYSNPTPP-LSSFTHLLSGLAKIKHYSQVFYLYNQMRLSGISPDCCTLNILLN 139

Query: 61  CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP 120
           C C + RV  G  V+  ILR  + PD VT+T+LIKGLC E RI +AA LFT+++  GC P
Sbjct: 140 CLCNVNRVGEGLAVMAGILRRGYIPDIVTYTTLIKGLCMEHRISKAALLFTRMQKLGCTP 199

Query: 121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD 180
           +  TY TL+ GLCRTG+  +AL L +EM N +  +G+  KP  I+YS I D LCK+   D
Sbjct: 200 NAITYGTLMKGLCRTGNISIALKLHQEMLNDSSLYGINFKPVVISYSIIIDALCKDRRED 259

Query: 181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM 240
           +A++LF +MK + + P V++YTSLI GFC    W EAK LF EM++QGVQPNVVTFNV++
Sbjct: 260 EARDLFEEMKVQGMTPTVISYTSLIHGFCCGGKWEEAKRLFNEMVNQGVQPNVVTFNVLI 319

Query: 241 NELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM 300
           + LCK GK+ EA  LLE+MIQ G+ P+   YN+L++GFCL G +N A+ELFVSM S GC 
Sbjct: 320 DVLCKEGKVIEAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSMPSKGCE 379

Query: 301 RDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTY 341
            DV  Y +LINGYCK  ++E A+ LY+ ML  G RP V TY
Sbjct: 380 PDVICYTVLINGYCKTSKVEEAMKLYNGMLQVGKRPDVKTY 420

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520325|ref|XP_004167184.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  351 bits (900), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 171/340 (50%), Positives = 230/340 (67%), Gaps = 1/340 (0%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F  M+R  P+P  + SFN L   LAK KHY  V SL+ ++   GL  D  T NIL+NC C
Sbjct: 57  FHLMMRSTPTPS-LSSFNHLLSGLAKIKHYSQVFSLYNQMRLSGLSSDRCTLNILLNCLC 115

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
            + R+  GF     ILR  ++P+ VT+ +LIKGLC E RI EA  LF +++  GC PDV 
Sbjct: 116 NVNRLREGFAAFAGILRRGYSPNIVTYNTLIKGLCMEHRISEATRLFLRMQKLGCTPDVV 175

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           TY TLI GLC TG+  +AL L +EM N    + + CKP+ ITY+ I DGLCK G  D+AK
Sbjct: 176 TYGTLIKGLCGTGNINIALKLHQEMLNDISRYEINCKPNVITYNIIVDGLCKVGREDEAK 235

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
           +LF +MK + + P +++Y SLI GFC A  W E+K L  EM+DQG+QP++VTFNV+++ L
Sbjct: 236 QLFEEMKTQGMIPSIISYNSLIHGFCCAGKWEESKRLLDEMLDQGLQPDMVTFNVLIDTL 295

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK GK+ EA +LL +MI+ G+ PD   YN+L++GFC+ G +N A+ELFVSM S GC  DV
Sbjct: 296 CKEGKVIEAKKLLGVMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDV 355

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            SY +LINGY K  ++E A+ LY+EML  G RP V+TY++
Sbjct: 356 ISYNVLINGYSKTLKVEEAMKLYNEMLLVGKRPNVITYDS 395

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462477|ref|XP_004148967.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  337 bits (864), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 171/341 (50%), Positives = 227/341 (66%), Gaps = 9/341 (2%)

Query: 1   FCIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILIN 60
           F  F  M+  +P+PP + SF  L   LAK KHY  V  L+ ++   G+ PD  T NIL+N
Sbjct: 81  FQFFHLMMYSNPTPP-LSSFTHLLSGLAKIKHYSQVFYLYNQMRLSGISPDCCTLNILLN 139

Query: 61  CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP 120
           C C + RV  G  V+  ILR  + PD VT+T+LIKGLC E RI +AA LFT+++  GC P
Sbjct: 140 CLCNVNRVGEGLAVMAGILRRGYIPDIVTYTTLIKGLCMEHRISKAALLFTRMQKLGCTP 199

Query: 121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD 180
           +  TY TL+ GLCRTG+  +AL L +EM N +  +G+  KP  I+YS I D LCK+   D
Sbjct: 200 NAITYGTLMKGLCRTGNISIALKLHQEMLNDSSLYGINFKPVVISYSIIIDALCKDRRED 259

Query: 181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM 240
           +A++LF +MK + + P V++YTSL+        W EAK LF EM++QGVQPNVVTFNV++
Sbjct: 260 EARDLFEEMKVQGMTPTVISYTSLM--------WEEAKRLFNEMVNQGVQPNVVTFNVLI 311

Query: 241 NELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM 300
           + LCK GK+ EA  LLE+MIQ G+ P+   YN+L++GFCL G +N A+ELFVSM S GC 
Sbjct: 312 DVLCKEGKVIEAKDLLEVMIQRGIVPNLLTYNSLIEGFCLVGDLNSARELFVSMPSKGCE 371

Query: 301 RDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTY 341
            DV  Y +LINGYCK  ++E A+ LY+ ML  G RP V TY
Sbjct: 372 PDVICYTVLINGYCKTSKVEEAMKLYNGMLQVGKRPDVKTY 412

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462479|ref|XP_004148968.1| PREDICTED: pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Cucumis sativus]

 Score =  311 bits (797), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 159/340 (46%), Positives = 215/340 (63%), Gaps = 26/340 (7%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F  M+R  P+P  + SFN L   LAK KHY  V SL+ ++   GL  D  T NIL+NC C
Sbjct: 57  FHLMMRSTPTPS-LSSFNHLLSGLAKIKHYSQVFSLYNQMRLSGLSSDRCTLNILLNCLC 115

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
            + R+  GF     ILR  ++P+ VT+ +LIKGLC E RI EA  LF +++  GC PDV 
Sbjct: 116 NVNRLREGFAAFAGILRRGYSPNIVTYNTLIKGLCMEHRISEATRLFLRMQKLGCTPDVV 175

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           TY TLI GLC TG+  +AL L +EM N    + + CKP+ ITY+ I DGLCK G  D+AK
Sbjct: 176 TYGTLIKGLCGTGNINIALKLHQEMLNDISRYEINCKPNVITYNIIVDGLCKVGREDEAK 235

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
           +LF +MK + + P+                         EM+DQG+QP++VTFNV+++ L
Sbjct: 236 QLFEEMKTQGMIPN-------------------------EMLDQGLQPDMVTFNVLIDTL 270

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK GK+ EA +LL +MI+ G+ PD   YN+L++GFC+ G +N A+ELFVSM S GC  DV
Sbjct: 271 CKEGKVIEAKKLLGVMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSMPSKGCEPDV 330

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            SY +LINGY K  ++E A+ LY+EML  G RP V+TY++
Sbjct: 331 ISYNVLINGYSKTLKVEEAMKLYNEMLLVGKRPNVITYDS 370

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488005|ref|XP_002263693.2| PREDICTED: putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial-like [Vitis vinifera]

 Score =  300 bits (767), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 151/340 (44%), Positives = 208/340 (61%), Gaps = 7/340 (2%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F+ ML MHP PP    FN L   +AK K Y TV SL  +++S G+ PD+YT NILIN FC
Sbjct: 57  FNRMLHMHP-PPSTVDFNRLLTSIAKTKQYPTVFSLSNQMDSFGIPPDVYTLNILINSFC 115

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
            + R+   F VL +IL+    PD  TFT+LI+GLC E +I +A  LF K+   G +P+V 
Sbjct: 116 HLNRLGFAFSVLAKILKLGHQPDTATFTTLIRGLCVEGKIGDALHLFDKMIGEGFQPNVV 175

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           TY TLINGLC+ G+T  A+ L   M  GN      C+PD + Y++I D LCK+  V +A 
Sbjct: 176 TYGTLINGLCKVGNTNAAIRLLRSMEQGN------CQPDVVVYTSIIDSLCKDRQVTEAF 229

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
            LF KM  + I+PD+ TYTSLI   C   +W     L  +M++  + P+VV F+ +++ L
Sbjct: 230 NLFSKMVGQGISPDIFTYTSLIHSLCNLCEWKHVTTLLNQMINSKIMPDVVIFSTVVDAL 289

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK GK+ EA  ++++MI  GV P+   YN LMDG CL   ++ A ++F +M  NG   +V
Sbjct: 290 CKEGKITEAHDVVDMMIIRGVEPNVVTYNALMDGHCLQSEMDEAVKVFDTMVHNGYAPNV 349

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            SY  LINGYCK + ++ A  L+ EM  K + P  VTYNT
Sbjct: 350 ISYNTLINGYCKIQRMDKATYLFEEMCQKELIPNTVTYNT 389

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225451354|ref|XP_002275019.1| PREDICTED: putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial-like [Vitis vinifera]

 Score =  299 bits (766), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 152/340 (44%), Positives = 208/340 (61%), Gaps = 7/340 (2%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F+ +L MHP PP +  F  L   +AK KHY TVLSL  +++S G+ P++YT NILIN FC
Sbjct: 44  FNRLLHMHP-PPSIVDFAKLLTSIAKMKHYSTVLSLSTQMDSFGVPPNVYTLNILINSFC 102

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
            + RV   F VL +IL+    PD  TFT+LI+GLC E +I EA  LF K+   G +P+V 
Sbjct: 103 HLNRVGFAFSVLAKILKLGHQPDPTTFTTLIRGLCVEGKIGEALHLFDKMIDEGFQPNVV 162

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           TY TLINGLC+ G+T  A+ L   M  GN      C+PD + Y++I D LCK+  V +A 
Sbjct: 163 TYGTLINGLCKVGNTSAAIRLLRSMEQGN------CQPDVVIYTSIIDSLCKDRQVTEAF 216

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
            LF +M  + I+PD+ TYTSL+   C   +W     L  +M++  + P+VV F+ +++ L
Sbjct: 217 NLFSQMVGQGISPDIFTYTSLVHALCNLCEWKHVTTLLNQMVNSKILPDVVIFSTVVDAL 276

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK GK+ EA  ++++MIQ GV PD   Y TLMDG CL   ++ A ++F  M   G   DV
Sbjct: 277 CKEGKVTEAHEIVDMMIQRGVEPDVVTYTTLMDGHCLQSEMDEAVKVFDMMVRKGFAPDV 336

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            SY  LINGYCK  +I+ A+ L+ EM  K   P   TYNT
Sbjct: 337 ISYTTLINGYCKIHKIDKAMYLFEEMCRKEWIPDTKTYNT 376

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133106|ref|XP_002327962.1| predicted protein [Populus trichocarpa] gi|222837371|gb|EEE75750.1| predicted protein [Populus trichocarpa]

 Score =  299 bits (765), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 146/340 (42%), Positives = 219/340 (64%), Gaps = 7/340 (2%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC 63
           F++M+  HP  P +  F+ L   L + KHY TVLSL KR+  + +  D++ +NILINCF 
Sbjct: 72  FNHMIHKHP-LPCIVEFDKLLSALVRIKHYGTVLSLSKRIELLRIERDVFHFNILINCFS 130

Query: 64  KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF 123
           ++ RV   F VLG+I++  F PDAVTF+SLI GLC E +   A   F ++ A G +P++ 
Sbjct: 131 RLQRVDFAFSVLGKIIKLGFEPDAVTFSSLINGLCFEDKFARAMEFFDEMVASGYQPNLH 190

Query: 124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK 183
           TY T+I G C+ G T VA+ L ++M    G      +PD + Y+TI DGLCK+  V +A 
Sbjct: 191 TYNTIIKGFCKIGKTTVAVGLLKKMDKAGG------RPDIVIYNTIIDGLCKDRLVSEAL 244

Query: 184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL 243
           ++F ++K + + PDV TY+ L+ G C ++   EA  LF EMM   + P+VVTFN+++++L
Sbjct: 245 DIFSEIKGKGVRPDVFTYSILMHGLCNSDQKEEASALFNEMMSLNIMPDVVTFNILVDKL 304

Query: 244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
           CK G + EA  ++++MI+ GV P+ + YN+LM+G+CL  +V  A+ +F +M + GCM +V
Sbjct: 305 CKEGMLSEAQGIIKIMIEKGVEPNYATYNSLMNGYCLQNKVFEARMVFDAMITKGCMPNV 364

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
            SY ILINGYCK + I+ A  L+ EM  +G+ P    YNT
Sbjct: 365 VSYNILINGYCKAQRIDEARELFDEMSFRGLIPNTFNYNT 404

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	343
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.930	0.519	0.372	7.9e-62
TAIR|locus:2015208	630	AT1G63130 [Arabidopsis thalian	0.973	0.530	0.369	3.9e-60
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.973	0.531	0.375	6.4e-60
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.930	0.515	0.375	1e-59
TAIR|locus:2034760	637	AT1G12300 [Arabidopsis thalian	0.953	0.513	0.362	2.7e-59
TAIR|locus:2015213	629	AT1G63150 [Arabidopsis thalian	0.973	0.531	0.363	3.5e-59
TAIR|locus:2203916	634	AT1G62590 [Arabidopsis thalian	0.930	0.503	0.363	7.3e-59
TAIR|locus:2031301	577	AT1G63400 [Arabidopsis thalian	0.973	0.578	0.363	1.2e-58
TAIR|locus:2163041	527	AT5G41170 [Arabidopsis thalian	0.970	0.631	0.352	4.6e-57
TAIR|locus:2015218	590	AT1G63070 [Arabidopsis thalian	0.973	0.566	0.356	5.9e-57

TAIR|locus:2015228 AT1G63080 [Arabidopsis thaliana (taxid:3702)]

 Score = 632 (227.5 bits), Expect = 7.9e-62, P = 7.9e-62
 Identities = 121/325 (37%), Positives = 191/325 (58%)

Query:    19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRI 78
             ++NI+  CL +       L++  ++  +G  P + T N L+N FC   R+S    ++ ++
Sbjct:   102 TYNIMINCLCRRSQLSFALAILGKMMKLGYGPSIVTLNSLLNGFCHGNRISEAVALVDQM 161

Query:    79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT 138
             +   + PD VTFT+L+ GL   ++  EA AL  ++   GC+PD+ TY  +INGLC+ G  
Sbjct:   162 VEMGYQPDTVTFTTLVHGLFQHNKASEAVALVERMVVKGCQPDLVTYGAVINGLCKRGEP 221

Query:   139 IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV 198
              +ALNL  +M  G  E       D + YST+ D LCK   VD A  LF +M ++ I PDV
Sbjct:   222 DLALNLLNKMEKGKIE------ADVVIYSTVIDSLCKYRHVDDALNLFTEMDNKGIRPDV 275

Query:   199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLEL 258
              TY+SLI   C    W++A  L  +M+++ + PNVVTFN +++   K GK+ EA +L + 
Sbjct:   276 FTYSSLISCLCNYGRWSDASRLLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDE 335

Query:   259 MIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE 318
             MIQ  + P+   YN+L++GFC+  R++ A+++F  M S  C+ DV +Y  LING+CK K+
Sbjct:   336 MIQRSIDPNIVTYNSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKK 395

Query:   319 IEGALSLYSEMLSKGIRPTVVTYNT 343
             +   + L+ +M  +G+    VTY T
Sbjct:   396 VVDGMELFRDMSRRGLVGNTVTYTT 420

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 616 (221.9 bits), Expect = 3.9e-60, P = 3.9e-60
 Identities = 126/341 (36%), Positives = 200/341 (58%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F  M++  P P  +  F+ L   +AK   +D V+SL +++ ++G+  +LYTY+ILINCF
Sbjct:    68 LFGDMVKSRPFPS-IVEFSKLLSAIAKMNKFDLVISLGEQMQNLGISHNLYTYSILINCF 126

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  ++S    VL ++++  + PD VT  SL+ G C  +RI +A +L  ++   G +PD 
Sbjct:   127 CRRSQLSLALAVLAKMMKLGYEPDIVTLNSLLNGFCHGNRISDAVSLVGQMVEMGYQPDS 186

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
             FT+ TLI+GL R      A+ L + M    G     C+PD +TY  + +GLCK G +D A
Sbjct:   187 FTFNTLIHGLFRHNRASEAVALVDRMVV-KG-----CQPDLVTYGIVVNGLCKRGDIDLA 240

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L  KM+   I P VV Y ++I   C   + N+A  LF EM ++G++PNVVT+N ++  
Sbjct:   241 LSLLKKMEQGKIEPGVVIYNTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRC 300

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             LC  G+  +ASRLL  MI+  + P+   ++ L+D F   G++  A++L+  M       D
Sbjct:   301 LCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPD 360

Query:   303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
             +F+Y  LING+C +  ++ A  ++  M+SK   P VVTYNT
Sbjct:   361 IFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNT 401

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 128/341 (37%), Positives = 197/341 (57%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F  M++  P P  +  FN L   +AK   +D V+SL +R+ ++ +  DLY+YNILINCF
Sbjct:    67 LFGEMVQSRPLPS-IVEFNKLLSAIAKMNKFDLVISLGERMQNLRISYDLYSYNILINCF 125

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  ++     VLG++++  + PD VT +SL+ G C   RI EA AL  ++     +P+ 
Sbjct:   126 CRRSQLPLALAVLGKMMKLGYEPDIVTLSSLLNGYCHGKRISEAVALVDQMFVMEYQPNT 185

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
              T+ TLI+GL        A+ L + M    G     C+PD  TY T+ +GLCK G +D A
Sbjct:   186 VTFNTLIHGLFLHNKASEAVALIDRMV-ARG-----CQPDLFTYGTVVNGLCKRGDIDLA 239

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L  KM+   I  DVV YT++I   C   + N+A  LF EM ++G++PNVVT+N ++  
Sbjct:   240 LSLLKKMEKGKIEADVVIYTTIIDALCNYKNVNDALNLFTEMDNKGIRPNVVTYNSLIRC 299

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             LC  G+  +ASRLL  MI+  + P+   ++ L+D F   G++  A++L+  M       D
Sbjct:   300 LCNYGRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPD 359

Query:   303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
             +F+Y  LING+C +  ++ A  ++  M+SK   P VVTYNT
Sbjct:   360 IFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNT 400

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

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

 Score = 612 (220.5 bits), Expect = 1.0e-59, P = 1.0e-59
 Identities = 122/325 (37%), Positives = 186/325 (57%)

Query:    19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRI 78
             +  I+  C  + K      S+  R   +G  PD  T++ L+N FC  GRVS    ++ R+
Sbjct:   107 TMTIMINCYCRKKKLLFAFSVLGRAWKLGYEPDTITFSTLVNGFCLEGRVSEAVALVDRM 166

Query:    79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT 138
             +     PD VT ++LI GLC + R+ EA  L  ++  +G +PD  TY  ++N LC++G++
Sbjct:   167 VEMKQRPDLVTVSTLINGLCLKGRVSEALVLIDRMVEYGFQPDEVTYGPVLNRLCKSGNS 226

Query:   139 IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV 198
              +AL+LF +M   N       K   + YS + D LCK+G  D A  LF +M+ + I  DV
Sbjct:   227 ALALDLFRKMEERN------IKASVVQYSIVIDSLCKDGSFDDALSLFNEMEMKGIKADV 280

Query:   199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLEL 258
             VTY+SLI G C    W++   +  EM+ + + P+VVTF+ +++   K GK+ EA  L   
Sbjct:   281 VTYSSLIGGLCNDGKWDDGAKMLREMIGRNIIPDVVTFSALIDVFVKEGKLLEAKELYNE 340

Query:   259 MIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE 318
             MI  G+ PD   YN+L+DGFC    ++ A ++F  M S GC  D+ +Y ILIN YCK K 
Sbjct:   341 MITRGIAPDTITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCKAKR 400

Query:   319 IEGALSLYSEMLSKGIRPTVVTYNT 343
             ++  + L+ E+ SKG+ P  +TYNT
Sbjct:   401 VDDGMRLFREISSKGLIPNTITYNT 425

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2034760 AT1G12300 [Arabidopsis thaliana (taxid:3702)]

 Score = 608 (219.1 bits), Expect = 2.7e-59, P = 2.7e-59
 Identities = 121/334 (36%), Positives = 194/334 (58%)

Query:    10 MHPSP-PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRV 68
             +H  P P V  F+ LF  +AK K YD VL+L K++   G+  +LYT +I+INCFC+  ++
Sbjct:    80 IHSRPLPTVIDFSRLFSAIAKTKQYDLVLALCKQMELKGIAHNLYTLSIMINCFCRCRKL 139

Query:    69 SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL 128
                F  +G+I++  + P+ +TF++LI GLC E R+ EA  L  ++   G KPD+ T  TL
Sbjct:   140 CLAFSAMGKIIKLGYEPNTITFSTLINGLCLEGRVSEALELVDRMVEMGHKPDLITINTL 199

Query:   129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK 188
             +NGLC +G    A+ L ++M     E+G  C+P+A+TY  + + +CK G    A EL  K
Sbjct:   200 VNGLCLSGKEAEAMLLIDKMV----EYG--CQPNAVTYGPVLNVMCKSGQTALAMELLRK 253

Query:   189 MKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK 248
             M++ NI  D V Y+ +I G C     + A  LF EM  +G+  N++T+N+++   C  G+
Sbjct:   254 MEERNIKLDAVKYSIIIDGLCKHGSLDNAFNLFNEMEMKGITTNIITYNILIGGFCNAGR 313

Query:   249 MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGI 308
              D+ ++LL  MI+  + P+   ++ L+D F   G++  A+EL   M   G   D  +Y  
Sbjct:   314 WDDGAKLLRDMIKRKINPNVVTFSVLIDSFVKEGKLREAEELHKEMIHRGIAPDTITYTS 373

Query:   309 LINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYN 342
             LI+G+CK   ++ A  +   M+SKG  P + T+N
Sbjct:   374 LIDGFCKENHLDKANQMVDLMVSKGCDPNIRTFN 407

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015213 AT1G63150 [Arabidopsis thaliana (taxid:3702)]

 Score = 607 (218.7 bits), Expect = 3.5e-59, P = 3.5e-59
 Identities = 124/341 (36%), Positives = 195/341 (57%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F  M++  P P  +  FN L   +AK   ++ V+SL +++ ++G+  DLYTY+I INCF
Sbjct:    70 LFGDMVKSRPFPS-IVEFNKLLSAVAKMNKFELVISLGEQMQTLGISHDLYTYSIFINCF 128

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  ++S    VL ++++  + PD VT +SL+ G C   RI +A AL  ++   G KPD 
Sbjct:   129 CRRSQLSLALAVLAKMMKLGYEPDIVTLSSLLNGYCHSKRISDAVALVDQMVEMGYKPDT 188

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
             FT+TTLI+GL        A+ L ++M    G     C+PD +TY T+ +GLCK G +D A
Sbjct:   189 FTFTTLIHGLFLHNKASEAVALVDQMVQ-RG-----CQPDLVTYGTVVNGLCKRGDIDLA 242

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L  KM+   I  +VV + ++I   C       A  LF EM  +G++PNVVT+N ++N 
Sbjct:   243 LNLLNKMEAARIKANVVIFNTIIDSLCKYRHVEVAVDLFTEMETKGIRPNVVTYNSLINC 302

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             LC  G+  +ASRLL  M++  + P+   +N L+D F   G++  A++L   M       D
Sbjct:   303 LCNYGRWSDASRLLSNMLEKKINPNVVTFNALIDAFFKEGKLVEAEKLHEEMIQRSIDPD 362

Query:   303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
               +Y +LING+C +  ++ A  ++  M+SK   P + TYNT
Sbjct:   363 TITYNLLINGFCMHNRLDEAKQMFKFMVSKDCLPNIQTYNT 403

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 604 (217.7 bits), Expect = 7.3e-59, P = 7.3e-59
 Identities = 118/325 (36%), Positives = 189/325 (58%)

Query:    19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRI 78
             ++NIL  C  +       L+L  ++  +G  P + T + L+N +C   R+S    ++ ++
Sbjct:   122 TYNILINCFCRRSQISLALALLGKMMKLGYEPSIVTLSSLLNGYCHGKRISDAVALVDQM 181

Query:    79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT 138
             +   + PD +TFT+LI GL   ++  EA AL  ++   GC+P++ TY  ++NGLC+ G T
Sbjct:   182 VEMGYRPDTITFTTLIHGLFLHNKASEAVALVDRMVQRGCQPNLVTYGVVVNGLCKRGDT 241

Query:   139 IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV 198
              +ALNL  +M     E       D + ++TI D LCK   VD A  LF +M+ + I P+V
Sbjct:   242 DLALNLLNKMEAAKIE------ADVVIFNTIIDSLCKYRHVDDALNLFKEMETKGIRPNV 295

Query:   199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLEL 258
             VTY+SLI   C    W++A  L  +M+++ + PN+VTFN +++   K GK  EA +L + 
Sbjct:   296 VTYSSLISCLCSYGRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDD 355

Query:   259 MIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE 318
             MI+  + PD   YN+L++GFC+  R+++AK++F  M S  C  DV +Y  LI G+CK+K 
Sbjct:   356 MIKRSIDPDIFTYNSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKR 415

Query:   319 IEGALSLYSEMLSKGIRPTVVTYNT 343
             +E    L+ EM  +G+    VTY T
Sbjct:   416 VEDGTELFREMSHRGLVGDTVTYTT 440

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 124/341 (36%), Positives = 199/341 (58%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F  M++  P P  +  FN L   +AK K +D V+SL +++  +G+  +LYTYNILINCF
Sbjct:    72 LFGGMVKSRPLPS-IFEFNKLLSAIAKMKKFDLVISLGEKMQRLGISHNLYTYNILINCF 130

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  ++S    +LG++++  + P  VT +SL+ G C   RI +A AL  ++   G +PD 
Sbjct:   131 CRRSQISLALALLGKMMKLGYEPSIVTLSSLLNGYCHGKRISDAVALVDQMVEMGYRPDT 190

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
              T+TTLI+GL        A+ L + M    G     C+P+ +TY  + +GLCK G +D A
Sbjct:   191 ITFTTLIHGLFLHNKASEAVALVDRMVQ-RG-----CQPNLVTYGVVVNGLCKRGDIDLA 244

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L  KM+   I  +VV Y+++I   C     ++A  LF EM ++GV+PNV+T++ +++ 
Sbjct:   245 FNLLNKMEAAKIEANVVIYSTVIDSLCKYRHEDDALNLFTEMENKGVRPNVITYSSLISC 304

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             LC   +  +ASRLL  MI+  + P+   +N L+D F   G++  A++L+  M       D
Sbjct:   305 LCNYERWSDASRLLSDMIERKINPNVVTFNALIDAFVKEGKLVEAEKLYDEMIKRSIDPD 364

Query:   303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
             +F+Y  LING+C +  ++ A  ++  M+SK   P VVTYNT
Sbjct:   365 IFTYSSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNT 405

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 587 (211.7 bits), Expect = 4.6e-57, P = 4.6e-57
 Identities = 120/340 (35%), Positives = 192/340 (56%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F +M+   P P  +  F  L   +AK K +D V++L   L  +G+  DLYT N+L+NCF
Sbjct:    59 LFTHMVESRPLPS-IIDFTKLLNVIAKMKKFDVVINLCDHLQIMGVSHDLYTCNLLMNCF 117

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  +       LG++++  F PD VTFTSLI G C  +R+ EA ++  ++   G KPDV
Sbjct:   118 CQSSQPYLASSFLGKMMKLGFEPDIVTFTSLINGFCLGNRMEEAMSMVNQMVEMGIKPDV 177

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
               YTT+I+ LC+ GH   AL+LF++M N    +G+  +PD + Y+++ +GLC  G    A
Sbjct:   178 VMYTTIIDSLCKNGHVNYALSLFDQMEN----YGI--RPDVVMYTSLVNGLCNSGRWRDA 231

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L   M    I PDV+T+ +LI  F     + +A+ L+ EM+   + PN+ T+  ++N 
Sbjct:   232 DSLLRGMTKRKIKPDVITFNALIDAFVKEGKFLDAEELYNEMIRMSIAPNIFTYTSLING 291

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
              C  G +DEA ++  LM   G  PD   Y +L++GFC   +V+ A ++F  M   G   +
Sbjct:   292 FCMEGCVDEARQMFYLMETKGCFPDVVAYTSLINGFCKCKKVDDAMKIFYEMSQKGLTGN 351

Query:   303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYN 342
               +Y  LI G+ +  +   A  ++S M+S+G+ P + TYN
Sbjct:   352 TITYTTLIQGFGQVGKPNVAQEVFSHMVSRGVPPNIRTYN 391

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015218 AT1G63070 [Arabidopsis thaliana (taxid:3702)]

 Score = 586 (211.3 bits), Expect = 5.9e-57, P = 5.9e-57
 Identities = 122/342 (35%), Positives = 196/342 (57%)

Query:     3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
             +F  M++  P P  +  F+ L   +AK   +D V+SL +++ ++G+  +LYTY+I IN F
Sbjct:    62 LFGDMVKSRPFPS-IVEFSKLLSAIAKMNKFDLVISLGEQMQNLGISHNLYTYSIFINYF 120

Query:    63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             C+  ++S    +LG++++  + P  VT  SL+ G C  +RI EA AL  ++   G +PD 
Sbjct:   121 CRRSQLSLALAILGKMMKLGYGPSIVTLNSLLNGFCHGNRISEAVALVDQMVEMGYQPDT 180

Query:   123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA 182
              T+TTL++GL +      A+ L E M    G     C+PD +TY  + +GLCK G  D A
Sbjct:   181 VTFTTLVHGLFQHNKASEAVALVERMVV-KG-----CQPDLVTYGAVINGLCKRGEPDLA 234

Query:   183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE 242
               L  KM+   I  DVV Y ++I G C     ++A  LF +M  +G++P+V T+N +++ 
Sbjct:   235 LNLLNKMEKGKIEADVVIYNTIIDGLCKYKHMDDAFDLFNKMETKGIKPDVFTYNPLISC 294

Query:   243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM-ESNGCMR 301
             LC  G+  +ASRLL  M++  + PD   +N L+D F   G++  A++L+  M +S  C  
Sbjct:   295 LCNYGRWSDASRLLSDMLEKNINPDLVFFNALIDAFVKEGKLVEAEKLYDEMVKSKHCFP 354

Query:   302 DVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
             DV +Y  LI G+CK K +E  + ++ EM  +G+    VTY T
Sbjct:   355 DVVAYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYTT 396

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00023872001 SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (660 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	343
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-32
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-20
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	9e-18
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	5e-17
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-16
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-16
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-14
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-13
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-13
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-13
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	9e-13
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-12
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-10
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-10
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-09
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-09
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	9e-09
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-07
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-06
pfam01535	31	pfam01535, PPR, PPR repeat	2e-06
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-06
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	5e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	1e-05
pfam01535	31	pfam01535, PPR, PPR repeat	4e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	4e-05
pfam01535	31	pfam01535, PPR, PPR repeat	5e-05
pfam01535	31	pfam01535, PPR, PPR repeat	5e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	6e-05
pfam01535	31	pfam01535, PPR, PPR repeat	1e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	1e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-04
pfam12854	34	pfam12854, PPR_1, PPR repeat	3e-04
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	4e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	4e-04
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.004

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

 Score =  128 bits (324), Expect = 1e-32
 Identities = 85/328 (25%), Positives = 152/328 (46%), Gaps = 6/328 (1%)

Query: 15  PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVV 74
           P + +FN+L    A ++  D  L + + +   GL  D   Y  LI+   K G+V   F V
Sbjct: 435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEV 494

Query: 75  LGRILRSCFTPDAVTFTSLIKGLCAES-RIMEAAALFTKLRAFGCKPDVFTYTTLINGLC 133
              ++ +    +  TF +LI G CA + ++ +A   +  +R+   KPD   +  LI+   
Sbjct: 495 FHEMVNAGVEANVHTFGALIDG-CARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACG 553

Query: 134 RTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN 193
           ++G    A ++  EM     E   +  PD IT   +       G VD+AKE++  + + N
Sbjct: 554 QSGAVDRAFDVLAEM---KAETHPI-DPDHITVGALMKACANAGQVDRAKEVYQMIHEYN 609

Query: 194 INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEAS 253
           I      YT  +       DW+ A  ++ +M  +GV+P+ V F+ +++     G +D+A 
Sbjct: 610 IKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAF 669

Query: 254 RLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY 313
            +L+   + G++     Y++LM          +A EL+  ++S      V +   LI   
Sbjct: 670 EILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITAL 729

Query: 314 CKNKEIEGALSLYSEMLSKGIRPTVVTY 341
           C+  ++  AL + SEM   G+ P  +TY
Sbjct: 730 CEGNQLPKALEVLSEMKRLGLCPNTITY 757

Length = 1060

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

 Score = 91.4 bits (227), Expect = 3e-20
 Identities = 90/376 (23%), Positives = 155/376 (41%), Gaps = 64/376 (17%)

Query: 3   IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF 62
           +FD M R         S+N +     +N      L LF  +  + + PDL T   +I+  
Sbjct: 244 VFDRMPRRD-----CISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAC 298

Query: 63  CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
             +G    G  + G ++++ F  D     SLI+   +     EA  +F+++     K D 
Sbjct: 299 ELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME---TK-DA 354

Query: 123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAIT----------------- 165
            ++T +I+G  + G    AL  +  M   N        PD IT                 
Sbjct: 355 VSWTAMISGYEKNGLPDKALETYALMEQDN------VSPDEITIASVLSACACLGDLDVG 408

Query: 166 --------------YSTITDGL------CKEGFVDKAKELFLKMKDENINPDVVTYTSLI 205
                         Y  + + L      CK   +DKA E+F  + ++    DV+++TS+I
Sbjct: 409 VKLHELAERKGLISYVVVANALIEMYSKCKC--IDKALEVFHNIPEK----DVISWTSII 462

Query: 206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR 265
            G    N   EA  +F   M   ++PN VT    ++   + G +     +   +++ G+ 
Sbjct: 463 AGLRLNNRCFEA-LIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIG 521

Query: 266 PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSL 325
            D  + N L+D +   GR+N A   F     N   +DV S+ IL+ GY  + +   A+ L
Sbjct: 522 FDGFLPNALLDLYVRCGRMNYAWNQF-----NSHEKDVVSWNILLTGYVAHGKGSMAVEL 576

Query: 326 YSEMLSKGIRPTVVTY 341
           ++ M+  G+ P  VT+
Sbjct: 577 FNRMVESGVNPDEVTF 592

Length = 857

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

 Score = 84.2 bits (208), Expect = 9e-18
 Identities = 74/325 (22%), Positives = 128/325 (39%), Gaps = 53/325 (16%)

Query: 50  PDLYTYNILINCFCKMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGLCAESRIMEAA 107
           PD   +N LI+   + G V   F VL  +        PD +T  +L+K      ++  A 
Sbjct: 540 PDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAK 599

Query: 108 ALFTKLRAFGCK--PDVFTYTTLINGLCRTGHTIVALNLFEEM----------------- 148
            ++  +  +  K  P+V  YT  +N   + G    AL+++++M                 
Sbjct: 600 EVYQMIHEYNIKGTPEV--YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVD 657

Query: 149 ANGNGE-----FGVV-------CKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINP 196
             G+       F ++        K   ++YS++           KA EL+  +K   + P
Sbjct: 658 VAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRP 717

Query: 197 DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLL 256
            V T  +LI   C  N   +A  +  EM   G+ PN +T+++++    +    D    LL
Sbjct: 718 TVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL 777

Query: 257 ELMIQIGVRPDASVYNTLMDGFCLTGRVNRA---KELFVSMESNGCMRDVFSYGILINGY 313
               + G++P+  +   +  G CL  R  +A    E  VS +S                 
Sbjct: 778 SQAKEDGIKPNLVMCRCIT-GLCLR-RFEKACALGEPVVSFDSG-------------RPQ 822

Query: 314 CKNKEIEGALSLYSEMLSKGIRPTV 338
            +NK    AL +Y E +S G  PT+
Sbjct: 823 IENKWTSWALMVYRETISAGTLPTM 847

Length = 1060

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

 Score = 81.8 bits (202), Expect = 5e-17
 Identities = 58/273 (21%), Positives = 116/273 (42%), Gaps = 20/273 (7%)

Query: 85  PDAVTFTSLIK-----------GLCAESRIMEAA-ALFTKLRAFGCKPDVFTYTTLINGL 132
            +A  F  LI+            +CA S+ ++ A  +   ++  G K D   YTTLI+  
Sbjct: 423 KEAFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTC 482

Query: 133 CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE 192
            ++G       +F EM N   E       +  T+  + DG  + G V KA   +  M+ +
Sbjct: 483 AKSGKVDAMFEVFHEMVNAGVE------ANVHTFGALIDGCARAGQVAKAFGAYGIMRSK 536

Query: 193 NINPDVVTYTSLIRGFCYANDWNEAKCLFIEMM--DQGVQPNVVTFNVIMNELCKNGKMD 250
           N+ PD V + +LI     +   + A  +  EM      + P+ +T   +M      G++D
Sbjct: 537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVD 596

Query: 251 EASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILI 310
            A  + +++ +  ++    VY   ++     G  + A  ++  M+  G   D   +  L+
Sbjct: 597 RAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALV 656

Query: 311 NGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
           +      +++ A  +  +   +GI+   V+Y++
Sbjct: 657 DVAGHAGDLDKAFEILQDARKQGIKLGTVSYSS 689

Length = 1060

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

 Score = 79.9 bits (197), Expect = 2e-16
 Identities = 77/354 (21%), Positives = 138/354 (38%), Gaps = 60/354 (16%)

Query: 27  LAKNKHYDTVLSLFKRLNSIGLFP-DLYTYNILINCFCKMGRVSPGFV--VLGRILRSCF 83
           L     +   L LF+ L +   F     TY+ L+     +   S   V  V   +  S F
Sbjct: 97  LVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALK--SIRCVKAVYWHVESSGF 154

Query: 84  TPDAVTFTSLIK-----GLCAESRIMEAAALFTKLRAFGCKPD--VFTYTTLINGLCRTG 136
            PD      ++      G+  ++R           R F   P+  + ++ T+I GL   G
Sbjct: 155 EPDQYMMNRVLLMHVKCGMLIDAR-----------RLFDEMPERNLASWGTIIGGLVDAG 203

Query: 137 HTIVALNLFEEM-----ANGNGEFGVVCKPDAITYST----------------------- 168
           +   A  LF EM           F V+ +  A   S                        
Sbjct: 204 NYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSC 263

Query: 169 -ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ 227
            + D   K G ++ A+ +F  M ++      V + S++ G+       EA CL+ EM D 
Sbjct: 264 ALIDMYSKCGDIEDARCVFDGMPEKT----TVAWNSMLAGYALHGYSEEALCLYYEMRDS 319

Query: 228 GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA 287
           GV  +  TF++++    +   ++ A +    +I+ G   D      L+D +   GR+  A
Sbjct: 320 GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDA 379

Query: 288 KELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTY 341
           + +F  M      +++ S+  LI GY  +     A+ ++  M+++G+ P  VT+
Sbjct: 380 RNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTF 429

Length = 697

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

 Score = 71.7 bits (177), Expect = 2e-16
 Identities = 25/49 (51%), Positives = 35/49 (71%)

Query: 161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFC 209
           PD +TY+T+ DG CK+G V++A +LF +MK   I P+V TY+ LI G C
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 79.1 bits (195), Expect = 4e-16
 Identities = 83/365 (22%), Positives = 150/365 (41%), Gaps = 64/365 (17%)

Query: 17  VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTY--------------------- 55
           + S+N+L G  AK  ++D  L L+ R+   G+ PD+YT+                     
Sbjct: 152 LFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHA 211

Query: 56  --------------NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES 101
                         N LI  + K G V    +V  R+ R     D +++ ++I G     
Sbjct: 212 HVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRR----DCISWNAMISGYFENG 267

Query: 102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP 161
             +E   LF  +R     PD+ T T++          I A  L  +   G    G V K 
Sbjct: 268 ECLEGLELFFTMRELSVDPDLMTITSV----------ISACELLGDERLGREMHGYVVKT 317

Query: 162 ----DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEA 217
               D    +++       G   +A+++F +M+ +    D V++T++I G+   N   + 
Sbjct: 318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEK-NGLPDK 372

Query: 218 KCLFIEMMDQ-GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD 276
                 +M+Q  V P+ +T   +++     G +D   +L EL  + G+     V N L++
Sbjct: 373 ALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIE 432

Query: 277 GFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRP 336
            +     +++A E+F ++      +DV S+  +I G   N     AL  + +ML   ++P
Sbjct: 433 MYSKCKCIDKALEVFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKP 487

Query: 337 TVVTY 341
             VT 
Sbjct: 488 NSVTL 492

Length = 857

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

 Score = 71.3 bits (176), Expect = 4e-16
 Identities = 24/50 (48%), Positives = 35/50 (70%)

Query: 196 PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK 245
           PDVVTY +LI G+C      EA  LF EM  +G++PNV T++++++ LCK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 69.0 bits (170), Expect = 2e-15
 Identities = 20/49 (40%), Positives = 34/49 (69%)

Query: 231 PNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC 279
           P+VVT+N +++  CK GK++EA +L   M + G++P+   Y+ L+DG C
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 66.3 bits (163), Expect = 2e-14
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 266 PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK 315
           PD   YNTL+DG+C  G+V  A +LF  M+  G   +V++Y ILI+G CK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 64.7 bits (159), Expect = 7e-14
 Identities = 23/50 (46%), Positives = 36/50 (72%)

Query: 85  PDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR 134
           PD VT+ +LI G C + ++ EA  LF +++  G KP+V+TY+ LI+GLC+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 62.8 bits (154), Expect = 3e-13
 Identities = 27/56 (48%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 120 PDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK 175
           PDV TY TLI+G C+ G    AL LF EM           KP+  TYS + DGLCK
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRG------IKPNVYTYSILIDGLCK 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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 62.8 bits (154), Expect = 3e-13
 Identities = 21/42 (50%), Positives = 30/42 (71%)

Query: 302 DVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
           DV +Y  LI+GYCK  ++E AL L++EM  +GI+P V TY+ 
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSI 43

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

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

 Score = 69.5 bits (170), Expect = 7e-13
 Identities = 73/322 (22%), Positives = 130/322 (40%), Gaps = 55/322 (17%)

Query: 51  DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK---GLCAESRIMEAA 107
           DL+++N+L+  + K G       +  R+L +   PD  TF  +++   G+   +R  E  
Sbjct: 151 DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVH 210

Query: 108 ALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS 167
           A   +   FG + DV     LI    + G  + A  +F+ M           + D I+++
Sbjct: 211 AHVVR---FGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----------RRDCISWN 257

Query: 168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLI---------------------R 206
            +  G  + G   +  ELF  M++ +++PD++T TS+I                      
Sbjct: 258 AMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT 317

Query: 207 GFC--------------YANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEA 252
           GF                   W EA+ +F  M  +    + V++  +++   KNG  D+A
Sbjct: 318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK----DAVSWTAMISGYEKNGLPDKA 373

Query: 253 SRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILING 312
                LM Q  V PD     +++      G ++   +L    E  G +  V     LI  
Sbjct: 374 LETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEM 433

Query: 313 YCKNKEIEGALSLYSEMLSKGI 334
           Y K K I+ AL ++  +  K +
Sbjct: 434 YSKCKCIDKALEVFHNIPEKDV 455

Length = 857

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

 Score = 69.1 bits (169), Expect = 9e-13
 Identities = 64/283 (22%), Positives = 114/283 (40%), Gaps = 39/283 (13%)

Query: 34  DTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL 93
           D  + L +     GL   +   N LI  + K   +     V   I       D +++TS+
Sbjct: 406 DVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEK----DVISWTSI 461

Query: 94  IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG----------HTIVA-- 141
           I GL   +R  EA   F ++     KP+  T    ++   R G          H +    
Sbjct: 462 IAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGI 520

Query: 142 ----------LNLF---EEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK 188
                     L+L+     M     +F    + D ++++ +  G    G    A ELF +
Sbjct: 521 GFDGFLPNALLDLYVRCGRMNYAWNQFNS-HEKDVVSWNILLTGYVAHGKGSMAVELFNR 579

Query: 189 MKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ-GVQPNVVTFNVIMNELCKNG 247
           M +  +NPD VT+ SL+     +    +    F  M ++  + PN+  +  +++ L + G
Sbjct: 580 MVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAG 639

Query: 248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKEL 290
           K+ EA   +  M    + PD +V+  L++  C   R++R  EL
Sbjct: 640 KLTEAYNFINKM---PITPDPAVWGALLNA-C---RIHRHVEL 675

Length = 857

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

 Score = 67.2 bits (164), Expect = 3e-12
 Identities = 51/242 (21%), Positives = 103/242 (42%), Gaps = 15/242 (6%)

Query: 47  GLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEA 106
           G+  D +    LI+ + K G +     V   +         V + S++ G        EA
Sbjct: 254 GVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEK----TTVAWNSMLAGYALHGYSEEA 309

Query: 107 AALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY 166
             L+ ++R  G   D FT++ +I    R       L   ++   G    G     D +  
Sbjct: 310 LCLYYEMRDSGVSIDQFTFSIMIRIFSRLA----LLEHAKQAHAGLIRTGF--PLDIVAN 363

Query: 167 STITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMD 226
           + + D   K G ++ A+ +F +M  +N+    +++ +LI G+       +A  +F  M+ 
Sbjct: 364 TALVDLYSKWGRMEDARNVFDRMPRKNL----ISWNALIAGYGNHGRGTKAVEMFERMIA 419

Query: 227 QGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI-GVRPDASVYNTLMDGFCLTGRVN 285
           +GV PN VTF  +++    +G  ++   + + M +   ++P A  Y  +++     G ++
Sbjct: 420 EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLD 479

Query: 286 RA 287
            A
Sbjct: 480 EA 481

Length = 697

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

 Score = 60.7 bits (147), Expect = 4e-10
 Identities = 61/257 (23%), Positives = 102/257 (39%), Gaps = 15/257 (5%)

Query: 88  VTFTSLIKGLCAESRIMEAAALFTKLRA-FGCKPDVFTYTTLINGLCRTGHTIVALNLFE 146
           V+  S I+ L A  R  EA  LF  L A         TY  L+              ++ 
Sbjct: 88  VSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYW 147

Query: 147 EMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIR 206
            + +   E      PD    + +     K G +  A+ LF +M + N+     ++ ++I 
Sbjct: 148 HVESSGFE------PDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNL----ASWGTIIG 197

Query: 207 GFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRP 266
           G   A ++ EA  LF EM + G      TF V++      G      +L   +++ GV  
Sbjct: 198 GLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVG 257

Query: 267 DASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLY 326
           D  V   L+D +   G +  A+ +F  M      +   ++  ++ GY  +   E AL LY
Sbjct: 258 DTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLY 313

Query: 327 SEMLSKGIRPTVVTYNT 343
            EM   G+     T++ 
Sbjct: 314 YEMRDSGVSIDQFTFSI 330

Length = 697

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

 Score = 53.9 bits (131), Expect = 4e-10
 Identities = 19/33 (57%), Positives = 22/33 (66%)

Query: 116 FGCKPDVFTYTTLINGLCRTGHTIVALNLFEEM 148
            G KPDV TY TLI+GLCR G    A+ L +EM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 53.6 bits (130), Expect = 7e-10
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK 64
          P V ++N L     K    +  L LF  +   G+ P++YTY+ILI+  CK
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 58.7 bits (142), Expect = 2e-09
 Identities = 46/158 (29%), Positives = 77/158 (48%), Gaps = 12/158 (7%)

Query: 185 LFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC 244
           +F KM +     D+ ++  L+ G+  A  ++EA CL+  M+  GV+P+V TF  ++   C
Sbjct: 143 VFGKMPER----DLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRT-C 197

Query: 245 KNGKMDEA-SRLLEL-MIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
             G  D A  R +   +++ G   D  V N L+  +   G V  A+ +F  M      RD
Sbjct: 198 -GGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRD 252

Query: 303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVT 340
             S+  +I+GY +N E    L L+  M    + P ++T
Sbjct: 253 CISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMT 290

Length = 857

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

 Score = 51.6 bits (125), Expect = 2e-09
 Identities = 15/33 (45%), Positives = 27/33 (81%)

Query: 227 QGVQPNVVTFNVIMNELCKNGKMDEASRLLELM 259
           +G++P+VVT+N +++ LC+ G++DEA  LL+ M
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 56.8 bits (137), Expect = 7e-09
 Identities = 37/140 (26%), Positives = 57/140 (40%), Gaps = 39/140 (27%)

Query: 237 NVIMNELCKNGKMDEASRLLELMIQIGVRPDASVY------------------------- 271
           N  +  LC +G++++A +LLE M ++ V  D   Y                         
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS 114

Query: 272 ----------NTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEG 321
                     N ++  F   G +  A  +F  M      RD+FS+ +L+ GY K    + 
Sbjct: 115 SHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPE----RDLFSWNVLVGGYAKAGYFDE 170

Query: 322 ALSLYSEMLSKGIRPTVVTY 341
           AL LY  ML  G+RP V T+
Sbjct: 171 ALCLYHRMLWAGVRPDVYTF 190

Length = 857

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

 Score = 56.4 bits (136), Expect = 9e-09
 Identities = 63/288 (21%), Positives = 114/288 (39%), Gaps = 32/288 (11%)

Query: 19  SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGF--VVLG 76
           S+  + G L    +Y    +LF+ +   G   +  T       F  M R S G      G
Sbjct: 191 SWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRT-------FVVMLRASAGLGSARAG 243

Query: 77  RILRSCFTPDAV---TFTS--LIKGLCAESRIMEAAALFTKLRAFGCKPD--VFTYTTLI 129
           + L  C     V   TF S  LI        I +A         F   P+     + +++
Sbjct: 244 QQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDAR------CVFDGMPEKTTVAWNSML 297

Query: 130 NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKM 189
            G    G++  AL L+ EM +     GV    D  T+S +     +   ++ AK+    +
Sbjct: 298 AGYALHGYSEEALCLYYEMRDS----GV--SIDQFTFSIMIRIFSRLALLEHAKQAHAGL 351

Query: 190 KDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM 249
                  D+V  T+L+  +       +A+ +F + M +    N++++N ++     +G+ 
Sbjct: 352 IRTGFPLDIVANTALVDLYSKWGRMEDARNVF-DRMPR---KNLISWNALIAGYGNHGRG 407

Query: 250 DEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN 297
            +A  + E MI  GV P+   +  ++     +G   +  E+F SM  N
Sbjct: 408 TKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN 455

Length = 697

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

 Score = 49.7 bits (120), Expect = 1e-08
 Identities = 17/32 (53%), Positives = 24/32 (75%)

Query: 159 CKPDAITYSTITDGLCKEGFVDKAKELFLKMK 190
            KPD +TY+T+ DGLC+ G VD+A EL  +M+
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

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

 Score = 46.3 bits (111), Expect = 2e-07
 Identities = 16/35 (45%), Positives = 21/35 (60%)

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV 338
            +Y  LI+G CK   +E AL L+ EM  +GI P V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 45.8 bits (110), Expect = 3e-07
 Identities = 18/33 (54%), Positives = 22/33 (66%)

Query: 263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSME 295
           G++PD   YNTL+DG C  GRV+ A EL   ME
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

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

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 28/120 (23%), Positives = 53/120 (44%), Gaps = 1/120 (0%)

Query: 14  PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFV 73
                S++ L G  +  K++   L L++ + SI L P + T N LI   C+  ++     
Sbjct: 681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE 740

Query: 74  VLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC 133
           VL  + R    P+ +T++ L+     +        L ++ +  G KP++     +  GLC
Sbjct: 741 VLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCIT-GLC 799

Length = 1060

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

 Score = 44.3 bits (106), Expect = 1e-06
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 297 NGCMRDVFSYGILINGYCKNKEIEGALSLYSEM 329
            G   DV +Y  LI+G C+   ++ A+ L  EM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 43.6 bits (104), Expect = 2e-06
 Identities = 17/35 (48%), Positives = 23/35 (65%)

Query: 199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV 233
           VTY +LI G C A    EA  LF EM ++G++P+V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 43.6 bits (104), Expect = 2e-06
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 304 FSYGILINGYCKNKEIEGALSLYSEMLSKGI 334
            +Y  LI+GYCK  ++E AL L+ EM  KG+
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 48.7 bits (116), Expect = 3e-06
 Identities = 58/296 (19%), Positives = 120/296 (40%), Gaps = 47/296 (15%)

Query: 2   CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINC 61
           C+FD M    P    V   ++L G  A + + +  L L+  +   G+  D +T++I+I  
Sbjct: 280 CVFDGM----PEKTTVAWNSMLAG-YALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRI 334

Query: 62  FCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPD 121
           F ++  +         ++R+ F  D V  T+L+       R+ +A  +F ++     + +
Sbjct: 335 FSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKN 390

Query: 122 VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDK 181
           + ++  LI G    G    A+ +FE M       GV   P+ +T+  +       G  ++
Sbjct: 391 LISWNALIAGYGNHGRGTKAVEMFERMIAE----GVA--PNHVTFLAVLSACRYSGLSEQ 444

Query: 182 AKELFLKM-KDENINPDVVTYTSLIRGFCYANDWNEA-----KCLFIEMMDQ-------- 227
             E+F  M ++  I P  + Y  +I         +EA     +  F   ++         
Sbjct: 445 GWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTAC 504

Query: 228 -----------------GVQPNVV-TFNVIMNELCKNGKMDEASRLLELMIQIGVR 265
                            G+ P  +  + V++N    +G+  EA++++E + + G+ 
Sbjct: 505 RIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLS 560

Length = 697

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

 Score = 42.7 bits (102), Expect = 4e-06
 Identities = 16/32 (50%), Positives = 19/32 (59%)

Query: 193 NINPDVVTYTSLIRGFCYANDWNEAKCLFIEM 224
            + PDVVTY +LI G C A   +EA  L  EM
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 47.9 bits (114), Expect = 5e-06
 Identities = 62/272 (22%), Positives = 109/272 (40%), Gaps = 22/272 (8%)

Query: 29  KNKHYDTVLSLFKRLNSIGLFPDLYTY-NILINCFCKMGRVSPGFVVLGRILRSCFTPDA 87
           KN   D  L  +  +    + PD  T  ++L  C C +G +  G  +     R       
Sbjct: 366 KNGLPDKALETYALMEQDNVSPDEITIASVLSACAC-LGDLDVGVKLHELAERKGLISYV 424

Query: 88  VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP--DVFTYTTLINGLCRTGHTIVALNLF 145
           V   +LI+ + ++ + ++ A     L  F   P  DV ++T++I GL        AL  F
Sbjct: 425 VVANALIE-MYSKCKCIDKA-----LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFF 478

Query: 146 EEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLI 205
            +M        +  KP+++T         + G +   KE+   +    I  D     +L+
Sbjct: 479 RQML-------LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALL 531

Query: 206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR 265
             +      N A   F        + +VV++N+++     +GK   A  L   M++ GV 
Sbjct: 532 DLYVRCGRMNYAWNQF-----NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVN 586

Query: 266 PDASVYNTLMDGFCLTGRVNRAKELFVSMESN 297
           PD   + +L+     +G V +  E F SME  
Sbjct: 587 PDEVTFISLLCACSRSGMVTQGLEYFHSMEEK 618

Length = 857

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

 Score = 42.3 bits (101), Expect = 5e-06
 Identities = 13/22 (59%), Positives = 16/22 (72%)

Query: 47 GLFPDLYTYNILINCFCKMGRV 68
          GL PD+ TYN LI+  C+ GRV
Sbjct: 2  GLKPDVVTYNTLIDGLCRAGRV 23

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

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

 Score = 41.3 bits (98), Expect = 1e-05
 Identities = 20/35 (57%), Positives = 27/35 (77%)

Query: 164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV 198
           +TY+T+ DGLCK G V++A ELF +MK+  I PDV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 39.7 bits (94), Expect = 4e-05
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 234 VTFNVIMNELCKNGKMDEASRLLELMIQIGV 264
           VT+N +++  CK GK++EA  L + M + GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 303 VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRP 336
           + +Y  L+    K  + + AL++  EM + G++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

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

 Score = 39.4 bits (93), Expect = 5e-05
 Identities = 17/31 (54%), Positives = 20/31 (64%)

Query: 199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGV 229
           VTY SLI G+C A    EA  LF EM ++GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 39.4 bits (93), Expect = 5e-05
 Identities = 12/31 (38%), Positives = 23/31 (74%)

Query: 164 ITYSTITDGLCKEGFVDKAKELFLKMKDENI 194
           +TY+++  G CK G +++A ELF +MK++ +
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 39.4 bits (93), Expect = 6e-05
 Identities = 18/34 (52%), Positives = 20/34 (58%)

Query: 270 VYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV 303
            YNTL+DG C  GRV  A ELF  M+  G   DV
Sbjct: 2   TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 38.6 bits (91), Expect = 1e-04
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 269 SVYNTLMDGFCLTGRVNRAKELFVSMESNGC 299
             YN+L+ G+C  G++  A ELF  M+  G 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 233 VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRP 266
           + T+N ++  L K G  D A  +LE M   G++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

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

 Score = 38.2 bits (90), Expect = 2e-04
 Identities = 14/35 (40%), Positives = 24/35 (68%)

Query: 234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDA 268
           VT+N +++ LCK G+++EA  L + M + G+ PD 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 37.3 bits (88), Expect = 3e-04
 Identities = 13/28 (46%), Positives = 16/28 (57%)

Query: 83  FTPDAVTFTSLIKGLCAESRIMEAAALF 110
             PD VT+ +LI GLC   R+ EA  L 
Sbjct: 3   LKPDVVTYNTLIDGLCRAGRVDEAVELL 30

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

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

 Score = 37.4 bits (88), Expect = 3e-04
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 123 FTYTTLINGLCRTGHTIVALNLFEEM 148
            TY +LI+G C+ G    AL LF+EM
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEM 26

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

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

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 88  VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV 122
           VT+ +LI GLC   R+ EA  LF +++  G +PDV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 10/34 (29%), Positives = 17/34 (50%)

Query: 198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP 231
           + TY +L+     A D + A  +  EM   G++P
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

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

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 36/150 (24%), Positives = 62/150 (41%), Gaps = 12/150 (8%)

Query: 17  VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC-KMGRVSPGFVVL 75
           V S+NIL      +      + LF R+   G+ PD  T+  L+ C C + G V+ G    
Sbjct: 554 VVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLL-CACSRSGMVTQGLEYF 612

Query: 76  GRI-LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR 134
             +  +   TP+   +  ++  L    ++ EA     K+      PD   +  L+N  CR
Sbjct: 613 HSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPI---TPDPAVWGALLNA-CR 668

Query: 135 TGHTI-----VALNLFEEMANGNGEFGVVC 159
               +      A ++FE   N  G + ++C
Sbjct: 669 IHRHVELGELAAQHIFELDPNSVGYYILLC 698

Length = 857

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

 Score = 34.0 bits (79), Expect = 0.004
 Identities = 12/35 (34%), Positives = 15/35 (42%)

Query: 53 YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA 87
           TYN LI+  CK GRV     +   +      PD 
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	343
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.96
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.95
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.95
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.94
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.92
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.9
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.89
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.88
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.87
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.87
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.87
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.86
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.84
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.83
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.81
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.81
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.81
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.8
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.8
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.8
PRK14574	822	hmsH outer membrane protein; Provisional	99.79
PRK14574	822	hmsH outer membrane protein; Provisional	99.76
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.76
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.75
KOG1126	638	consensus DNA-binding cell division cycle control	99.75
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.75
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.74
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.72
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.72
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.71
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.71
KOG2076	895	consensus RNA polymerase III transcription factor	99.7
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.67
KOG1126	638	consensus DNA-binding cell division cycle control	99.66
KOG2076	895	consensus RNA polymerase III transcription factor	99.65
PRK12370	553	invasion protein regulator; Provisional	99.65
PRK12370	553	invasion protein regulator; Provisional	99.64
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.63
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.61
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.61
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.61
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.61
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.61
KOG2003	840	consensus TPR repeat-containing protein [General f	99.6
KOG2003	840	consensus TPR repeat-containing protein [General f	99.59
KOG1129	478	consensus TPR repeat-containing protein [General f	99.58
KOG1129	478	consensus TPR repeat-containing protein [General f	99.57
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.56
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.56
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.55
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.55
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.52
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.52
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.5
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.48
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.46
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.46
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.45
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.45
PRK11189	296	lipoprotein NlpI; Provisional	99.44
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.44
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.44
PRK11189	296	lipoprotein NlpI; Provisional	99.43
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.42
PF13041	50	PPR_2: PPR repeat family	99.41
PF13041	50	PPR_2: PPR repeat family	99.4
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.37
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.37
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.34
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.28
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.26
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.25
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.25
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.24
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.23
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.22
KOG1125	579	consensus TPR repeat-containing protein [General f	99.22
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.16
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.15
PLN02789	320	farnesyltranstransferase	99.13
KOG1125	579	consensus TPR repeat-containing protein [General f	99.13
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.12
PLN02789	320	farnesyltranstransferase	99.12
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.1
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.06
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.04
PRK04841	903	transcriptional regulator MalT; Provisional	99.03
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	99.03
KOG1128	777	consensus Uncharacterized conserved protein, conta	99.0
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.99
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.98
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.97
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.96
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.95
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.95
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.94
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.93
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.93
PRK04841	903	transcriptional regulator MalT; Provisional	98.92
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.92
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.91
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.9
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.9
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.89
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.87
PRK15359	144	type III secretion system chaperone protein SscB;	98.87
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.87
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.85
PF12854	34	PPR_1: PPR repeat	98.83
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.83
PRK15359	144	type III secretion system chaperone protein SscB;	98.8
PF12854	34	PPR_1: PPR repeat	98.78
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.78
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.76
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.75
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.75
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.73
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.71
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.66
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.64
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.64
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.58
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.57
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.56
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.56
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.55
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.53
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.53
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.51
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.5
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.48
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.48
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.45
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.45
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.45
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.44
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.41
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.38
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.38
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.36
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.36
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.33
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.29
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.28
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.28
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.26
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.24
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.22
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.18
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.18
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.16
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.16
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.15
KOG0553	304	consensus TPR repeat-containing protein [General f	98.14
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.11
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.11
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.11
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.1
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.1
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	98.09
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.06
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.06
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	98.05
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.05
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.03
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.02
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	98.01
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.01
PF12688	120	TPR_5: Tetratrico peptide repeat	98.0
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.99
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.98
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.96
KOG0553	304	consensus TPR repeat-containing protein [General f	97.95
PF12688	120	TPR_5: Tetratrico peptide repeat	97.94
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.94
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.9
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.89
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.87
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.85
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.84
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.83
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.82
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.82
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.79
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.75
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.72
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.7
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.7
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.69
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.69
PRK10803	263	tol-pal system protein YbgF; Provisional	97.6
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.59
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.56
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.52
PRK15331	165	chaperone protein SicA; Provisional	97.51
PRK10803	263	tol-pal system protein YbgF; Provisional	97.49
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.47
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.41
PF13371	73	TPR_9: Tetratricopeptide repeat	97.36
PF13371	73	TPR_9: Tetratricopeptide repeat	97.36
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.35
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.32
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.32
PRK15331	165	chaperone protein SicA; Provisional	97.3
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.28
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.28
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.27
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	97.24
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.16
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.12
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.1
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.08
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.02
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.98
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	96.95
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.93
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.81
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.77
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.68
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.65
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.65
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.62
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.62
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.59
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.57
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.56
PF13428	44	TPR_14: Tetratricopeptide repeat	96.48
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.45
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.45
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.45
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.44
PF13512	142	TPR_18: Tetratricopeptide repeat	96.39
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.37
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.36
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.35
PF13512	142	TPR_18: Tetratricopeptide repeat	96.33
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.26
KOG1585	308	consensus Protein required for fusion of vesicles	96.22
KOG1585	308	consensus Protein required for fusion of vesicles	96.15
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.09
KOG3941	406	consensus Intermediate in Toll signal transduction	95.98
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.96
KOG3941	406	consensus Intermediate in Toll signal transduction	95.96
PF13428	44	TPR_14: Tetratricopeptide repeat	95.95
KOG1550	552	consensus Extracellular protein SEL-1 and related	95.94
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.92
KOG4555	175	consensus TPR repeat-containing protein [Function	95.88
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.85
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.82
KOG4555	175	consensus TPR repeat-containing protein [Function	95.76
COG4105	254	ComL DNA uptake lipoprotein [General function pred	95.74
PRK11906	458	transcriptional regulator; Provisional	95.73
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.71
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.63
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.59
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.56
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.52
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.5
PRK11906	458	transcriptional regulator; Provisional	95.42
COG1747	711	Uncharacterized N-terminal domain of the transcrip	95.33
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.28
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.27
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.19
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.19
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.18
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.16
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.13
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.12
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.01
KOG1550	552	consensus Extracellular protein SEL-1 and related	95.01
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	94.98
PF13431	34	TPR_17: Tetratricopeptide repeat	94.9
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.86
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	94.8
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.63
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.59
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.46
COG0457	291	NrfG FOG: TPR repeat [General function prediction	94.42
COG0457	291	NrfG FOG: TPR repeat [General function prediction	94.4
PF13431	34	TPR_17: Tetratricopeptide repeat	94.36
KOG4570	418	consensus Uncharacterized conserved protein [Funct	94.19
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	94.05
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.97
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	93.91
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	93.9
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.86
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	93.85
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.81
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.44
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	93.4
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.23
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.23
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	93.2
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	92.87
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	92.82
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	92.65
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	92.61
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.57
KOG4648	536	consensus Uncharacterized conserved protein, conta	92.38
PRK11619	644	lytic murein transglycosylase; Provisional	92.36
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	92.36
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	92.14
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	91.93
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	91.82
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	91.8
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	91.78
KOG4234	271	consensus TPR repeat-containing protein [General f	91.67
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	91.31
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	91.31
KOG1258	577	consensus mRNA processing protein [RNA processing	91.26
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	91.23
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	90.99
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	90.9
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	90.75
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.6
PF13929	292	mRNA_stabil: mRNA stabilisation	90.52
COG1747	711	Uncharacterized N-terminal domain of the transcrip	90.32
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.3
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.2
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.03
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	90.0
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	89.82
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	89.56
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	89.45
KOG4234	271	consensus TPR repeat-containing protein [General f	89.42
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	89.19
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	89.15
KOG4648	536	consensus Uncharacterized conserved protein, conta	88.95
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	88.85
COG4455	273	ImpE Protein of avirulence locus involved in tempe	88.48
COG4455	273	ImpE Protein of avirulence locus involved in tempe	88.38
PF13929	292	mRNA_stabil: mRNA stabilisation	88.06
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	87.44
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	87.41
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	87.37
PRK09687	280	putative lyase; Provisional	87.09
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	86.42
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	86.27
COG3947	361	Response regulator containing CheY-like receiver a	86.25
PF07575	566	Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR0	85.89
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	85.51
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	84.58
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	84.32
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	84.32
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	84.28
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	83.21
KOG4507	886	consensus Uncharacterized conserved protein, conta	82.71
COG5159	421	RPN6 26S proteasome regulatory complex component [	82.68
PRK09687	280	putative lyase; Provisional	82.29
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	81.79
KOG0687	393	consensus 26S proteasome regulatory complex, subun	81.12

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.7e-59  Score=415.25  Aligned_cols=335  Identities=21%  Similarity=0.347  Sum_probs=296.2

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ++|+.|.+.|.. |+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|+.|.+.
T Consensus       458 ~lf~~M~~~Gl~-pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~  536 (1060)
T PLN03218        458 RVLRLVQEAGLK-ADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK  536 (1060)
T ss_pred             HHHHHHHHcCCC-CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            578888888887 8888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHh--cCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccc
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRA--FGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      |+.||..+|+.++.+|++.|++++|.++|++|..  .|+.||..+|+.++.+|++.|++++|.++|+.|.+.+      +
T Consensus       537 Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~g------i  610 (1060)
T PLN03218        537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYN------I  610 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC------C
Confidence            8888888888888888888888888888888876  5678888888888888888888888888888888887      7


Q ss_pred             cCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          160 KPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVI  239 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  239 (343)
                      +|+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++++.|.+.|+.|+..+|+.+
T Consensus       611 ~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsL  690 (1060)
T PLN03218        611 KGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSL  690 (1060)
T ss_pred             CCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            88888889999999989999999999988888888888888999999888888999999999988888888888889999


Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCCh
Q 040261          240 MNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEI  319 (343)
Q Consensus       240 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  319 (343)
                      +.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|.+.|++
T Consensus       691 I~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~l  770 (1060)
T PLN03218        691 MGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDA  770 (1060)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCH
Confidence            99999999999999999888888888888889999999999999999999999888888888999999999889888999


Q ss_pred             HHHHHHHHHHHhCCCCCCccccCC
Q 040261          320 EGALSLYSEMLSKGIRPTVVTYNT  343 (343)
Q Consensus       320 ~~a~~~~~~~~~~~~~p~~~t~~~  343 (343)
                      ++|.+++++|.+.|+.||..+|++
T Consensus       771 e~A~~l~~~M~k~Gi~pd~~tyns  794 (1060)
T PLN03218        771 DVGLDLLSQAKEDGIKPNLVMCRC  794 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHH
Confidence            999999999988888888888763

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=8.7e-59  Score=411.99  Aligned_cols=325  Identities=25%  Similarity=0.432  Sum_probs=316.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      |+..+|+.++.+|++.|++++|.++|+.|.+.|+.||..+|+.++.+|++.|+++.|.++|++|.+.|+.||..+|+.+|
T Consensus       435 pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI  514 (1060)
T PLN03218        435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI  514 (1060)
T ss_pred             CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      .+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|...+..    +.|+..+|+.++.+|+
T Consensus       515 ~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~g----i~PD~vTynaLI~ay~  590 (1060)
T PLN03218        515 DGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHP----IDPDHITVGALMKACA  590 (1060)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCC----CCCcHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999863211    6899999999999999


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      +.|++++|.++|+.|.+.|+.|+..+|+.++.+|++.|++++|..+|++|.+.|+.||..+|+.++.+|++.|++++|.+
T Consensus       591 k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~  670 (1060)
T PLN03218        591 NAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFE  670 (1060)
T ss_pred             HCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 040261          255 LLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  334 (343)
                      ++++|.+.|++|+..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|...|+
T Consensus       671 l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi  750 (1060)
T PLN03218        671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGL  750 (1060)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCccccCC
Q 040261          335 RPTVVTYNT  343 (343)
Q Consensus       335 ~p~~~t~~~  343 (343)
                      .||..||++
T Consensus       751 ~Pd~~Ty~s  759 (1060)
T PLN03218        751 CPNTITYSI  759 (1060)
T ss_pred             CCCHHHHHH
Confidence            999999863

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

Probab=100.00  E-value=1.8e-52  Score=368.46  Aligned_cols=324  Identities=20%  Similarity=0.344  Sum_probs=255.5

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ++|++|...++.+|+..+|+.++.++.+.++++.+.+++..|.+.|+.||..+|+.++.+|++.|+++.|.++|++|.  
T Consensus       108 ~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~--  185 (697)
T PLN03081        108 ELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMP--  185 (697)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCC--
Confidence            577777776655577778888888888888888888888888887877888888888888888888888888887774  


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHH-----------------------------------HH
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFT-----------------------------------YT  126 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----------------------------------~~  126 (343)
                        .||..+|+.++.+|++.|++++|+++|++|.+.|+.|+..+                                   ++
T Consensus       186 --~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n  263 (697)
T PLN03081        186 --ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSC  263 (697)
T ss_pred             --CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHH
Confidence              36777788888888888888888888887776666665554                                   45


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHH
Q 040261          127 TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIR  206 (343)
Q Consensus       127 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  206 (343)
                      .++.+|++.|++++|.++|+.|.          .++..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.++.
T Consensus       264 ~Li~~y~k~g~~~~A~~vf~~m~----------~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~  333 (697)
T PLN03081        264 ALIDMYSKCGDIEDARCVFDGMP----------EKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIR  333 (697)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCC----------CCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            66677777777777777777763          34677788888888888888888888888877788888888888888


Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHH
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNR  286 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  286 (343)
                      +|++.|++++|.+++..|.+.|+.|+..+|+.|+.+|++.|++++|.++|++|.    .||..+|+.++.+|++.|+.++
T Consensus       334 a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d~~t~n~lI~~y~~~G~~~~  409 (697)
T PLN03081        334 IFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTK  409 (697)
T ss_pred             HHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCCeeeHHHHHHHHHHcCCHHH
Confidence            888888888888888888888888888888888888888888888888888774    4677788888888888888888


Q ss_pred             HHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh-CCCCCCccccCC
Q 040261          287 AKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS-KGIRPTVVTYNT  343 (343)
Q Consensus       287 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~p~~~t~~~  343 (343)
                      |.++|++|.+.|+.||..||+.++.+|.+.|+.++|.++|+.|.+ .|+.|+..+|++
T Consensus       410 A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~  467 (697)
T PLN03081        410 AVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYAC  467 (697)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHh
Confidence            888888888888888888888888888888888888888888875 488888888764

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

Probab=100.00  E-value=8.4e-52  Score=364.28  Aligned_cols=320  Identities=17%  Similarity=0.280  Sum_probs=275.8

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +++..|.+.|.. |+..+|+.++..|++.|++++|.++|++|.+    ||..+|+.++.+|++.|++++|.++|++|.+.
T Consensus       144 ~l~~~m~~~g~~-~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~----~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~  218 (697)
T PLN03081        144 AVYWHVESSGFE-PDQYMMNRVLLMHVKCGMLIDARRLFDEMPE----RNLASWGTIIGGLVDAGNYREAFALFREMWED  218 (697)
T ss_pred             HHHHHHHHhCCC-cchHHHHHHHHHHhcCCCHHHHHHHHhcCCC----CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence            355566666655 5566666666666666666666666666542    55556666666666666666666666665544


Q ss_pred             -----------------------------------CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHH
Q 040261           82 -----------------------------------CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYT  126 (343)
Q Consensus        82 -----------------------------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  126 (343)
                                                         |..||..+|+.++.+|++.|++++|.++|++|..    +|..+|+
T Consensus       219 g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n  294 (697)
T PLN03081        219 GSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWN  294 (697)
T ss_pred             CCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHH
Confidence                                               4455666778889999999999999999999964    5899999


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHH
Q 040261          127 TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIR  206 (343)
Q Consensus       127 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  206 (343)
                      .++.+|++.|+.++|.++|++|.+.+      +.||..+|+.++.+|++.|++++|.+++..|.+.|+.|+..+|+.++.
T Consensus       295 ~li~~y~~~g~~~eA~~lf~~M~~~g------~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~  368 (697)
T PLN03081        295 SMLAGYALHGYSEEALCLYYEMRDSG------VSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVD  368 (697)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHH
Confidence            99999999999999999999999988      899999999999999999999999999999999999999999999999


Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHH
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNR  286 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  286 (343)
                      +|++.|++++|.++|++|.    .||..+|+.++.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|++++
T Consensus       369 ~y~k~G~~~~A~~vf~~m~----~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~  444 (697)
T PLN03081        369 LYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ  444 (697)
T ss_pred             HHHHCCCHHHHHHHHHhCC----CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHH
Confidence            9999999999999999985    478999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHh-CCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCccccCC
Q 040261          287 AKELFVSMES-NGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT  343 (343)
Q Consensus       287 a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~t~~~  343 (343)
                      |.++|+.|.+ .|+.|+..+|+.++++|.+.|++++|.+++++|   ++.|+..+|++
T Consensus       445 a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~  499 (697)
T PLN03081        445 GWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRA---PFKPTVNMWAA  499 (697)
T ss_pred             HHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHC---CCCCCHHHHHH
Confidence            9999999986 699999999999999999999999999999876   68899998864

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.1e-50  Score=361.50  Aligned_cols=314  Identities=22%  Similarity=0.300  Sum_probs=189.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      +++.+|+.++..|++.|++++|.++|++|..    ||..+|+.++.+|++.|++++|+++|.+|.+.|+.||..+|+.++
T Consensus       220 ~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~----~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll  295 (857)
T PLN03077        220 LDVDVVNALITMYVKCGDVVSARLVFDRMPR----RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVI  295 (857)
T ss_pred             cccchHhHHHHHHhcCCCHHHHHHHHhcCCC----CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHH
Confidence            4444555566666666666666666666542    455666666666666666666666666666666666666666666


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      .+|.+.|+.+.+.+++..|.+.|+.||..+|+.++.+|++.|++++|.++|++|.          .|+..+|+.++.+|.
T Consensus       296 ~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----------~~d~~s~n~li~~~~  365 (857)
T PLN03077        296 SACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME----------TKDAVSWTAMISGYE  365 (857)
T ss_pred             HHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC----------CCCeeeHHHHHHHHH
Confidence            6666666666666666666666666666666666666666666666666666653          244556666666666


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      +.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++++.+.+.|+.|+..+|+.|+.+|++.|++++|.+
T Consensus       366 ~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~  445 (857)
T PLN03077        366 KNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALE  445 (857)
T ss_pred             hCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHH
Confidence            66666666666666666666666666666666666666666666666666666655555555555555555555555555


Q ss_pred             HHHHHHHc------------------------------CCCC--------------------------------------
Q 040261          255 LLELMIQI------------------------------GVRP--------------------------------------  266 (343)
Q Consensus       255 ~~~~~~~~------------------------------~~~~--------------------------------------  266 (343)
                      +|++|.+.                              +++|                                      
T Consensus       446 vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~  525 (857)
T PLN03077        446 VFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGF  525 (857)
T ss_pred             HHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccce
Confidence            55443221                              1233                                      


Q ss_pred             ---------------------------CHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCCh
Q 040261          267 ---------------------------DASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEI  319 (343)
Q Consensus       267 ---------------------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  319 (343)
                                                 |..+|+.++.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|++
T Consensus       526 ~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v  605 (857)
T PLN03077        526 LPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMV  605 (857)
T ss_pred             echHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChH
Confidence                                       33445555555555666666666666666666666666666666666666666


Q ss_pred             HHHHHHHHHHH-hCCCCCCccccC
Q 040261          320 EGALSLYSEML-SKGIRPTVVTYN  342 (343)
Q Consensus       320 ~~a~~~~~~~~-~~~~~p~~~t~~  342 (343)
                      ++|.++|++|. ..|+.|+..+|+
T Consensus       606 ~ea~~~f~~M~~~~gi~P~~~~y~  629 (857)
T PLN03077        606 TQGLEYFHSMEEKYSITPNLKHYA  629 (857)
T ss_pred             HHHHHHHHHHHHHhCCCCchHHHH
Confidence            66666666665 446666655554

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.4e-50  Score=361.32  Aligned_cols=315  Identities=24%  Similarity=0.421  Sum_probs=264.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHH-----------------------------------HHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTY-----------------------------------NILI   59 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----------------------------------~~l~   59 (343)
                      ++..+|+.++.+|++.|++++|+++|++|...|+.||..+|                                   +.++
T Consensus       150 ~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li  229 (857)
T PLN03077        150 RDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALI  229 (857)
T ss_pred             CCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHH
Confidence            45556666666666666666666666666655555555554                                   5566


Q ss_pred             HHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH
Q 040261           60 NCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI  139 (343)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  139 (343)
                      .+|++.|+++.|.++|++|.    .||..+|+.++.+|++.|++++|+++|++|.+.|+.||..+|+.++.+|.+.|+.+
T Consensus       230 ~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~  305 (857)
T PLN03077        230 TMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDER  305 (857)
T ss_pred             HHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChH
Confidence            66666677777777777664    35777888888888888888888888888888888889999999999999999999


Q ss_pred             HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHH
Q 040261          140 VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKC  219 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  219 (343)
                      .+.+++..+.+.+      ..|+..+|+.++.+|++.|++++|.++|+.|..    ||..+|+.++.+|++.|++++|..
T Consensus       306 ~a~~l~~~~~~~g------~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s~n~li~~~~~~g~~~~A~~  375 (857)
T PLN03077        306 LGREMHGYVVKTG------FAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMISGYEKNGLPDKALE  375 (857)
T ss_pred             HHHHHHHHHHHhC------CccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeeeHHHHHHHHHhCCCHHHHHH
Confidence            9999998888887      789999999999999999999999999999864    688899999999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC-
Q 040261          220 LFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG-  298 (343)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-  298 (343)
                      +|++|.+.|+.||..+|+.++.+|++.|+++.|.++++.+.+.|+.|+..+++.|+.+|++.|++++|.++|++|.+.+ 
T Consensus       376 lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~  455 (857)
T PLN03077        376 TYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDV  455 (857)
T ss_pred             HHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCe
Confidence            9999999999999999999999999999999999999999999999999999999999999999999988887764421 


Q ss_pred             -----------------------------C--------------------------------------------------
Q 040261          299 -----------------------------C--------------------------------------------------  299 (343)
Q Consensus       299 -----------------------------~--------------------------------------------------  299 (343)
                                                   +                                                  
T Consensus       456 vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~  535 (857)
T PLN03077        456 ISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYV  535 (857)
T ss_pred             eeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHH
Confidence                                         1                                                  


Q ss_pred             ---------------CccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCccccCC
Q 040261          300 ---------------MRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT  343 (343)
Q Consensus       300 ---------------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~t~~~  343 (343)
                                     .||..+|+.++.+|.+.|+.++|.++|++|.+.|+.||.+||++
T Consensus       536 k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~  594 (857)
T PLN03077        536 RCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFIS  594 (857)
T ss_pred             HcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHH
Confidence                           35666788888999999999999999999999999999999863

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.96  E-value=7.2e-25  Score=182.25  Aligned_cols=309  Identities=14%  Similarity=0.074  Sum_probs=254.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc---HHHHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD---AVTFTSLIK   95 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~   95 (343)
                      ........+...|++++|...|+++.+.+ +.+..++..+...+...|++++|..+++.+......++   ...+..+..
T Consensus        37 ~~y~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~  115 (389)
T PRK11788         37 RDYFKGLNFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQ  115 (389)
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            34444556778899999999999999865 44667899999999999999999999999987532222   356788899


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC---cchHHHHHHH
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD---AITYSTITDG  172 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~  172 (343)
                      .+.+.|++++|.++|+++.+.. +.+..++..++..+.+.|++++|.+.++.+.+.++.     ++.   ...+..+...
T Consensus       116 ~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-----~~~~~~~~~~~~la~~  189 (389)
T PRK11788        116 DYLKAGLLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGD-----SLRVEIAHFYCELAQQ  189 (389)
T ss_pred             HHHHCCCHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCC-----cchHHHHHHHHHHHHH
Confidence            9999999999999999998763 346778999999999999999999999999876521     111   1245667778


Q ss_pred             HHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHH
Q 040261          173 LCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEA  252 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  252 (343)
                      +.+.|++++|...++++.+.. +.+...+..+...+.+.|++++|..+++++.+.+......++..++.++...|++++|
T Consensus       190 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A  268 (389)
T PRK11788        190 ALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEG  268 (389)
T ss_pred             HHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHH
Confidence            899999999999999998764 3356678888899999999999999999999864222346788899999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh---cCChHHHHHHHHHH
Q 040261          253 SRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK---NKEIEGALSLYSEM  329 (343)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~  329 (343)
                      ...++++.+.  .|+...+..++..+.+.|++++|..+++++.+.  .|+...+..++..+..   .|+.++++.++++|
T Consensus       269 ~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~  344 (389)
T PRK11788        269 LEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDL  344 (389)
T ss_pred             HHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHH
Confidence            9999999886  456667788999999999999999999998876  5888889888887664   56899999999999


Q ss_pred             HhCCCCCCcc
Q 040261          330 LSKGIRPTVV  339 (343)
Q Consensus       330 ~~~~~~p~~~  339 (343)
                      .++++.|+..
T Consensus       345 ~~~~~~~~p~  354 (389)
T PRK11788        345 VGEQLKRKPR  354 (389)
T ss_pred             HHHHHhCCCC
Confidence            9988777654

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

Probab=99.95  E-value=1.1e-23  Score=193.97  Aligned_cols=312  Identities=12%  Similarity=0.048  Sum_probs=176.5

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      +|+.+...++  .+...+..++..+.+.|++++|..+++.+.+.. +.+...|..+..++...|++++|...++++.+..
T Consensus       555 ~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  631 (899)
T TIGR02917       555 WLEKAAELNP--QEIEPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ  631 (899)
T ss_pred             HHHHHHHhCc--cchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            4455544444  355566666666666667777766666665533 3455566666666666666666666666666543


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                       +.+...+..+..++.+.|++++|...++++.+.... +..++..+...+...|++++|.++++.+....       +.+
T Consensus       632 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------~~~  702 (899)
T TIGR02917       632 -PDSALALLLLADAYAVMKNYAKAITSLKRALELKPD-NTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-------PKA  702 (899)
T ss_pred             -CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-------cCC
Confidence             224555666666666666666666666666654322 45556666666666666666666666665543       334


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      ...+..+...+...|++++|...++.+...+  |+..++..+..++.+.|++++|...++.+.+.. +.+...+..+...
T Consensus       703 ~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~  779 (899)
T TIGR02917       703 ALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAEL  779 (899)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            4455555556666666666666666655543  333445555555555666666666665555542 3345555555555


Q ss_pred             HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHH
Q 040261          243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGA  322 (343)
Q Consensus       243 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  322 (343)
                      +...|++++|...|+++.+.. +.+..++..+...+...|+ .+|...++++.+.. +.++..+..+...+...|++++|
T Consensus       780 ~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A  856 (899)
T TIGR02917       780 YLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA-PNIPAILDTLGWLLVEKGEADRA  856 (899)
T ss_pred             HHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHH
Confidence            555666666666665555543 3445555555555555555 44555555554432 22334444455555555555555


Q ss_pred             HHHHHHHHhC
Q 040261          323 LSLYSEMLSK  332 (343)
Q Consensus       323 ~~~~~~~~~~  332 (343)
                      .+.++++++.
T Consensus       857 ~~~~~~a~~~  866 (899)
T TIGR02917       857 LPLLRKAVNI  866 (899)
T ss_pred             HHHHHHHHhh
Confidence            5555555544

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=99.95  E-value=2.7e-23  Score=191.29  Aligned_cols=299  Identities=14%  Similarity=0.087  Sum_probs=171.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...|..+..++.+.|++++|...|+++.+.. +.+...+..+..++.+.|++++|..+++++.+.. +.+..++..+..
T Consensus       600 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  677 (899)
T TIGR02917       600 SPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQ  677 (899)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            55556666666666666666666666655433 2344455555566666666666666666665543 224555555666


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+...|++++|.++++.+.+.+. .+...+..+...+...|++++|.+.++++....        |+..++..+..++.+
T Consensus       678 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--------~~~~~~~~l~~~~~~  748 (899)
T TIGR02917       678 LLLAAKRTESAKKIAKSLQKQHP-KAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--------PSSQNAIKLHRALLA  748 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCc-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--------CCchHHHHHHHHHHH
Confidence            66666666666666666655532 244455555556666666666666666655543        333455555566666


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      .|++++|.+.++.+.+.. +.+...+..+...|...|++++|..+++++.+.. +.+...+..+...+...|+ .+|+.+
T Consensus       749 ~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~  825 (899)
T TIGR02917       749 SGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEY  825 (899)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHH
Confidence            666666666666655543 3345555555666666666666666666665553 3445555566666666666 556666


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          256 LELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      ++++.+.. +-+..++..+...+...|++++|...++++.+.+. .+..++..+..++.+.|++++|.+++++|+
T Consensus       826 ~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       826 AEKALKLA-PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAP-EAAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             HHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            66655543 33344555555556666666666666666665542 255556666666666666666666666554

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=99.94  E-value=1.3e-23  Score=174.67  Aligned_cols=289  Identities=15%  Similarity=0.115  Sum_probs=241.0

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHH
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD---LYTYNILINCFCKMGRVSPGFVVLGRI   78 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~   78 (343)
                      +.|..+...+|  .+..++..+...+...|++++|..+++.+...+..++   ...+..+...+.+.|++++|..+|+++
T Consensus        56 ~~~~~al~~~p--~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~  133 (389)
T PRK11788         56 DLFIEMLKVDP--ETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQL  133 (389)
T ss_pred             HHHHHHHhcCc--ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            56788888765  4788999999999999999999999999987542221   246788899999999999999999999


Q ss_pred             HHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHHccCCC
Q 040261           79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV----FTYTTLINGLCRTGHTIVALNLFEEMANGNGE  154 (343)
Q Consensus        79 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  154 (343)
                      .+.. +.+..++..++..+.+.|++++|.+.++.+.+.+..+..    ..+..+...+.+.|++++|...++++.+..  
T Consensus       134 l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--  210 (389)
T PRK11788        134 VDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD--  210 (389)
T ss_pred             HcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC--
Confidence            8763 446788999999999999999999999999887544322    245567778899999999999999998864  


Q ss_pred             CCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHH
Q 040261          155 FGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVV  234 (343)
Q Consensus       155 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  234 (343)
                           +.+...+..+...+.+.|++++|.+.++++...+......+++.++.+|...|++++|...++.+.+.  .|+..
T Consensus       211 -----p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~  283 (389)
T PRK11788        211 -----PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--YPGAD  283 (389)
T ss_pred             -----cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCch
Confidence                 34456788888999999999999999999987643323466888999999999999999999999886  46666


Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc---CCchHHHHHHHHHHHhCCCCccHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL---TGRVNRAKELFVSMESNGCMRDVF  304 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~  304 (343)
                      .+..++..+.+.|++++|..+++++.+.  .|+...+..++..+..   .|+.+++..+++++.++++.|++.
T Consensus       284 ~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        284 LLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence            7788999999999999999999999886  6888888888877664   558999999999999877777665

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.92  E-value=7.7e-21  Score=165.81  Aligned_cols=313  Identities=11%  Similarity=0.020  Sum_probs=254.0

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      +++......|.  +...+..++.+....|++++|.+.++++.+.. |.+...+..+...+...|++++|...++++.+..
T Consensus        64 l~~~~l~~~p~--~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~  140 (656)
T PRK15174         64 LLSDRVLTAKN--GRDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAF  140 (656)
T ss_pred             HhHHHHHhCCC--chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            45555665664  66778888888889999999999999998865 4566788888999999999999999999999864


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                       +.+...+..+...+...|++++|...++.+...... +...+..+ ..+...|++++|...++.+....      ..++
T Consensus       141 -P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~-~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~------~~~~  211 (656)
T PRK15174        141 -SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPP-RGDMIATC-LSFLNKSRLPEDHDLARALLPFF------ALER  211 (656)
T ss_pred             -CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC-CHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcC------CCcc
Confidence             335778888999999999999999999988776443 33333333 34788999999999999987764      1233


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHH----HHHHHHHHHHcCCCCCHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNE----AKCLFIEMMDQGVQPNVVTFNV  238 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~  238 (343)
                      ......+..++...|++++|...++++.... +.+...+..+...+...|++++    |...+++..+.. +.+...+..
T Consensus       212 ~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~  289 (656)
T PRK15174        212 QESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTL  289 (656)
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHH
Confidence            4445556778889999999999999998765 3467788889999999999986    899999998863 445778889


Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH-HHHHHHHHHHHhcC
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV-FSYGILINGYCKNK  317 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~  317 (343)
                      +...+...|++++|...++++.+.. +.+...+..+..++.+.|++++|...++++.+..  |+. ..+..+..++...|
T Consensus       290 lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~--P~~~~~~~~~a~al~~~G  366 (656)
T PRK15174        290 YADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLAREK--GVTSKWNRYAAAALLQAG  366 (656)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHCC
Confidence            9999999999999999999999875 4566778888999999999999999999998763  544 33444567889999


Q ss_pred             ChHHHHHHHHHHHhC
Q 040261          318 EIEGALSLYSEMLSK  332 (343)
Q Consensus       318 ~~~~a~~~~~~~~~~  332 (343)
                      ++++|...|++..+.
T Consensus       367 ~~deA~~~l~~al~~  381 (656)
T PRK15174        367 KTSEAESVFEHYIQA  381 (656)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998865

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.90  E-value=1.4e-19  Score=157.93  Aligned_cols=300  Identities=10%  Similarity=0.031  Sum_probs=248.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      -...++..+.+.|++++|..+++...... +-+...+..++.+....|+++.|...++++....+ .+...+..+...+.
T Consensus        44 ~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P-~~~~a~~~la~~l~  121 (656)
T PRK15174         44 NIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNV-CQPEDVLLVASVLL  121 (656)
T ss_pred             CHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHH
Confidence            45566778889999999999999988765 34455666777788889999999999999998753 36778888899999


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      ..|++++|...+++....... +...+..+...+...|++++|...++.+....       +.+...+..+ ..+...|+
T Consensus       122 ~~g~~~~Ai~~l~~Al~l~P~-~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~-------P~~~~a~~~~-~~l~~~g~  192 (656)
T PRK15174        122 KSKQYATVADLAEQAWLAFSG-NSQIFALHLRTLVLMDKELQAISLARTQAQEV-------PPRGDMIATC-LSFLNKSR  192 (656)
T ss_pred             HcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-------CCCHHHHHHH-HHHHHcCC
Confidence            999999999999999987433 56788889999999999999999999887754       2233344333 34788999


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhH----HHH
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDE----ASR  254 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~  254 (343)
                      +++|...++.+.+....++...+..+..++...|++++|...++.+.+.. +.+...+..+...+...|++++    |..
T Consensus       193 ~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~  271 (656)
T PRK15174        193 LPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAE  271 (656)
T ss_pred             HHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHH
Confidence            99999999998776433445555666778889999999999999999874 4457778889999999999986    899


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          255 LLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .++++.+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+..++.+.|++++|...++++...
T Consensus       272 ~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~  347 (656)
T PRK15174        272 HWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLARE  347 (656)
T ss_pred             HHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            999999875 5567889999999999999999999999999864 335667788889999999999999999999865

>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=99.89  E-value=2.4e-18  Score=150.60  Aligned_cols=233  Identities=14%  Similarity=0.050  Sum_probs=139.0

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      .+..+...+...|++++|+..+++..+.... ....|..+..++...|++++|...++++.+..       +.+..++..
T Consensus       333 a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~-~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-------p~~~~~~~~  404 (615)
T TIGR00990       333 ALNLRGTFKCLKGKHLEALADLSKSIELDPR-VTQSYIKRASMNLELGDPDKAEEDFDKALKLN-------SEDPDIYYH  404 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHH
Confidence            3444444555556666666666666554221 24455556666666666666666666665543       334556666


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  248 (343)
                      +...+...|++++|...|++..+.. +.+...+..+..++.+.|++++|...++...+.. +.+...++.+..++...|+
T Consensus       405 lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~  482 (615)
T TIGR00990       405 RAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNK  482 (615)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccC
Confidence            6666666777777777776666543 2245555566666667777777777777666542 3345666666777777777


Q ss_pred             hhHHHHHHHHHHHcCCCCCH------HHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHH
Q 040261          249 MDEASRLLELMIQIGVRPDA------SVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGA  322 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  322 (343)
                      +++|...|++..+.....+.      ..++.....+...|++++|..++++..+.. +.+...+..+...+.+.|++++|
T Consensus       483 ~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eA  561 (615)
T TIGR00990       483 FDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEA  561 (615)
T ss_pred             HHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHH
Confidence            77777777776664311111      011112222334577777777777766543 23344667777778888888888


Q ss_pred             HHHHHHHHhC
Q 040261          323 LSLYSEMLSK  332 (343)
Q Consensus       323 ~~~~~~~~~~  332 (343)
                      ++.|++..+.
T Consensus       562 i~~~e~A~~l  571 (615)
T TIGR00990       562 LKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHH
Confidence            8888777643

>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=99.88  E-value=4.5e-18  Score=148.92  Aligned_cols=304  Identities=12%  Similarity=0.002  Sum_probs=242.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      .+......+.+.|++++|+..|++.++.  .|+...|..+..+|.+.|++++|++.+++.++... .+...+..+..++.
T Consensus       129 ~~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p-~~~~a~~~~a~a~~  205 (615)
T TIGR00990       129 KLKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDP-DYSKALNRRANAYD  205 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHH
Confidence            4667788999999999999999998874  57888899999999999999999999999998753 35778888999999


Q ss_pred             hcCcHHHHHHHHHHHHhcCCC----------------------------CC-HHHHHHH---------------------
Q 040261           99 AESRIMEAAALFTKLRAFGCK----------------------------PD-VFTYTTL---------------------  128 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~----------------------------~~-~~~~~~l---------------------  128 (343)
                      ..|++++|+..+......+..                            |. ...+..+                     
T Consensus       206 ~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (615)
T TIGR00990       206 GLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNE  285 (615)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccc
Confidence            999999998766544322100                            00 0000000                     


Q ss_pred             ---------HHHH------HhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          129 ---------INGL------CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       129 ---------~~~~------~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                               +...      ...+++++|.+.|+.....+..    .+.....+..+...+...|++++|+..+++..+..
T Consensus       286 ~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~----~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~  361 (615)
T TIGR00990       286 LDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKL----GEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD  361 (615)
T ss_pred             cccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCC----ChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence                     0000      1125788899999998875410    12345678888888999999999999999998764


Q ss_pred             CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          194 INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNT  273 (343)
Q Consensus       194 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  273 (343)
                       +.....|..+..++...|++++|...++.+.+.. +.+...+..+...+...|++++|...|++.++.. +.+...+..
T Consensus       362 -P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~  438 (615)
T TIGR00990       362 -PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQ  438 (615)
T ss_pred             -CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHH
Confidence             2246688888899999999999999999998874 4457888899999999999999999999999875 556778888


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      +...+.+.|++++|...+++..+.. +.+...++.+...+...|++++|++.|++.+...
T Consensus       439 la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~  497 (615)
T TIGR00990       439 LGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELE  497 (615)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            9999999999999999999988753 4467889999999999999999999999988653

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

Probab=99.87  E-value=2.8e-19  Score=144.99  Aligned_cols=301  Identities=18%  Similarity=0.190  Sum_probs=178.3

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           13 SPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        13 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      .|.-.++|..+...+-..|++++|+.+++.+++.. +..+..|..+..++...|+.+.|.+.|...++.  .|+.....+
T Consensus       112 ~~q~ae~ysn~aN~~kerg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s  188 (966)
T KOG4626|consen  112 NPQGAEAYSNLANILKERGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARS  188 (966)
T ss_pred             cchHHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--Ccchhhhhc
Confidence            34567899999999999999999999999999865 346778999999999999999999999988875  444433222


Q ss_pred             -HHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHH
Q 040261           93 -LIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITD  171 (343)
Q Consensus        93 -l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  171 (343)
                       +...+...|+.++|...|.+.++.... =...|+.|...+...|+...|++.|++..+.+       +.-...|..|..
T Consensus       189 ~lgnLlka~Grl~ea~~cYlkAi~~qp~-fAiawsnLg~~f~~~Gei~~aiq~y~eAvkld-------P~f~dAYiNLGn  260 (966)
T KOG4626|consen  189 DLGNLLKAEGRLEEAKACYLKAIETQPC-FAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLD-------PNFLDAYINLGN  260 (966)
T ss_pred             chhHHHHhhcccchhHHHHHHHHhhCCc-eeeeehhcchHHhhcchHHHHHHHHHHhhcCC-------CcchHHHhhHHH
Confidence             333334456777777777666654221 23456666666666666666666666666654       222445666666


Q ss_pred             HHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChh
Q 040261          172 GLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMD  250 (343)
Q Consensus       172 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~  250 (343)
                      .|...+.++.|...+.+..... +.....+..+...|...|..+-|++.+++.++.  .|+ ...|+.|..++...|+..
T Consensus       261 V~ke~~~~d~Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~  337 (966)
T KOG4626|consen  261 VYKEARIFDRAVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVT  337 (966)
T ss_pred             HHHHHhcchHHHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchH
Confidence            6666666666665555544431 112344444444555555555555555555543  233 445555555555555555


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc-HHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          251 EASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD-VFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       251 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      +|.+.+.+..... +-.....+.|...|...|.+++|.++|....+-  .|. ...++.|...|-+.|+.++|+.-|++.
T Consensus       338 ea~~cYnkaL~l~-p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykea  414 (966)
T KOG4626|consen  338 EAVDCYNKALRLC-PNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEA  414 (966)
T ss_pred             HHHHHHHHHHHhC-CccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHH
Confidence            5555555555442 223344444555555555555555555544442  122 233444445555555555555555544


Q ss_pred             H
Q 040261          330 L  330 (343)
Q Consensus       330 ~  330 (343)
                      +
T Consensus       415 l  415 (966)
T KOG4626|consen  415 L  415 (966)
T ss_pred             H
Confidence            4

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.87  E-value=1.2e-17  Score=155.53  Aligned_cols=301  Identities=13%  Similarity=0.070  Sum_probs=208.0

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH-----------
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS-----------   92 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-----------   92 (343)
                      ...+.+.|++++|...|+++.+.. +.+...+..+..++...|++++|.+.|+++.+.... +...+..           
T Consensus       358 g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~~~~~~  435 (1157)
T PRK11447        358 GDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYRQQSPE  435 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCHH
Confidence            445677888888888888887754 345667777788888888888888888888765322 2322222           


Q ss_pred             -------------------------------HHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHH
Q 040261           93 -------------------------------LIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVA  141 (343)
Q Consensus        93 -------------------------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  141 (343)
                                                     +...+...|++++|++.+++..+..+. +...+..+...|.+.|++++|
T Consensus       436 ~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~-~~~~~~~LA~~~~~~G~~~~A  514 (1157)
T PRK11447        436 KALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPG-SVWLTYRLAQDLRQAGQRSQA  514 (1157)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHH
Confidence                                           233345678888888888888877543 566777788888999999999


Q ss_pred             HHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC-----------------------------
Q 040261          142 LNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE-----------------------------  192 (343)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----------------------------  192 (343)
                      ...++++....       +.+...+..+...+...++.++|+..++.+...                             
T Consensus       515 ~~~l~~al~~~-------P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G  587 (1157)
T PRK11447        515 DALMRRLAQQK-------PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSG  587 (1157)
T ss_pred             HHHHHHHHHcC-------CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCC
Confidence            99998887654       223333333333333444444444443332110                             


Q ss_pred             ----------CCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          193 ----------NINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       193 ----------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                                ..+.+...+..+...+.+.|++++|...++.+.+.. +.+...+..++..+...|++++|...++.+.+.
T Consensus       588 ~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~  666 (1157)
T PRK11447        588 KEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPAT  666 (1157)
T ss_pred             CHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence                      123445566677788888899999999999888863 445777888888898999999999999887765


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCC--c---cHHHHHHHHHHHHhcCChHHHHHHHHHHHh-CCCCC
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM--R---DVFSYGILINGYCKNKEIEGALSLYSEMLS-KGIRP  336 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~p  336 (343)
                      . +.+...+..+..++...|++++|.++++++......  |   +...+..+...+...|++++|+..|++.+. .|+.|
T Consensus       667 ~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~  745 (1157)
T PRK11447        667 A-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITP  745 (1157)
T ss_pred             C-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCC
Confidence            3 345566677778888899999999999988765311  1   224555567788888999999999988864 24544

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.87  E-value=1.1e-17  Score=155.84  Aligned_cols=317  Identities=9%  Similarity=0.031  Sum_probs=227.0

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC-CHHHH------------HHHHHHHHhcCCc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP-DLYTY------------NILINCFCKMGRV   68 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~------------~~l~~~~~~~~~~   68 (343)
                      ..|+...+..|  .+..++..+..++.+.|++++|+..|++..+..... +...+            ......+.+.|++
T Consensus       290 ~~l~~aL~~~P--~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~  367 (1157)
T PRK11447        290 PELQQAVRANP--KDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNL  367 (1157)
T ss_pred             HHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCH
Confidence            35666666665  478889999999999999999999999987754211 11111            1224456788999


Q ss_pred             chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHH--------------------
Q 040261           69 SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL--------------------  128 (343)
Q Consensus        69 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------------  128 (343)
                      ++|...|+++.+... .+...+..+...+...|++++|++.|++..+.... +...+..+                    
T Consensus       368 ~eA~~~~~~Al~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~~~~~~~A~~~l~~l~  445 (1157)
T PRK11447        368 AQAERLYQQARQVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYRQQSPEKALAFIASLS  445 (1157)
T ss_pred             HHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCHHHHHHHHHhCC
Confidence            999999999988753 35667778889999999999999999998876432 23333222                    


Q ss_pred             ----------------------HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHH
Q 040261          129 ----------------------INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELF  186 (343)
Q Consensus       129 ----------------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  186 (343)
                                            ...+...|++++|.+.+++..+..       +.+...+..+...|.+.|++++|...+
T Consensus       446 ~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-------P~~~~~~~~LA~~~~~~G~~~~A~~~l  518 (1157)
T PRK11447        446 ASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-------PGSVWLTYRLAQDLRQAGQRSQADALM  518 (1157)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence                                  233456788888888888888764       345667777888888999999999999


Q ss_pred             HHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---------------------------------------
Q 040261          187 LKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---------------------------------------  227 (343)
Q Consensus       187 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------------------------------------  227 (343)
                      +++.+.. +.+...+..+...+...++.++|...++.+...                                       
T Consensus       519 ~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~  597 (1157)
T PRK11447        519 RRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLR  597 (1157)
T ss_pred             HHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHH
Confidence            8887643 223333333333333444444444443322100                                       


Q ss_pred             CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHH
Q 040261          228 GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYG  307 (343)
Q Consensus       228 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  307 (343)
                      ..+.+...+..+...+.+.|++++|+..|+++.+.. +.+...+..++..+...|++++|.+.++.+.+.. +.+...+.
T Consensus       598 ~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~-p~~~~~~~  675 (1157)
T PRK11447        598 QQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPATA-NDSLNTQR  675 (1157)
T ss_pred             hCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccC-CCChHHHH
Confidence            123445566778888889999999999999998875 5578888999999999999999999999887652 23456677


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          308 ILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       308 ~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .+..++...|++++|.+++++++..
T Consensus       676 ~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        676 RVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            7888888999999999999998865

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

Probab=99.86  E-value=1.1e-18  Score=141.68  Aligned_cols=317  Identities=15%  Similarity=0.177  Sum_probs=216.6

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHH-HHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYT-YNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      ..++.+.+..|  ..++.|-.+..++...|+.+.|.+.|...++.+  |+... ...+...+-..|+..+|...|.+.++
T Consensus       137 ~~y~~aiel~p--~fida~inla~al~~~~~~~~a~~~~~~alqln--P~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~  212 (966)
T KOG4626|consen  137 ALYRAAIELKP--KFIDAYINLAAALVTQGDLELAVQCFFEALQLN--PDLYCARSDLGNLLKAEGRLEEAKACYLKAIE  212 (966)
T ss_pred             HHHHHHHhcCc--hhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcC--cchhhhhcchhHHHHhhcccchhHHHHHHHHh
Confidence            34556666555  488899999999999999999999888877743  54432 22233344445666666666555554


Q ss_pred             cCC--------------------------------Ccc-HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           81 SCF--------------------------------TPD-AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        81 ~~~--------------------------------~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      ...                                .|+ ...|-.|...|...+.+++|+..|.+....... ....+..
T Consensus       213 ~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lrpn-~A~a~gN  291 (966)
T KOG4626|consen  213 TQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNLRPN-HAVAHGN  291 (966)
T ss_pred             hCCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhcCCc-chhhccc
Confidence            321                                122 233444444444444445555444444433111 2334444


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHH
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG  207 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  207 (343)
                      +...|...|.++.|+..+++..+..       +.-...|+.|..++-..|++.+|.+.+.+..... +.-..+.+.+..+
T Consensus       292 la~iYyeqG~ldlAI~~Ykral~~~-------P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam~NLgni  363 (966)
T KOG4626|consen  292 LACIYYEQGLLDLAIDTYKRALELQ-------PNFPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAMNNLGNI  363 (966)
T ss_pred             eEEEEeccccHHHHHHHHHHHHhcC-------CCchHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            4445556667777777777766654       3335678888888888888888888888777653 2235667777888


Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHhcCCchH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD-ASVYNTLMDGFCLTGRVN  285 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~  285 (343)
                      +...|.+++|..++....+-  .|. ...++.|...|-+.|++++|+..+++.++.  +|+ ...++.+...|...|+.+
T Consensus       364 ~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI--~P~fAda~~NmGnt~ke~g~v~  439 (966)
T KOG4626|consen  364 YREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRI--KPTFADALSNMGNTYKEMGDVS  439 (966)
T ss_pred             HHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhc--CchHHHHHHhcchHHHHhhhHH
Confidence            88888888888888877764  343 567788888888899999999999888875  444 567888888899999999


Q ss_pred             HHHHHHHHHHhCCCCcc-HHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCcc
Q 040261          286 RAKELFVSMESNGCMRD-VFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVV  339 (343)
Q Consensus       286 ~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~  339 (343)
                      .|.+.+.+.+..  .|. ...++.|...|...|+..+|+.-|++.+  .++||..
T Consensus       440 ~A~q~y~rAI~~--nPt~AeAhsNLasi~kDsGni~~AI~sY~~aL--klkPDfp  490 (966)
T KOG4626|consen  440 AAIQCYTRAIQI--NPTFAEAHSNLASIYKDSGNIPEAIQSYRTAL--KLKPDFP  490 (966)
T ss_pred             HHHHHHHHHHhc--CcHHHHHHhhHHHHhhccCCcHHHHHHHHHHH--ccCCCCc
Confidence            999999888875  354 4678889999999999999999999998  4567653

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.84  E-value=1.4e-16  Score=142.24  Aligned_cols=321  Identities=11%  Similarity=0.028  Sum_probs=224.7

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      +|......  .|.+...+..+...+.+.|++++|.++|++..+.. +.+...+..+..++...|++++|...++++.+..
T Consensus        37 ~~~~~~~~--~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~  113 (765)
T PRK10049         37 VYNRYRVH--MQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAGQYDEALVKAKQLVSGA  113 (765)
T ss_pred             HHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            44555442  33567779999999999999999999999988754 4556777888888999999999999999998874


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHH----------------
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFE----------------  146 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----------------  146 (343)
                       +.+.. +..+..++...|+.++|+..++++.+..+. +...+..+..++...+..++|++.++                
T Consensus       114 -P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~  190 (765)
T PRK10049        114 -PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADA  190 (765)
T ss_pred             -CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHH
Confidence             33556 888888899999999999999999987544 45555566666666666665554444                


Q ss_pred             ------------------------------HHHccCCCCCccccCCcc-hH----HHHHHHHHhcCChHHHHHHHHHhhh
Q 040261          147 ------------------------------EMANGNGEFGVVCKPDAI-TY----STITDGLCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       147 ------------------------------~~~~~~~~~~~~~~~~~~-~~----~~l~~~~~~~~~~~~a~~~~~~~~~  191 (343)
                                                    .+.+...     ..|+.. .+    ...+.++...|++++|+..|+.+.+
T Consensus       191 ~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~-----~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~  265 (765)
T PRK10049        191 AAELVRLSFMPTRSEKERYAIADRALAQYDALEALWH-----DNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKA  265 (765)
T ss_pred             HHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcc-----cCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence                                          3332210     011111 11    1113345677899999999999887


Q ss_pred             CCCC-CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC---
Q 040261          192 ENIN-PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP---NVVTFNVIMNELCKNGKMDEASRLLELMIQIGV---  264 (343)
Q Consensus       192 ~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---  264 (343)
                      .+.+ |+. ....+..++...|++++|...++.+.+.....   .......+..++.+.|++++|..+++.+.+...   
T Consensus       266 ~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~  344 (765)
T PRK10049        266 EGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFL  344 (765)
T ss_pred             cCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceE
Confidence            6532 221 22224668888899999999999887653111   123455666677888999999999888876521   


Q ss_pred             --------CCC---HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          265 --------RPD---ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       265 --------~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                              .|+   ...+..+...+...|+.++|.+.++++.... +.+...+..+...+...|++++|++.+++.+.. 
T Consensus       345 ~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l-  422 (765)
T PRK10049        345 RLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVL-  422 (765)
T ss_pred             eecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh-
Confidence                    123   2344566677788888888888888887753 445677778888888888888888888888754 


Q ss_pred             CCCCc
Q 040261          334 IRPTV  338 (343)
Q Consensus       334 ~~p~~  338 (343)
                       .|+.
T Consensus       423 -~Pd~  426 (765)
T PRK10049        423 -EPRN  426 (765)
T ss_pred             -CCCC
Confidence             4664

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.83  E-value=4.5e-16  Score=139.01  Aligned_cols=322  Identities=13%  Similarity=0.065  Sum_probs=236.7

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ++|+......|  .++..+..++..+.+.|++++|+..++++.+.. +.+.. +..+..++...|+.++|+..++++.+.
T Consensus        70 ~~~~~al~~~P--~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~  145 (765)
T PRK10049         70 TLWQKALSLEP--QNDDYQRGLILTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPR  145 (765)
T ss_pred             HHHHHHHHhCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            35566666555  478888899999999999999999999998764 44566 888888999999999999999999987


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHH----------------------------------------------HHHHHHHh
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAA----------------------------------------------ALFTKLRA  115 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~----------------------------------------------~~~~~~~~  115 (343)
                      .+. +...+..+..++...+..+.|+                                              +.++.+.+
T Consensus       146 ~P~-~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~  224 (765)
T PRK10049        146 APQ-TQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEA  224 (765)
T ss_pred             CCC-CHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHh
Confidence            533 4555555666665555554444                                              34444443


Q ss_pred             c-CCCCCHH-HHH----HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHh
Q 040261          116 F-GCKPDVF-TYT----TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKM  189 (343)
Q Consensus       116 ~-~~~~~~~-~~~----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  189 (343)
                      . ...|+.. .+.    ..+..+...|++++|...|+++...+.     ..|+ .....+..+|...|++++|+..|+++
T Consensus       225 ~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~-----~~P~-~a~~~la~~yl~~g~~e~A~~~l~~~  298 (765)
T PRK10049        225 LWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQ-----IIPP-WAQRWVASAYLKLHQPEKAQSILTEL  298 (765)
T ss_pred             hcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCC-----CCCH-HHHHHHHHHHHhcCCcHHHHHHHHHH
Confidence            2 1122211 111    113345677999999999999988641     0122 12233577899999999999999998


Q ss_pred             hhCCCCC---ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCC-----------CCC---HHHHHHHHHHHHhCCChhHH
Q 040261          190 KDENINP---DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGV-----------QPN---VVTFNVIMNELCKNGKMDEA  252 (343)
Q Consensus       190 ~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~~~~~~l~~~~~~~~~~~~a  252 (343)
                      .......   .......+..++...|++++|..+++.+.+...           .|+   ...+..+...+...|++++|
T Consensus       299 l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA  378 (765)
T PRK10049        299 FYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQA  378 (765)
T ss_pred             hhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHH
Confidence            7653111   124456667788999999999999999987631           123   23455677888999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          253 SRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +.+++++.... +.+...+..+...+...|++++|++.+++..+.. +.+...+..++..+...|++++|..+++++++.
T Consensus       379 ~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~-Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        379 EMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVLE-PRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            99999998875 6678899999999999999999999999999864 334667777778899999999999999999965


Q ss_pred             CCCCCc
Q 040261          333 GIRPTV  338 (343)
Q Consensus       333 ~~~p~~  338 (343)
                        .|+.
T Consensus       457 --~Pd~  460 (765)
T PRK10049        457 --EPQD  460 (765)
T ss_pred             --CCCC
Confidence              4543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.81  E-value=1e-15  Score=119.32  Aligned_cols=246  Identities=15%  Similarity=0.207  Sum_probs=181.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      |.+.+++..+|..+++--..+.|.+++++..+...+.+..+||.+|.+-+-...    .++..+|.+..+.||..|+|++
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHH
Confidence            468899999999999999999999999998887778899999999977554333    7889999999999999999999


Q ss_pred             HHHHhhcCcHHH----HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHH-HHHHHHHHHcc--CCCCCccccCCcchH
Q 040261           94 IKGLCAESRIME----AAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIV-ALNLFEEMANG--NGEFGVVCKPDAITY  166 (343)
Q Consensus        94 ~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~--~~~~~~~~~~~~~~~  166 (343)
                      +++..+.|+++.    |.+++.+|++.|+.|...+|..++..+.+.++..+ +..++..+...  |..+.+..+.+...|
T Consensus       280 L~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF  359 (625)
T KOG4422|consen  280 LSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFF  359 (625)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHH
Confidence            999999998765    56788999999999999999999999999888754 44555554432  223333234455667


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhC----CCCCC---hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDE----NINPD---VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVI  239 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  239 (343)
                      ...+..|.+..+.+.|.++..-+...    -+.|+   ..-|..+....++....+.....++.|.-.-+-|+..+...+
T Consensus       360 ~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~  439 (625)
T KOG4422|consen  360 QSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHL  439 (625)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHH
Confidence            77788888888888888776555432    12222   122444555556666666667777777665556666666667


Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcC
Q 040261          240 MNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       240 ~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      +++....|.++-.-++|..++..|
T Consensus       440 lrA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  440 LRALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             HHHHhhcCcchhHHHHHHHHHHhh
Confidence            776666666666666666655544

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

Probab=99.81  E-value=5.2e-19  Score=139.79  Aligned_cols=262  Identities=17%  Similarity=0.135  Sum_probs=83.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCC-CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIG-LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE  100 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  100 (343)
                      .+...+.+.|++++|+++++...... .+.+...|..+.......++++.|.+.++++...+.. +...+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            44666666777777777775433222 1233444455555556666777777777777665422 44455555555 466


Q ss_pred             CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH
Q 040261          101 SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD  180 (343)
Q Consensus       101 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  180 (343)
                      +++++|.++++...+.  .++...+..++..+.+.++++++..+++.+.....     .+.+...|..+...+.+.|+.+
T Consensus        91 ~~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~~~~~~~~a~~~~~~G~~~  163 (280)
T PF13429_consen   91 GDPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPA-----APDSARFWLALAEIYEQLGDPD  163 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T--------T-HHHHHHHHHHHHHCCHHH
T ss_pred             cccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccC-----CCCCHHHHHHHHHHHHHcCCHH
Confidence            6677776666655443  23445555666666667777777777666654321     2345556666666666777777


Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      +|++.+++..+.. |.+......++..+...|+.+++..+++...+.. +.+...+..+..++...|+.++|..++++..
T Consensus       164 ~A~~~~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~  241 (280)
T PF13429_consen  164 KALRDYRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKAL  241 (280)
T ss_dssp             HHHHHHHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccc
Confidence            7777777666643 2245556666666666677666666666665552 3444555666666666677777777776666


Q ss_pred             HcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          261 QIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       261 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      +.. +.|+.....+..++...|+.++|.++.+++.
T Consensus       242 ~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  242 KLN-PDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHS-TT-HHHHHHHHHHHT----------------
T ss_pred             ccc-ccccccccccccccccccccccccccccccc
Confidence            653 4466666666666777777777766665543

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.81  E-value=2.1e-15  Score=124.62  Aligned_cols=286  Identities=13%  Similarity=0.105  Sum_probs=223.5

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHH-HHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHH--HHHHHHhhcCcHHH
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYT-YNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFT--SLIKGLCAESRIME  105 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~  105 (343)
                      -.|+++.|.+.+....+..  +++.. |.....+..+.|+++.|.+++.++.+.  .|+.....  .....+...|+++.
T Consensus        96 ~eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~  171 (398)
T PRK10747         96 AEGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHA  171 (398)
T ss_pred             hCCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHH
Confidence            3699999998888765532  22333 433455558999999999999999875  44543332  33677888999999


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc------chHHHHHHHHHhcCCh
Q 040261          106 AAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA------ITYSTITDGLCKEGFV  179 (343)
Q Consensus       106 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~  179 (343)
                      |.+.++++.+..+. ++.....+...|.+.|++++|.+++..+.+...     ..+..      .+|..++.......+.
T Consensus       172 Al~~l~~~~~~~P~-~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~-----~~~~~~~~l~~~a~~~l~~~~~~~~~~  245 (398)
T PRK10747        172 ARHGVDKLLEVAPR-HPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHV-----GDEEHRAMLEQQAWIGLMDQAMADQGS  245 (398)
T ss_pred             HHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCC-----CCHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence            99999999988654 678888999999999999999999999998762     11111      2334444444555667


Q ss_pred             HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          180 DKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       180 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      +...++++.+.+. .+.++.....+...+...|+.++|..++++..+.  +|+....  ++.+....++.+++.+..+..
T Consensus       246 ~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~  320 (398)
T PRK10747        246 EGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQ  320 (398)
T ss_pred             HHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHH
Confidence            7777777777553 3457888889999999999999999999999884  5555322  233344569999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          260 IQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       260 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .+.. +-|...+..+...+.+.+++++|.+.|+...+.  .|+...+..+...+.+.|+.++|.+.+++.+..
T Consensus       321 lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~  390 (398)
T PRK10747        321 IKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLML  390 (398)
T ss_pred             HhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            8874 556778889999999999999999999999986  599999999999999999999999999988653

>TIGR00540 hemY_coli hemY protein

Probab=99.80  E-value=9.7e-16  Score=127.30  Aligned_cols=291  Identities=11%  Similarity=0.064  Sum_probs=214.0

Q ss_pred             HhcCChhHHHHHHHHhHhCCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHH
Q 040261           28 AKNKHYDTVLSLFKRLNSIGLFPDL-YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEA  106 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  106 (343)
                      ...|+++.|.+.+.+..+..  |+. ..+-....+..+.|+.+.|.+++.+..+....+...........+...|+++.|
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            46899999999998877643  443 344555678888999999999999988764333333444457888889999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH-HHHHH---HHhcCChHHH
Q 040261          107 AALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS-TITDG---LCKEGFVDKA  182 (343)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~---~~~~~~~~~a  182 (343)
                      .+.++.+.+..+. +......+...+...|++++|.+.+..+.+.+.       .+...+. .-..+   ....+..++.
T Consensus       173 l~~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~-------~~~~~~~~l~~~a~~~~l~~~~~~~~  244 (409)
T TIGR00540       173 RHGVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGL-------FDDEEFADLEQKAEIGLLDEAMADEG  244 (409)
T ss_pred             HHHHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCC-------CCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999998654 677888999999999999999999999998751       2222221 11111   1222333333


Q ss_pred             HHHHHHhhhCC---CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHH--H-HHHHHHHHhCCChhHHHHHH
Q 040261          183 KELFLKMKDEN---INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVT--F-NVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       183 ~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~-~~l~~~~~~~~~~~~a~~~~  256 (343)
                      .+.+..+....   .+.+...+..+...+...|+.++|..++++..+..  |+...  + ..........++.+.+.+.+
T Consensus       245 ~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~  322 (409)
T TIGR00540       245 IDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLI  322 (409)
T ss_pred             HHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHH
Confidence            34444444432   12378888899999999999999999999999873  44331  1 11122223457788899999


Q ss_pred             HHHHHcCCCCCH--HHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          257 ELMIQIGVRPDA--SVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       257 ~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      +...+.. +-|+  .....+...+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.++|++...
T Consensus       323 e~~lk~~-p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       323 EKQAKNV-DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HHHHHhC-CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            8887763 4445  677789999999999999999999544433468988899999999999999999999998754

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.

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

Probab=99.80  E-value=5.1e-19  Score=139.86  Aligned_cols=262  Identities=18%  Similarity=0.141  Sum_probs=115.1

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHHcC-CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 040261           57 ILINCFCKMGRVSPGFVVLGRILRSC-FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRT  135 (343)
Q Consensus        57 ~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  135 (343)
                      .+...+.+.|++++|++++....... .+.+...|..+...+...++++.|.+.++++...+.. +...+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            56788899999999999997655443 2335566666777777889999999999999987644 56677777777 789


Q ss_pred             CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCChhhHHHHHHHHhccCcH
Q 040261          136 GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPDVVTYTSLIRGFCYANDW  214 (343)
Q Consensus       136 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~  214 (343)
                      +++++|.++++...+..        +++..+..++..+.+.++++++.++++.+.... .+.+...|..+...+.+.|+.
T Consensus        91 ~~~~~A~~~~~~~~~~~--------~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~  162 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--------GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDP  162 (280)
T ss_dssp             -----------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHH
T ss_pred             ccccccccccccccccc--------cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCH
Confidence            99999999998876543        456777888899999999999999999976542 345778888999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          215 NEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       215 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      ++|...+++..+.. +-+......++..+...|+.+++..+++...+.. +.|+..+..+..++...|+.++|...+++.
T Consensus       163 ~~A~~~~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~  240 (280)
T PF13429_consen  163 DKALRDYRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKA  240 (280)
T ss_dssp             HHHHHHHHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccc
Confidence            99999999999973 3357788899999999999999999998888764 556678889999999999999999999998


Q ss_pred             HhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          295 ESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       295 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      .+.. +.|+.....+..++...|+.++|.++.+++..
T Consensus       241 ~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  241 LKLN-PDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHS-TT-HHHHHHHHHHHT-----------------
T ss_pred             cccc-cccccccccccccccccccccccccccccccc
Confidence            8853 45788888999999999999999999887754

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.80  E-value=7e-15  Score=132.17  Aligned_cols=315  Identities=10%  Similarity=0.034  Sum_probs=237.2

Q ss_pred             HHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhC-C-CCCCHHHHHHHHHHHHhcCCcc---hHHHH----
Q 040261            4 FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSI-G-LFPDLYTYNILINCFCKMGRVS---PGFVV----   74 (343)
Q Consensus         4 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~~~~~---~a~~~----   74 (343)
                      +..|.+..+  .+....-.+.....+.|+.++|.++++..... + ..++......++..+.+.+...   ++..+    
T Consensus       365 ~~~~y~~~~--~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~  442 (987)
T PRK09782        365 ARLLYQQEP--ANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPL  442 (987)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhcccc
Confidence            444555544  37777778888888999999999999998762 1 1233444556777777765522   22222    


Q ss_pred             ------------------HHHHHHc-CC-Cc--cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040261           75 ------------------LGRILRS-CF-TP--DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGL  132 (343)
Q Consensus        75 ------------------~~~~~~~-~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  132 (343)
                                        ++..... +. ++  +...|..+..++.. ++.++|...+.+....  .|+......+...+
T Consensus       443 ~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al  519 (987)
T PRK09782        443 PLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQA  519 (987)
T ss_pred             ccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHH
Confidence                              2222111 11 23  56677778877776 7888999988887776  35655544555666


Q ss_pred             HhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccC
Q 040261          133 CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAN  212 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  212 (343)
                      ...|++++|...++++...        +|+...+..+..++.+.|+.++|...+++..+.. +.....+..+.......|
T Consensus       520 ~~~Gr~eeAi~~~rka~~~--------~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~G  590 (987)
T PRK09782        520 YQVEDYATALAAWQKISLH--------DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPG  590 (987)
T ss_pred             HHCCCHHHHHHHHHHHhcc--------CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCC
Confidence            7899999999999998664        3445556777888899999999999999998764 223333434444455669


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHH
Q 040261          213 DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFV  292 (343)
Q Consensus       213 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  292 (343)
                      ++++|...+++..+.  .|+...+..+..++.+.|++++|...+++..+.. +.+...+..+..++...|++++|...++
T Consensus       591 r~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~  667 (987)
T PRK09782        591 QPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLE  667 (987)
T ss_pred             CHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999999986  4678889999999999999999999999999986 5677888889999999999999999999


Q ss_pred             HHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          293 SMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       293 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      +..+.. +-+...+..+..++...|++++|...+++.+..  .|+.
T Consensus       668 ~AL~l~-P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l--~P~~  710 (987)
T PRK09782        668 RAHKGL-PDDPALIRQLAYVNQRLDDMAATQHYARLVIDD--IDNQ  710 (987)
T ss_pred             HHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCC
Confidence            998864 346788899999999999999999999999865  4543

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.79  E-value=1.2e-14  Score=128.10  Aligned_cols=145  Identities=14%  Similarity=-0.009  Sum_probs=76.3

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.|+...+..|. ..+.++ .++..+...|+.++|+..+++..... +.+......+...+...|++++|+++|+++.+.
T Consensus        55 ~~L~qaL~~~P~-~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~-n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~  131 (822)
T PRK14574         55 DYLQEESKAGPL-QSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSM-NISSRGLASAARAYRNEKRWDQALALWQSSLKK  131 (822)
T ss_pred             HHHHHHHhhCcc-chhhHH-HHHHHHHHcCCcHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            345555555543 111222 55566666666666666666665211 112222333344566666666666666666665


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      .+. +...+..++..+...++.++|++.++++...  .|+...+..++..+...++..+|++.++++.+..
T Consensus       132 dP~-n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~  199 (822)
T PRK14574        132 DPT-NPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA  199 (822)
T ss_pred             CCC-CHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC
Confidence            432 3455555566666666666666666666655  3343344333333333444444666666665554

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.76  E-value=6e-14  Score=123.78  Aligned_cols=302  Identities=11%  Similarity=0.020  Sum_probs=173.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      ...+...+...|++++|+++|+++.+.. +.+...+..++..+...++.++|++.++++...  .|+...+..++..+..
T Consensus       105 llalA~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~  181 (822)
T PRK14574        105 LASAARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRA  181 (822)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHh
Confidence            3333557778888888888888887765 345566667777788888888888888888765  3444445444444444


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHH---------------------------------
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFE---------------------------------  146 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~---------------------------------  146 (343)
                      .++..+|++.++++.+..+. +...+..+..++.+.|-...|.++..                                 
T Consensus       182 ~~~~~~AL~~~ekll~~~P~-n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~  260 (822)
T PRK14574        182 TDRNYDALQASSEAVRLAPT-SEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSE  260 (822)
T ss_pred             cchHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccc
Confidence            55555688888888776432 44444555555444443333333222                                 


Q ss_pred             ---------------HHHccCCCCCccccCCcchH----HHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHH
Q 040261          147 ---------------EMANGNGEFGVVCKPDAITY----STITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG  207 (343)
Q Consensus       147 ---------------~~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  207 (343)
                                     .+...-+.    .|+....|    .-.+.++...|+..++++.++.+...+.+....+-..+..+
T Consensus       261 ~~r~~~~d~ala~~~~l~~~~~~----~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~ada  336 (822)
T PRK14574        261 TERFDIADKALADYQNLLTRWGK----DPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASA  336 (822)
T ss_pred             hhhHHHHHHHHHHHHHHHhhccC----CCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHH
Confidence                           22211100    11111111    12344556666677777777776666554444556666666


Q ss_pred             HhccCcHHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC-----------CCC---H
Q 040261          208 FCYANDWNEAKCLFIEMMDQG-----VQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV-----------RPD---A  268 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~  268 (343)
                      |...+++++|..+++.+....     ..++......|.-++...+++++|..+++.+.+...           .||   .
T Consensus       337 yl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~  416 (822)
T PRK14574        337 YIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWI  416 (822)
T ss_pred             HHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHH
Confidence            666666677766666665432     122233345566666666666666666666665210           122   1


Q ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          269 SVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       269 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      ..+..++..+...|+..+|++.++++.... +-|......+...+...|.+.+|.+.++...
T Consensus       417 ~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~  477 (822)
T PRK14574        417 EGQTLLVQSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALASIYLARDLPRKAEQELKAVE  477 (822)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence            233444555666666666666666665543 3456666666666666666666666665554

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

Probab=99.76  E-value=6.3e-14  Score=108.49  Aligned_cols=293  Identities=12%  Similarity=0.058  Sum_probs=239.9

Q ss_pred             cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHH
Q 040261           30 NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAAL  109 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  109 (343)
                      .|+|.+|..+..+-.+.+ +.....|..-.++.-+.|+.+.+-.++.++.+....++....-...+.....|+...|..-
T Consensus        97 eG~~~qAEkl~~rnae~~-e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHG-EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            699999999999987776 3345577778888899999999999999998864466677777888889999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC-------cchHHHHHHHHHhcCChHHH
Q 040261          110 FTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD-------AITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a  182 (343)
                      ++++.+.+.. .+........+|.+.|++.....++..+.+.+-      -.+       ..+|..++.-....+..+.-
T Consensus       176 v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~------l~~~e~~~le~~a~~glL~q~~~~~~~~gL  248 (400)
T COG3071         176 VDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGL------LSDEEAARLEQQAWEGLLQQARDDNGSEGL  248 (400)
T ss_pred             HHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccC------CChHHHHHHHHHHHHHHHHHHhccccchHH
Confidence            9999988765 677888999999999999999999999998873      222       24677777777777777777


Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ...++..... .+.++..-..++.-+.+.|+.++|.++.++..+++..|+..    ..-.+.+.++.+.-.+..+.-.+.
T Consensus       249 ~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~k~~e~~l~~  323 (400)
T COG3071         249 KTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLIKAAEKWLKQ  323 (400)
T ss_pred             HHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHHHHHHHHHHh
Confidence            7788777554 34467777788888999999999999999999987666621    223456778888888888776665


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      . +.++..+..|...|.+.+.|.+|...|+...+.  .|+..+|+.+.+++.+.|++.+|.+..++.+..-.+|+.
T Consensus       324 h-~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~~  396 (400)
T COG3071         324 H-PEDPLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPNL  396 (400)
T ss_pred             C-CCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCCC
Confidence            3 445678999999999999999999999988876  599999999999999999999999999998865555544

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

Probab=99.75  E-value=2e-14  Score=108.15  Aligned_cols=290  Identities=18%  Similarity=0.150  Sum_probs=225.4

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH------HHHHHHHHHHhhcCc
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA------VTFTSLIKGLCAESR  102 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~  102 (343)
                      -.++.++|+++|-+|.+.. +.+..+..++.+.|.+.|..+.|+.+.+.+.++   ||.      .....+..-|...|-
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl  122 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGL  122 (389)
T ss_pred             hhcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhh
Confidence            3578899999999998844 445567778899999999999999999999875   332      234456677888999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC---cchHHHHHHHHHhcCCh
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD---AITYSTITDGLCKEGFV  179 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~  179 (343)
                      ++.|+.+|..+.+.+.. -..+...|+..|....++++|+++-+++.+.++.     +.+   ...|.-+...+.-..+.
T Consensus       123 ~DRAE~~f~~L~de~ef-a~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q-----~~~~eIAqfyCELAq~~~~~~~~  196 (389)
T COG2956         123 LDRAEDIFNQLVDEGEF-AEGALQQLLNIYQATREWEKAIDVAERLVKLGGQ-----TYRVEIAQFYCELAQQALASSDV  196 (389)
T ss_pred             hhHHHHHHHHHhcchhh-hHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCc-----cchhHHHHHHHHHHHHHhhhhhH
Confidence            99999999999986533 5567888999999999999999999999887631     111   24567777777788999


Q ss_pred             HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          180 DKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       180 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      +.|..++++..+.+. .....--.+.+.+...|+++.|.+.++.+.+.+..--..+...|..+|...|+.++....+.++
T Consensus       197 d~A~~~l~kAlqa~~-~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~  275 (389)
T COG2956         197 DRARELLKKALQADK-KCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhhCc-cceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            999999999988652 2444555667888999999999999999999865555778889999999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh---cCChHHHHHHHHHHHhCC
Q 040261          260 IQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK---NKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       260 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~  333 (343)
                      .+..  +....-..+...-....-.+.|...+.+-...  .|+...+..++..-..   .|...+-+..+++|....
T Consensus       276 ~~~~--~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~  348 (389)
T COG2956         276 METN--TGADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGEQ  348 (389)
T ss_pred             HHcc--CCccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHHH
Confidence            8864  34444455555545555666676666555544  5999999999987654   355777788888887653

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

Probab=99.75  E-value=1.7e-15  Score=124.17  Aligned_cols=292  Identities=14%  Similarity=0.071  Sum_probs=226.7

Q ss_pred             CChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC--CccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           31 KHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF--TPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      =+.++|+..|..+... +.....+...+..+|...+++++|.++|+.+.+...  .-+..+|...+--+-   +.-+---
T Consensus       333 y~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq---~~v~Ls~  408 (638)
T KOG1126|consen  333 YNCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQ---DEVALSY  408 (638)
T ss_pred             HHHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHH---hhHHHHH
Confidence            3567899999995543 344456777888999999999999999999987531  125566766665432   2122222


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040261          109 LFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK  188 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  188 (343)
                      +-+.+.+.. +-.+.+|.++.++|.-+++.+.|++.|++..+.+       +....+|+.+..-+.....+|.|...|+.
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-------p~faYayTLlGhE~~~~ee~d~a~~~fr~  480 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-------PRFAYAYTLLGHESIATEEFDKAMKSFRK  480 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-------CccchhhhhcCChhhhhHHHHhHHHHHHh
Confidence            233344432 2367899999999999999999999999999976       34688999999999999999999999999


Q ss_pred             hhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCH
Q 040261          189 MKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDA  268 (343)
Q Consensus       189 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  268 (343)
                      ...... ..-..|.-+...|.+.++++.|+-.|+.+.+.+ +-+.+....+...+.+.|+.++|+.+++++...+ +.|+
T Consensus       481 Al~~~~-rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld-~kn~  557 (638)
T KOG1126|consen  481 ALGVDP-RHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLD-PKNP  557 (638)
T ss_pred             hhcCCc-hhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcC-CCCc
Confidence            876431 134455556788999999999999999998864 4457777888899999999999999999999886 4455


Q ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          269 SVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       269 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      ..--.-+..+...++.++|+..++++++. ++.+...|..+...|.+.|+.+.|+.-|.-+.+...++..
T Consensus       558 l~~~~~~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  558 LCKYHRASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             hhHHHHHHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            55555667778899999999999999986 2445677888889999999999999999888876555443

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.75  E-value=3.4e-14  Score=127.84  Aligned_cols=264  Identities=10%  Similarity=0.008  Sum_probs=209.4

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      +...|..+..++.. ++.++|...+.+....  .|+......+...+...|++++|...|+++...  .|+...+..+..
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~  550 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAAN  550 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHH
Confidence            56778888877776 8888999988888775  355544444555567899999999999998665  344555667788


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY  210 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (343)
                      ++.+.|+.++|...+++.....       +.....+..+.......|++++|...+++..+..  |+...+..+..++.+
T Consensus       551 all~~Gd~~eA~~~l~qAL~l~-------P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~  621 (987)
T PRK09782        551 TAQAAGNGAARDRWLQQAEQRG-------LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARATIYRQ  621 (987)
T ss_pred             HHHHCCCHHHHHHHHHHHHhcC-------CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHH
Confidence            8899999999999999998764       2333333344445556699999999999998764  578889999999999


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKEL  290 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  290 (343)
                      .|++++|...+++..+.. +.+...+..+..++...|++++|+..+++..+.. +-+...+..+..++...|++++|+..
T Consensus       622 lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~-P~~~~a~~nLA~al~~lGd~~eA~~~  699 (987)
T PRK09782        622 RHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLERAHKGL-PDDPALIRQLAYVNQRLDDMAATQHY  699 (987)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            999999999999999874 4457778888889999999999999999999875 55778899999999999999999999


Q ss_pred             HHHHHhCCCCccH-HHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          291 FVSMESNGCMRDV-FSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       291 ~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +++..+..  |+. .+.........+..+++.+.+.+++....
T Consensus       700 l~~Al~l~--P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~~  740 (987)
T PRK09782        700 ARLVIDDI--DNQALITPLTPEQNQQRFNFRRLHEEVGRRWTF  740 (987)
T ss_pred             HHHHHhcC--CCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhc
Confidence            99998863  543 45555666677777888888888776643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.74  E-value=4.8e-14  Score=116.64  Aligned_cols=263  Identities=10%  Similarity=0.021  Sum_probs=206.4

Q ss_pred             hhhHHHH-HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHH--HHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           17 VCSFNIL-FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYN--ILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        17 ~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      +..+..+ ..+..+.|+++.|.+.+.++.+.  .|+.....  .....+...|+++.|...++++.+..+ -+......+
T Consensus       117 p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P-~~~~al~ll  193 (398)
T PRK10747        117 PVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAP-RHPEVLRLA  193 (398)
T ss_pred             hHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CCHHHHHHH
Confidence            3444444 44448999999999999999874  45554333  346788899999999999999998763 367888899


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCH-------HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDV-------FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...|.+.|++++|.+++..+.+.+..++.       .+|..++.......+.+...++++.+...       .+.++...
T Consensus       194 ~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-------~~~~~~~~  266 (398)
T PRK10747        194 EQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK-------TRHQVALQ  266 (398)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-------HhCCHHHH
Confidence            99999999999999999999988755322       12333444444555666777777776554       35577888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN  246 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  246 (343)
                      ..+...+...|+.++|...+++..+.  +++....  ++.+....++.+++....+...+.. +-|...+..+...+.+.
T Consensus       267 ~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~  341 (398)
T PRK10747        267 VAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKH  341 (398)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHC
Confidence            99999999999999999999998874  3444222  3444456699999999999998873 44566788899999999


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          247 GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      +++++|...|+.+.+.  .|+...+..+...+.+.|+.++|.+.+++...
T Consensus       342 ~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        342 GEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            9999999999999986  68999999999999999999999999997754

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.72  E-value=6.6e-14  Score=109.46  Aligned_cols=308  Identities=16%  Similarity=0.200  Sum_probs=232.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC--CcchH-HHHHHHHHHcC---------
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG--RVSPG-FVVLGRILRSC---------   82 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a-~~~~~~~~~~~---------   82 (343)
                      ..+++=|.|+.. ...|...++.-+|+.|...|++.+...-..+++.-+-.+  ++--| .+.|-.|...|         
T Consensus       114 ~~V~~E~nL~km-IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~  192 (625)
T KOG4422|consen  114 LQVETENNLLKM-ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKS  192 (625)
T ss_pred             hhhcchhHHHHH-HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccccc
Confidence            344555555553 567899999999999999998888877666665433222  21111 11222221111         


Q ss_pred             ----------CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           83 ----------FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        83 ----------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                                .+-+..++..+|.++++.-..+.|.+++++-.....+.+..+||.++.+-+-..+    .+++.+|....
T Consensus       193 G~vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqk  268 (625)
T KOG4422|consen  193 GAVADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQK  268 (625)
T ss_pred             ccHHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhh
Confidence                      2346778999999999999999999999999988888899999999987654433    68888998888


Q ss_pred             CCCCccccCCcchHHHHHHHHHhcCChHH----HHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHH-HHHHHHHHHH-
Q 040261          153 GEFGVVCKPDAITYSTITDGLCKEGFVDK----AKELFLKMKDENINPDVVTYTSLIRGFCYANDWNE-AKCLFIEMMD-  226 (343)
Q Consensus       153 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~-  226 (343)
                            +.||..|+|+++.+..+.|+++.    |.+++.+|++-|+.|...+|..++..+.+.++..+ +..++.+++. 
T Consensus       269 ------m~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~  342 (625)
T KOG4422|consen  269 ------MTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNS  342 (625)
T ss_pred             ------cCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHh
Confidence                  89999999999999999998764    56778889999999999999999999999888744 4444444442 


Q ss_pred             ---cCCC---C-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC----CCCC---HHHHHHHHHHHhcCCchHHHHHHHH
Q 040261          227 ---QGVQ---P-NVVTFNVIMNELCKNGKMDEASRLLELMIQIG----VRPD---ASVYNTLMDGFCLTGRVNRAKELFV  292 (343)
Q Consensus       227 ---~~~~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~  292 (343)
                         +.+.   | +...|...+..|....|.+-|.++..-+....    +.|+   ..-|..+....++....+.....++
T Consensus       343 ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~  422 (625)
T KOG4422|consen  343 LTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYE  422 (625)
T ss_pred             hccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               2222   2 45667788888999999999998876664421    2233   2335667777788889999999999


Q ss_pred             HHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          293 SMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       293 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      .|.-.-.-|+..+...++++..-.|.++-.-++|.+++..|
T Consensus       423 ~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  423 DLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             HhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhh
Confidence            99988778899999999999999999998888888887766

>TIGR00540 hemY_coli hemY protein

Probab=99.72  E-value=1.4e-13  Score=114.51  Aligned_cols=269  Identities=8%  Similarity=-0.034  Sum_probs=196.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH--HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL--YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ..+-....+..+.|+++.|.+.+.+..+..  |+.  .........+...|+++.|...++.+.+..+. +...+..+..
T Consensus       119 ~~~llaA~aa~~~g~~~~A~~~l~~a~~~~--p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~-~~~~l~ll~~  195 (409)
T TIGR00540       119 LNLIKAAEAAQQRGDEARANQHLEEAAELA--GNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPR-HKEVLKLAEE  195 (409)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            344455677888999999999999987643  443  34444578888999999999999999998633 6778889999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHH-HHHHHH---HhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHH
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYT-TLINGL---CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITD  171 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  171 (343)
                      .+.+.|++++|.+.+..+.+.+.. +...+. ....++   ...+..+...+.+..+....+..   .+.+...+..+..
T Consensus       196 ~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~---~~~~~~l~~~~a~  271 (409)
T TIGR00540       196 AYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRH---RRHNIALKIALAE  271 (409)
T ss_pred             HHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHH---HhCCHHHHHHHHH
Confidence            999999999999999999998754 333332 111111   22333333334444444432100   1247788899999


Q ss_pred             HHHhcCChHHHHHHHHHhhhCCCCCChhh---HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhC
Q 040261          172 GLCKEGFVDKAKELFLKMKDENINPDVVT---YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV--VTFNVIMNELCKN  246 (343)
Q Consensus       172 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~  246 (343)
                      .+...|+.++|.+.+++..+..  |+...   ...........++.+.+...++...+.. +-+.  ....++...+.+.
T Consensus       272 ~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~-p~~~~~~ll~sLg~l~~~~  348 (409)
T TIGR00540       272 HLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNV-DDKPKCCINRALGQLLMKH  348 (409)
T ss_pred             HHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHHHc
Confidence            9999999999999999998864  33331   1222223344578889999998888762 3334  5666889999999


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          247 GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      |++++|.+.|+........|+...+..+...+.+.|+.++|.+++++...
T Consensus       349 ~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       349 GEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             ccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999654444578888899999999999999999999997643

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.

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

Probab=99.71  E-value=7.1e-14  Score=110.18  Aligned_cols=291  Identities=13%  Similarity=0.076  Sum_probs=214.6

Q ss_pred             HHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--ccHHHHHHHHHHHhhcCc
Q 040261           25 GCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  102 (343)
                      .++....+.+++.+=.+.+...|.+.+...-+....+.....++++|+.+|+++.+..+=  -|..+|..++-.-.....
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~sk  314 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSK  314 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHH
Confidence            444455677777777777777777666665566666667778889999999988876321  145566665544322222


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  182 (343)
                      ..---+....+.+    --+.|...+.+-|+-.++.++|...|++..+.+       +....+|+.+..-|....+...|
T Consensus       315 Ls~LA~~v~~idK----yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-------p~~~~aWTLmGHEyvEmKNt~AA  383 (559)
T KOG1155|consen  315 LSYLAQNVSNIDK----YRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-------PKYLSAWTLMGHEYVEMKNTHAA  383 (559)
T ss_pred             HHHHHHHHHHhcc----CCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-------cchhHHHHHhhHHHHHhcccHHH
Confidence            1111111111111    234567777888888999999999999999876       45577899999999999999999


Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ++.++...+-+ |.|-..|-.+.++|.-.+...=|+-.|++..+.. +-|...|.+|..+|.+.++.++|++.|.+....
T Consensus       384 i~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~  461 (559)
T KOG1155|consen  384 IESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILL  461 (559)
T ss_pred             HHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhc
Confidence            99999998875 4588899999999999999999999999998863 556889999999999999999999999999988


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CC-Cc-cHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN----GC-MR-DVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      | ..+...+..|.+.|-+.++..+|...+++..+.    |. .| .......|..-+.+.+++++|.......
T Consensus       462 ~-dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~  533 (559)
T KOG1155|consen  462 G-DTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLV  533 (559)
T ss_pred             c-ccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            7 557788999999999999999999998876652    22 22 2233333556677777877776654443

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

Probab=99.71  E-value=1.9e-13  Score=102.95  Aligned_cols=279  Identities=15%  Similarity=0.124  Sum_probs=220.2

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH------HHHHHHHHHHHhcCCcchHHHHH
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL------YTYNILINCFCKMGRVSPGFVVL   75 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~   75 (343)
                      +.|-+|.+..+.  +.++.-.|...|.+.|..++|+++.+.+.+.   ||.      .+...+..-|...|-++.|.++|
T Consensus        56 dlF~e~l~~d~~--t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f  130 (389)
T COG2956          56 DLFLEMLQEDPE--TFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLLDRAEDIF  130 (389)
T ss_pred             HHHHHHHhcCch--hhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence            678888886664  8888999999999999999999999998863   432      23455677788899999999999


Q ss_pred             HHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           76 GRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV----FTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        76 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      ..+.+.+ .--......++..|-...+|++|+++-+++.+.+.++..    ..|..+...+....+.+.|..++.+..+.
T Consensus       131 ~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa  209 (389)
T COG2956         131 NQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQA  209 (389)
T ss_pred             HHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh
Confidence            9998754 334667888999999999999999999999988765443    24556667777788999999999999987


Q ss_pred             CCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC
Q 040261          152 NGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP  231 (343)
Q Consensus       152 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  231 (343)
                      +       +..+.+-..+.+.....|+++.|.+.++.+.+.+..--+.+...+..+|.+.|+.++....+..+.+..  +
T Consensus       210 ~-------~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~--~  280 (389)
T COG2956         210 D-------KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN--T  280 (389)
T ss_pred             C-------ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc--C
Confidence            6       455667777889999999999999999999998755557788899999999999999999999998873  4


Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC---CchHHHHHHHHHHHhC
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT---GRVNRAKELFVSMESN  297 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~  297 (343)
                      ....-..+........-.+.|...+.+-.+.  +|+...+..++..-...   |...+-..+++.|...
T Consensus       281 g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge  347 (389)
T COG2956         281 GADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGE  347 (389)
T ss_pred             CccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHH
Confidence            4444455555555566667777776665554  79999999999865533   4466666677777643

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

Probab=99.70  E-value=4.4e-13  Score=113.88  Aligned_cols=318  Identities=13%  Similarity=0.106  Sum_probs=233.9

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +|+.++.+..|.  +...|..|..+|-+.|+.+++...+-..-..+ +.|...|..+.....+.|++++|.-+|.+.++.
T Consensus       160 ~i~~EvIkqdp~--~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~  236 (895)
T KOG2076|consen  160 EILMEVIKQDPR--NPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQARYCYSRAIQA  236 (895)
T ss_pred             HHHHHHHHhCcc--chhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHHHHHHHHHHhc
Confidence            467777777764  78889999999999999988888775554433 456678888888888889999999999998887


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHH----HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCc
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF----TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGV  157 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  157 (343)
                      . +++...+---...|-+.|+...|...|.++.....+.|..    ....+++.+...++.+.|.+.++.......    
T Consensus       237 ~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~----  311 (895)
T KOG2076|consen  237 N-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEK----  311 (895)
T ss_pred             C-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhcc----
Confidence            5 3455556667778888899999999998888874422322    223345667777777888888888777332    


Q ss_pred             cccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC---------------------------CCCChhhHHHHHHHHhc
Q 040261          158 VCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN---------------------------INPDVVTYTSLIRGFCY  210 (343)
Q Consensus       158 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~~~~~~~~~l~~~~~~  210 (343)
                       -..+...++.++..+.+...++.+...........                           ..++... -.++-++.+
T Consensus       312 -~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v-~rl~icL~~  389 (895)
T KOG2076|consen  312 -DEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRV-IRLMICLVH  389 (895)
T ss_pred             -ccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchh-HhHhhhhhc
Confidence             24456778888889999999999888877765511                           1112222 122334445


Q ss_pred             cCcHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQP--NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAK  288 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  288 (343)
                      .+..+....+...+.+..+.|  +...|.-+..++...|.+.+|+.++..+.....--+...|-.+..+|...|..+.|.
T Consensus       390 L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~  469 (895)
T KOG2076|consen  390 LKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAI  469 (895)
T ss_pred             ccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHH
Confidence            555555555666666665333  466788889999999999999999999988755556778999999999999999999


Q ss_pred             HHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          289 ELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      +.++...... +.+...-..|...+.+.|++++|.+.+..+.
T Consensus       470 e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  470 EFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             HHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            9999988763 3345555667778899999999999998876

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

Probab=99.67  E-value=3.4e-12  Score=99.12  Aligned_cols=271  Identities=13%  Similarity=0.071  Sum_probs=220.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ..-.|-.-..+.-+.|+.+.+-..+.+.-+..-.++...+-...+.....|+...|..-.+++.+.+.. ++.......+
T Consensus       117 p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr-~~~vlrLa~r  195 (400)
T COG3071         117 PVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMTPR-HPEVLRLALR  195 (400)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcC-ChHHHHHHHH
Confidence            444566667777889999999999999887533566777888888999999999999999999987644 7788899999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCH-------HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDV-------FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      +|.+.|++.....+...+.+.|.-.+.       .+|..+++-....+..+.-...|+.....       ...++..-..
T Consensus       196 ~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~-------lr~~p~l~~~  268 (400)
T COG3071         196 AYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK-------LRNDPELVVA  268 (400)
T ss_pred             HHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH-------hhcChhHHHH
Confidence            999999999999999999999865454       35677777777777777767777777665       3566778888


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  248 (343)
                      ++.-+.++|+.++|.++.++..+.+..|+   ... ...+.+-++...-.+..+.-.+. .+.++..+.+|...|.+.+.
T Consensus       269 ~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L~~-~~~~l~~~d~~~l~k~~e~~l~~-h~~~p~L~~tLG~L~~k~~~  343 (400)
T COG3071         269 YAERLIRLGDHDEAQEIIEDALKRQWDPR---LCR-LIPRLRPGDPEPLIKAAEKWLKQ-HPEDPLLLSTLGRLALKNKL  343 (400)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHhccChh---HHH-HHhhcCCCCchHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhH
Confidence            89999999999999999999998877665   222 23456778888877777776665 24456788899999999999


Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCc
Q 040261          249 MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMR  301 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  301 (343)
                      +.+|...|+...+.  .|+..+|+.+..++.+.|+..+|.++.++....-.+|
T Consensus       344 w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~  394 (400)
T COG3071         344 WGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLLTRQP  394 (400)
T ss_pred             HHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCC
Confidence            99999999987775  7899999999999999999999999998876443333

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

Probab=99.66  E-value=6.1e-14  Score=115.28  Aligned_cols=278  Identities=15%  Similarity=0.087  Sum_probs=217.7

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCC--CCCHHHHHHHHHHHHhcCCcchHHHHHH-HHH
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGL--FPDLYTYNILINCFCKMGRVSPGFVVLG-RIL   79 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~   79 (343)
                      .|..+..+..  .+..+...+..+|...+++++|..+|+.+.+...  .-+.+.|.+.+-.+-+    +-++.++. .+.
T Consensus       341 ~~~klp~h~~--nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~----~v~Ls~Laq~Li  414 (638)
T KOG1126|consen  341 LFEKLPSHHY--NTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD----EVALSYLAQDLI  414 (638)
T ss_pred             HHHhhHHhcC--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh----hHHHHHHHHHHH
Confidence            4555444444  3568888999999999999999999999987431  1256678877765533    22333333 333


Q ss_pred             HcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccc
Q 040261           80 RSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        80 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      ... +-.+.+|-++.++|.-+++.+.|++.|++..+.+.. ...+|+.+..-+....+++.|...|+.....+       
T Consensus       415 ~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~-faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~-------  485 (638)
T KOG1126|consen  415 DTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPR-FAYAYTLLGHESIATEEFDKAMKSFRKALGVD-------  485 (638)
T ss_pred             hhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCc-cchhhhhcCChhhhhHHHHhHHHHHHhhhcCC-------
Confidence            332 446889999999999999999999999999987432 67889999888999999999999999987754       


Q ss_pred             cCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          160 KPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVI  239 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  239 (343)
                      +.+-.+|-.+.-.|.+.++++.|+-.|+++.+-+ +-+.+....+...+.+.|+.++|+.+++++...+ +-|+..--..
T Consensus       486 ~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld-~kn~l~~~~~  563 (638)
T KOG1126|consen  486 PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLD-PKNPLCKYHR  563 (638)
T ss_pred             chhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcC-CCCchhHHHH
Confidence            2334556667788999999999999999998876 3367777888888999999999999999998875 3344444445


Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          240 MNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       240 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      +..+...+++++|+..++++.+. ++.+...|..+...|.+.|+.+.|..-|.-+.+..
T Consensus       564 ~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ld  621 (638)
T KOG1126|consen  564 ASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLD  621 (638)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCC
Confidence            66777889999999999999987 35567788889999999999999999998888753

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

Probab=99.65  E-value=3.4e-12  Score=108.64  Aligned_cols=304  Identities=13%  Similarity=0.087  Sum_probs=234.6

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      ....+...|++++|.+++.+.++.. +.+...|..|...|-+.|+.+++...+-.+...+ +-|...|..+.....+.|.
T Consensus       145 eAN~lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~  222 (895)
T KOG2076|consen  145 EANNLFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGN  222 (895)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhccc
Confidence            3444556699999999999998865 5677899999999999999999988877666554 3367889999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc----hHHHHHHHHHhcCC
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI----TYSTITDGLCKEGF  178 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~  178 (343)
                      +.+|.-+|.+.++..+. +...+-.-...|-+.|+...|..-|.++....+      +.+..    .-..++..+...++
T Consensus       223 i~qA~~cy~rAI~~~p~-n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p------~~d~er~~d~i~~~~~~~~~~~~  295 (895)
T KOG2076|consen  223 INQARYCYSRAIQANPS-NWELIYERSSLYQKTGDLKRAMETFLQLLQLDP------PVDIERIEDLIRRVAHYFITHNE  295 (895)
T ss_pred             HHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC------chhHHHHHHHHHHHHHHHHHhhH
Confidence            99999999999988543 555666677889999999999999999998751      12222    22334566777888


Q ss_pred             hHHHHHHHHHhhhC-CCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC---------------------------CC
Q 040261          179 VDKAKELFLKMKDE-NINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG---------------------------VQ  230 (343)
Q Consensus       179 ~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~  230 (343)
                      .+.|.+.++..... +-..+...++.++..+.+...++.+...........                           ..
T Consensus       296 ~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s  375 (895)
T KOG2076|consen  296 RERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELS  375 (895)
T ss_pred             HHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCC
Confidence            89999998887652 223466778899999999999999998887776521                           12


Q ss_pred             CCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHH
Q 040261          231 PNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR--PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGI  308 (343)
Q Consensus       231 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  308 (343)
                      ++..+ -.+.-++......+....+.....+.++.  -+...|..+..+|...|++.+|..++..+......-+...|..
T Consensus       376 ~~l~v-~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~  454 (895)
T KOG2076|consen  376 YDLRV-IRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYK  454 (895)
T ss_pred             ccchh-HhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHH
Confidence            22222 12333445556666666666666666633  4567889999999999999999999999998755567789999


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          309 LINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       309 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      +.++|...|.+++|.+.|+..+..  .|+.
T Consensus       455 ~a~c~~~l~e~e~A~e~y~kvl~~--~p~~  482 (895)
T KOG2076|consen  455 LARCYMELGEYEEAIEFYEKVLIL--APDN  482 (895)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHhc--CCCc
Confidence            999999999999999999999855  4543

>PRK12370 invasion protein regulator; Provisional

Probab=99.65  E-value=7.5e-13  Score=114.29  Aligned_cols=268  Identities=12%  Similarity=0.022  Sum_probs=179.8

Q ss_pred             CCCHHHHHHHHHHHHh-----cCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh---------hcCcHHHHHHHHHHHH
Q 040261           49 FPDLYTYNILINCFCK-----MGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC---------AESRIMEAAALFTKLR  114 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~  114 (343)
                      +.+...|...+++...     .+++++|...|++..+..+. +...|..+..++.         ..+++++|...+++..
T Consensus       253 ~~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~-~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al  331 (553)
T PRK12370        253 LNSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPN-SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKAT  331 (553)
T ss_pred             CCChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHH
Confidence            3455555555554322     23456888888888876422 4555555554443         2345788999999988


Q ss_pred             hcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC
Q 040261          115 AFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENI  194 (343)
Q Consensus       115 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  194 (343)
                      +.++. +...+..+...+...|++++|...++++.+.+       +.+...+..+..++...|++++|...+++..+.+.
T Consensus       332 ~ldP~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-------P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P  403 (553)
T PRK12370        332 ELDHN-NPQALGLLGLINTIHSEYIVGSLLFKQANLLS-------PISADIKYYYGWNLFMAGQLEEALQTINECLKLDP  403 (553)
T ss_pred             hcCCC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            87544 67778888888888999999999999988875       44566788888889999999999999999887642


Q ss_pred             CCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          195 NPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP-NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNT  273 (343)
Q Consensus       195 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  273 (343)
                      . +...+..++..+...|++++|...++++.+.. +| +...+..+..++...|+.++|...++++.... +.+....+.
T Consensus       404 ~-~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~  480 (553)
T PRK12370        404 T-RAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNL  480 (553)
T ss_pred             C-ChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHH
Confidence            2 22233344445666788999999998887663 34 34556677788888999999999998876542 223444555


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCC-CCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNG-CMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      +...|...|  ++|...++.+.+.. ..+....+  +-..+.-.|+.+.+..+ +++.+.+
T Consensus       481 l~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        481 LYAEYCQNS--ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             HHHHHhccH--HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHHHHH-HHhhccc
Confidence            656667777  47777777665431 11222222  34445566776666665 7776654

>PRK12370 invasion protein regulator; Provisional

Probab=99.64  E-value=1.7e-12  Score=112.09  Aligned_cols=266  Identities=12%  Similarity=0.054  Sum_probs=141.9

Q ss_pred             CChhhHHHHHHHHHh-----cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhc---------CCcchHHHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAK-----NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKM---------GRVSPGFVVLGRILR   80 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~   80 (343)
                      .+...|...+.+...     .+++++|.++|++..+.. +.+...|..+..++...         +++++|...+++..+
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            344445454444322     123456677777666543 22344455554444322         235566777777666


Q ss_pred             cCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcccc
Q 040261           81 SCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        81 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      .++. +...+..+...+...|++++|...+++..+.++. +...+..+..++...|++++|...+++..+.+       +
T Consensus       333 ldP~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~-------P  403 (553)
T PRK12370        333 LDHN-NPQALGLLGLINTIHSEYIVGSLLFKQANLLSPI-SADIKYYYGWNLFMAGQLEEALQTINECLKLD-------P  403 (553)
T ss_pred             cCCC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-------C
Confidence            5422 4556666666666667777777777777666432 44556666666777777777777777776654       1


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC-HHHHHHH
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN-VVTFNVI  239 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l  239 (343)
                      .+...+..++..+...|++++|...++++.....+-+...+..+..++...|++++|...+.++...  .|+ ....+.+
T Consensus       404 ~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l  481 (553)
T PRK12370        404 TRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLL  481 (553)
T ss_pred             CChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHH
Confidence            1222333334445556677777777766655432223444555666666677777777777665443  233 3333444


Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          240 MNELCKNGKMDEASRLLELMIQIG-VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       240 ~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...+...|  ++|...++.+.+.. ..+....+  +-..+.-.|+-+.+..+ +++.+.
T Consensus       482 ~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~  535 (553)
T PRK12370        482 YAEYCQNS--ERALPTIREFLESEQRIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNE  535 (553)
T ss_pred             HHHHhccH--HHHHHHHHHHHHHhhHhhcCchH--HHHHHHHHhhhHHHHHH-HHhhcc
Confidence            44555555  35555555554421 11111111  22334445555555554 555554

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

Probab=99.63  E-value=3.3e-12  Score=101.65  Aligned_cols=195  Identities=14%  Similarity=0.111  Sum_probs=148.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHH
Q 040261          125 YTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSL  204 (343)
Q Consensus       125 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  204 (343)
                      |.-+..+|....+.++..+.|......+       +.++.+|..-..++.-.+++++|..=|++..... +-+...|-.+
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~ld-------p~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~-pe~~~~~iQl  434 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAEDLD-------PENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD-PENAYAYIQL  434 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHhcC-------CCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC-hhhhHHHHHH
Confidence            5556667777788888888888887765       5567778777777778888888888888887754 2245566666


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC-------CCHHHHHHHHHH
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR-------PDASVYNTLMDG  277 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-------~~~~~~~~l~~~  277 (343)
                      .-+..+.+.++++...|++..++ ++-.+..|+.....+...+++++|.+.|+..++....       +.+.+...++..
T Consensus       435 ~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~  513 (606)
T KOG0547|consen  435 CCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVL  513 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhh
Confidence            66677888999999999999887 5666889999999999999999999999998875311       112222333322


Q ss_pred             HhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          278 FCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       278 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      - -.+++..|..++++..+.. +.....|..|...-.+.|+.++|+++|++..
T Consensus       514 q-wk~d~~~a~~Ll~KA~e~D-pkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  514 Q-WKEDINQAENLLRKAIELD-PKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             c-hhhhHHHHHHHHHHHHccC-chHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            2 3389999999999998864 3356788999999999999999999998764

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

Probab=99.61  E-value=2.7e-11  Score=100.01  Aligned_cols=303  Identities=11%  Similarity=0.042  Sum_probs=159.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...|......--..|..++...+|+++...- +-....|......+...|+...|..++..+.+.... +...|...+.
T Consensus       549 k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavK  626 (913)
T KOG0495|consen  549 KKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVK  626 (913)
T ss_pred             hhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHH
Confidence            44445444444444555555555555554421 222333444444444455555555555555544322 4445555555


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .-.....++.|..+|.+....  .|+...|.--+...--.+..++|.+++++..+..       +.-...|..+...+.+
T Consensus       627 le~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~f-------p~f~Kl~lmlGQi~e~  697 (913)
T KOG0495|consen  627 LEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEALRLLEEALKSF-------PDFHKLWLMLGQIEEQ  697 (913)
T ss_pred             HhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhC-------CchHHHHHHHhHHHHH
Confidence            555555555555555554443  3344444444444444455555555555554442       2223344444444444


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      .++.+.|...|..-.+. .+-.+..|-.+...--+.|.+-.|..++++..-++ +-+...|-..++.-.+.|+.+.|..+
T Consensus       698 ~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~l  775 (913)
T KOG0495|consen  698 MENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELL  775 (913)
T ss_pred             HHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHH
Confidence            44444444444333221 12223334444444444444444444444444332 22344444444444444444444444


Q ss_pred             HHHHHHc-----------------------------CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHH
Q 040261          256 LELMIQI-----------------------------GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSY  306 (343)
Q Consensus       256 ~~~~~~~-----------------------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  306 (343)
                      ..++.+.                             ...-|+.+...+...|....++++|++.|.+..+.+ +....+|
T Consensus       776 makALQecp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d-~d~GD~w  854 (913)
T KOG0495|consen  776 MAKALQECPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKD-PDNGDAW  854 (913)
T ss_pred             HHHHHHhCCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccC-CccchHH
Confidence            4333221                             013456667778888888899999999999998864 3456788


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          307 GILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       307 ~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ..+...+.++|.-++-.+++......
T Consensus       855 a~fykfel~hG~eed~kev~~~c~~~  880 (913)
T KOG0495|consen  855 AWFYKFELRHGTEEDQKEVLKKCETA  880 (913)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            88999999999888888888887644

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

Probab=99.61  E-value=4.3e-11  Score=94.83  Aligned_cols=166  Identities=12%  Similarity=0.049  Sum_probs=145.6

Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      .+.|...+...|+-.++.++|...|+...+.+. -....|+.+..-|....+...|..-+++.++-. +-|-..|-.|.+
T Consensus       329 R~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp-~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQ  406 (559)
T KOG1155|consen  329 RPETCCIIANYYSLRSEHEKAVMYFKRALKLNP-KYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQ  406 (559)
T ss_pred             CccceeeehhHHHHHHhHHHHHHHHHHHHhcCc-chhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhH
Confidence            345666677778888999999999999998763 357789999999999999999999999999874 667889999999


Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHH
Q 040261          242 ELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEG  321 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  321 (343)
                      +|.-.+.+.-|+-.|+++.+.. +-|...|.+|..+|.+.++.++|.+.|.+....| ..+...+..|...|-+.++.++
T Consensus       407 aYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~e  484 (559)
T KOG1155|consen  407 AYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNE  484 (559)
T ss_pred             HHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHH
Confidence            9999999999999999999875 6688999999999999999999999999999876 3366788999999999999999


Q ss_pred             HHHHHHHHHh
Q 040261          322 ALSLYSEMLS  331 (343)
Q Consensus       322 a~~~~~~~~~  331 (343)
                      |...|++-++
T Consensus       485 Aa~~yek~v~  494 (559)
T KOG1155|consen  485 AAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHH
Confidence            9999887765

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.61  E-value=1.6e-12  Score=100.39  Aligned_cols=202  Identities=12%  Similarity=0.078  Sum_probs=134.6

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      ....+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+++..+.... +...+..+..
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~  107 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPN-NGDVLNNYGT  107 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHH
Confidence            34566666777777777777777777776653 224556666677777777777777777777665433 4556666677


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY  210 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (343)
                      .+...|++++|.+.+++......     .+.....+..+..++...|++++|...+.+..... +.+...+..+...+..
T Consensus       108 ~~~~~g~~~~A~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  181 (234)
T TIGR02521       108 FLCQQGKYEQAMQQFEQAIEDPL-----YPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYL  181 (234)
T ss_pred             HHHHcccHHHHHHHHHHHHhccc-----cccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHH
Confidence            77777777777777777765421     12233455666677777778888877777776653 2245566677777777


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      .|++++|...+++..+. .+.+...+..+...+...|+.++|..+.+.+..
T Consensus       182 ~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       182 RGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             cCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            78888888777777765 234455566666777777788887777766654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.61  E-value=2.5e-12  Score=99.33  Aligned_cols=198  Identities=15%  Similarity=0.134  Sum_probs=105.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHH
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTS  203 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  203 (343)
                      .+..+...+...|++++|...+++.....       +.+...+..+...+...|++++|.+.+++..+.. +.+...+..
T Consensus        33 ~~~~la~~~~~~~~~~~A~~~~~~~l~~~-------p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~  104 (234)
T TIGR02521        33 IRVQLALGYLEQGDLEVAKENLDKALEHD-------PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNN  104 (234)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHH
Confidence            33444444445555555555555444432       2223344444455555555555555555544432 123334444


Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCC
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGV-QPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTG  282 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  282 (343)
                      +...+...|++++|...++...+... ......+..+...+...|++++|...+++..+.. +.+...+..+...+...|
T Consensus       105 ~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  183 (234)
T TIGR02521       105 YGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRG  183 (234)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcC
Confidence            45555555555555555555544311 1123344445556666666666666666666543 334455666666666677


Q ss_pred             chHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          283 RVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       283 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ++++|...+++..+. .+.+...+..+...+...|+.++|..+.+.+..
T Consensus       184 ~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       184 QYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             CHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            777777777666654 233455555566666666777777666665543

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.

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

Probab=99.61  E-value=2.5e-12  Score=110.27  Aligned_cols=279  Identities=13%  Similarity=0.073  Sum_probs=179.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc---CCCccH------HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRS---CFTPDA------VTFTSLIKGLCAESRIMEAAALFTKLRAFGCK  119 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  119 (343)
                      ++.+...|.+...+...|++..|...|......   ...++.      .+-..+.+..-..++++.|.+.|..+.+.  .
T Consensus       449 ~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilke--h  526 (1018)
T KOG2002|consen  449 QIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKE--H  526 (1018)
T ss_pred             CCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHH--C
Confidence            344555555555555556666666555555443   111111      11222334444445556666666655554  2


Q ss_pred             CC-HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCC
Q 040261          120 PD-VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPD  197 (343)
Q Consensus       120 ~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~  197 (343)
                      |. ...|..++......+...+|..+++.....+       ..++..+..+...+.+...+..|.+-|..+.+.- ..+|
T Consensus       527 p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-------~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D  599 (1018)
T KOG2002|consen  527 PGYIDAYLRLGCMARDKNNLYEASLLLKDALNID-------SSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTD  599 (1018)
T ss_pred             chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-------cCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCc
Confidence            22 2233333333333456667777777766654       3455666666667777777777777666655431 2245


Q ss_pred             hhhHHHHHHHHhc------------cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC
Q 040261          198 VVTYTSLIRGFCY------------ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR  265 (343)
Q Consensus       198 ~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  265 (343)
                      +.+.-.|...|.+            .+..+.|+.+|.++++.. +-|...-+-+..+++..|++..|..+|....+.. .
T Consensus       600 ~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~-~  677 (1018)
T KOG2002|consen  600 AYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREAT-S  677 (1018)
T ss_pred             hhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHH-h
Confidence            5554445544432            234678888888888874 5567777888888999999999999999998875 3


Q ss_pred             CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC-CCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          266 PDASVYNTLMDGFCLTGRVNRAKELFVSMESN-GCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       266 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      ....+|-.+.++|..+|++..|.++|+...+. .-..+......|.+++.+.|.+.+|.+.+.......+.-..
T Consensus       678 ~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~  751 (1018)
T KOG2002|consen  678 DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTS  751 (1018)
T ss_pred             hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccch
Confidence            34567888999999999999999999876554 33457788889999999999999999998888766443333

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

Probab=99.60  E-value=3.6e-12  Score=100.87  Aligned_cols=281  Identities=14%  Similarity=0.047  Sum_probs=207.5

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHH--HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNI--LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      ..-+.++|+++.|++++.-+....-+.....-+.  .++.+.--.++..|.++-+..+... ..++.....-.......|
T Consensus       426 a~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~d-ryn~~a~~nkgn~~f~ng  504 (840)
T KOG2003|consen  426 AGELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNID-RYNAAALTNKGNIAFANG  504 (840)
T ss_pred             HHHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhccc-ccCHHHhhcCCceeeecC
Confidence            4457789999999999988876432222222222  2222223346777877777766542 223333333334445578


Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHH
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDK  181 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  181 (343)
                      ++++|.+.|.+.......... ..-.+.-.+-..|+.++|+..|-++...       +..+..+...+...|....+..+
T Consensus       505 d~dka~~~ykeal~ndasc~e-alfniglt~e~~~~ldeald~f~klh~i-------l~nn~evl~qianiye~led~aq  576 (840)
T KOG2003|consen  505 DLDKAAEFYKEALNNDASCTE-ALFNIGLTAEALGNLDEALDCFLKLHAI-------LLNNAEVLVQIANIYELLEDPAQ  576 (840)
T ss_pred             cHHHHHHHHHHHHcCchHHHH-HHHHhcccHHHhcCHHHHHHHHHHHHHH-------HHhhHHHHHHHHHHHHHhhCHHH
Confidence            999999999999876433222 2233344577889999999999887654       35567788888899999999999


Q ss_pred             HHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          182 AKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       182 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      |++++.+.... ++.|+..++-+...|-+.|+-.+|+..+-.--+. ++.+..+...|...|....-+++++.+|++..-
T Consensus       577 aie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal  654 (840)
T KOG2003|consen  577 AIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL  654 (840)
T ss_pred             HHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence            99999887664 5668899999999999999999999887665554 567788888899999999999999999998765


Q ss_pred             cCCCCCHHHHHHHHHH-HhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          262 IGVRPDASVYNTLMDG-FCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       262 ~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                        +.|+..-|..++.. +.+.|++.+|.++++...+. ++.|..+...|++.+...|-
T Consensus       655 --iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  655 --IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             --cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence              48999999887764 55789999999999998876 56688888888888877663

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

Probab=99.59  E-value=3.7e-12  Score=100.77  Aligned_cols=186  Identities=13%  Similarity=0.119  Sum_probs=133.1

Q ss_pred             cCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcH
Q 040261          135 TGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDW  214 (343)
Q Consensus       135 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  214 (343)
                      .|++++|.+.+++....+.       .-....-.+.-.+-..|+.++|++.|-++..- +..+...+..+...|-...+.
T Consensus       503 ngd~dka~~~ykeal~nda-------sc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~  574 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDA-------SCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDP  574 (840)
T ss_pred             cCcHHHHHHHHHHHHcCch-------HHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCH
Confidence            4556666666666554430       11111222223455667777777777665442 123566666777777777788


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          215 NEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       215 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      .+|++++.+.... ++.|+.....|...|-+.|+..+|.+.+-.--+. ++-+..+...|...|....-++++...|++.
T Consensus       575 aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~eka  652 (840)
T KOG2003|consen  575 AQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKA  652 (840)
T ss_pred             HHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            8888887666554 4556888889999999999999998887554443 4678888888998999999999999999987


Q ss_pred             HhCCCCccHHHHHHHHHHH-HhcCChHHHHHHHHHHHhC
Q 040261          295 ESNGCMRDVFSYGILINGY-CKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       295 ~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~~~~~  332 (343)
                      .-  +.|+..-|..++..| .+.|+++.|+.+|++...+
T Consensus       653 al--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk  689 (840)
T KOG2003|consen  653 AL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK  689 (840)
T ss_pred             Hh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            66  469999999888765 5679999999999998654

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

Probab=99.58  E-value=1.3e-12  Score=98.91  Aligned_cols=231  Identities=16%  Similarity=0.036  Sum_probs=191.4

Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHH
Q 040261           91 TSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTIT  170 (343)
Q Consensus        91 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  170 (343)
                      +.+.++|.+.|.+.+|.+.++...+.  .|-+.||..|-+.|.+..+++.|+.++.+-.+..       |-++.....+.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f-------P~~VT~l~g~A  297 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF-------PFDVTYLLGQA  297 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC-------CchhhhhhhhH
Confidence            56788999999999999999888876  5667788889999999999999999999988763       44555556778


Q ss_pred             HHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChh
Q 040261          171 DGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMD  250 (343)
Q Consensus       171 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  250 (343)
                      +.+...++.++|.++++...+.. +.++.....+...|.-.++++-|+..++++++.|+ -+...|+.+.-+|.-.++++
T Consensus       298 Ri~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  298 RIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQID  375 (478)
T ss_pred             HHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchh
Confidence            88899999999999999988764 34677777777788888999999999999999984 47788999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHH
Q 040261          251 EASRLLELMIQIGVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSE  328 (343)
Q Consensus       251 ~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  328 (343)
                      -++.-|++....--.|+  ..+|-.+....+..||+..|.+.|+-...++ ..+...++.|.-.-.+.|+.++|..+++.
T Consensus       376 ~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~  454 (478)
T KOG1129|consen  376 LVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNA  454 (478)
T ss_pred             hhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHH
Confidence            99999998877643344  4567777778888999999999999888764 34567888888888899999999999998


Q ss_pred             HHhCC
Q 040261          329 MLSKG  333 (343)
Q Consensus       329 ~~~~~  333 (343)
                      .....
T Consensus       455 A~s~~  459 (478)
T KOG1129|consen  455 AKSVM  459 (478)
T ss_pred             hhhhC
Confidence            87553

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

Probab=99.57  E-value=1.3e-12  Score=98.90  Aligned_cols=230  Identities=14%  Similarity=0.074  Sum_probs=198.3

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHH-HHHHHHHHH
Q 040261           55 YNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFT-YTTLINGLC  133 (343)
Q Consensus        55 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~  133 (343)
                      -+.+..+|.+.|-+.+|.+-++..++.  .|-+.||..+-+.|.+..+...|+.++.+-.+.  .|-.+| ...+...+-
T Consensus       226 k~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~e  301 (478)
T KOG1129|consen  226 KQQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHE  301 (478)
T ss_pred             HHHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHH
Confidence            366889999999999999999998876  567788999999999999999999999998876  444444 456788889


Q ss_pred             hcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc
Q 040261          134 RTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND  213 (343)
Q Consensus       134 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  213 (343)
                      ..++.++|.++++...+..       +.++.....+...|.-.++++.|++.++++.+.|+. ++..|+.+.-+|.-.++
T Consensus       302 am~~~~~a~~lYk~vlk~~-------~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ  373 (478)
T KOG1129|consen  302 AMEQQEDALQLYKLVLKLH-------PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQ  373 (478)
T ss_pred             HHHhHHHHHHHHHHHHhcC-------CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcc
Confidence            9999999999999999875       556777777778888899999999999999999875 78999999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          214 WNEAKCLFIEMMDQGVQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      ++-++.-|.+.+..--.|+  ..+|..+.......||+..|.+.|+-...++ ..+...++.|.-.-.+.|+++.|..++
T Consensus       374 ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll  452 (478)
T KOG1129|consen  374 IDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLL  452 (478)
T ss_pred             hhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHH
Confidence            9999999999887643344  4567778888899999999999999998876 557788999998889999999999999


Q ss_pred             HHHHhC
Q 040261          292 VSMESN  297 (343)
Q Consensus       292 ~~~~~~  297 (343)
                      +.....
T Consensus       453 ~~A~s~  458 (478)
T KOG1129|consen  453 NAAKSV  458 (478)
T ss_pred             HHhhhh
Confidence            988875

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

Probab=99.56  E-value=8.7e-11  Score=98.59  Aligned_cols=297  Identities=12%  Similarity=0.105  Sum_probs=210.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      ..--....+...|++++|++.++.-.. .+.............+.+.|+.++|..++..+++.++. |...|..+..+..
T Consensus         6 ~lLY~~~il~e~g~~~~AL~~L~~~~~-~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPd-n~~Yy~~L~~~~g   83 (517)
T PF12569_consen    6 LLLYKNSILEEAGDYEEALEHLEKNEK-QILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPD-NYDYYRGLEEALG   83 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhhhh-hCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHh
Confidence            333455677899999999999987544 34444566777889999999999999999999998632 5555666666652


Q ss_pred             hc-----CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH-HHHHHHHHHHccCCCCCccccCCcchHHHHHHH
Q 040261           99 AE-----SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI-VALNLFEEMANGNGEFGVVCKPDAITYSTITDG  172 (343)
Q Consensus        99 ~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  172 (343)
                      -.     .+.+...++|+++...-  |.......+.-.+.....+. .+..++..+...|      +   +.+|..+-..
T Consensus        84 ~~~~~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~Kg------v---PslF~~lk~L  152 (517)
T PF12569_consen   84 LQLQLSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKG------V---PSLFSNLKPL  152 (517)
T ss_pred             hhcccccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcC------C---chHHHHHHHH
Confidence            22     35677888999887763  33333333322222222232 3445555666655      2   4567777777


Q ss_pred             HHhcCChHHHHHHHHHhhhC----C----------CCCCh--hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC-HHH
Q 040261          173 LCKEGFVDKAKELFLKMKDE----N----------INPDV--VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN-VVT  235 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~~----~----------~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~  235 (343)
                      |......+-..+++......    +          -+|+.  .++..+.+.|...|++++|+.+++..+++  .|+ ...
T Consensus       153 y~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~el  230 (517)
T PF12569_consen  153 YKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVEL  230 (517)
T ss_pred             HcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHH
Confidence            77665655556666554322    1          12333  34566678888999999999999999987  455 778


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHH------HH--H
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVF------SY--G  307 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~--~  307 (343)
                      |..-.+.+-..|++.+|...++.+...+ .-|..+-+-.+..+.++|++++|.+++..+.+.+..|...      .|  .
T Consensus       231 y~~KarilKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~  309 (517)
T PF12569_consen  231 YMTKARILKHAGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFET  309 (517)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHH
Confidence            8888999999999999999999999986 4577777788889999999999999999998876433221      22  3


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHh
Q 040261          308 ILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       308 ~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ....+|.+.|++..|++-|..+.+
T Consensus       310 e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  310 ECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHH
Confidence            446789999999999887776654

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 [], [].

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

Probab=99.56  E-value=2.3e-12  Score=109.46  Aligned_cols=254  Identities=14%  Similarity=0.118  Sum_probs=172.1

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +++-.+...|.. |+..+|..+|.-|+..|+.+.|- +|.-|.-...+.+...++.++.+....++.+.+.         
T Consensus        11 nfla~~e~~gi~-PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk---------   79 (1088)
T KOG4318|consen   11 NFLALHEISGIL-PNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK---------   79 (1088)
T ss_pred             hHHHHHHHhcCC-CchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC---------
Confidence            356778888888 88899999999999999999888 8888887777778889999999888888877765         


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHH---HHHHHHHHH----hcCCCCCHHHH--------------HHHHHHHHhcCChHH
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIME---AAALFTKLR----AFGCKPDVFTY--------------TTLINGLCRTGHTIV  140 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~----~~~~~~~~~~~--------------~~l~~~~~~~~~~~~  140 (343)
                        .|.+.+|..+..+|...||...   +.+.+..+.    ..|+-....-+              ...+....-.|.++.
T Consensus        80 --ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaq  157 (1088)
T KOG4318|consen   80 --EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQ  157 (1088)
T ss_pred             --CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHH
Confidence              6788899999999999998654   333222221    12221111111              112222233444445


Q ss_pred             HHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC-hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHH
Q 040261          141 ALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF-VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKC  219 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  219 (343)
                      +++++..+.....       ..  .+..+++-+..... +++-....+...+   .|++.+|..++.+-..+|+.+.|..
T Consensus       158 llkll~~~Pvsa~-------~~--p~~vfLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a~l~~alaag~~d~Ak~  225 (1088)
T KOG4318|consen  158 LLKLLAKVPVSAW-------NA--PFQVFLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHAVLKRALAAGDVDGAKN  225 (1088)
T ss_pred             HHHHHhhCCcccc-------cc--hHHHHHHHhccCCchHHHHHHHHHHhhc---CCChHHHHHHHHHHHhcCchhhHHH
Confidence            5554444332210       01  11112443333322 3333333333333   4788888888888888888888988


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          220 LFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      ++.+|.+.|++.+.+-|..|+-+   .++...+..+++-|.+.|+.|+..|+...+..+...|.
T Consensus       226 ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  226 LLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             HHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            88888888888888877777665   77888888888888888888888888888777777554

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

Probab=99.55  E-value=5.3e-11  Score=96.59  Aligned_cols=287  Identities=14%  Similarity=0.072  Sum_probs=221.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++...-...+.+...+++.+..++.+...+.. ++....+..-|.++...|+..+-+.+-.++.+.- +..+.+|-++.
T Consensus       242 ~~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg  319 (611)
T KOG1173|consen  242 ENLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVG  319 (611)
T ss_pred             hcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHH
Confidence            455566666777788889999999999888765 6677777777778889999888888888888764 44678888888


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      --|.-.|+..+|.+.|.+....+.. =...|......|+-.+..++|...+..+.+.-       +-...-+.-+.--|.
T Consensus       320 ~YYl~i~k~seARry~SKat~lD~~-fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~-------~G~hlP~LYlgmey~  391 (611)
T KOG1173|consen  320 CYYLMIGKYSEARRYFSKATTLDPT-FGPAWLAFGHSFAGEGEHDQAMAAYFTAARLM-------PGCHLPSLYLGMEYM  391 (611)
T ss_pred             HHHHHhcCcHHHHHHHHHHhhcCcc-ccHHHHHHhHHhhhcchHHHHHHHHHHHHHhc-------cCCcchHHHHHHHHH
Confidence            8888889999999999887765322 24578888899999999999998888877653       223333444556678


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc--CC----CCCHHHHHHHHHHHHhCCC
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ--GV----QPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~----~~~~~~~~~l~~~~~~~~~  248 (343)
                      +.++...|.+.|.+..... |-|+..++-+.-.....+.+.+|..+|+..+..  .+    .--..+++.|..+|.+.+.
T Consensus       392 ~t~n~kLAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~  470 (611)
T KOG1173|consen  392 RTNNLKLAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNK  470 (611)
T ss_pred             HhccHHHHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhh
Confidence            8899999999998887653 446777787877777888999999999887632  01    1134567888899999999


Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh
Q 040261          249 MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK  315 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  315 (343)
                      +++|+..++...... +.+..++..+.-.|...|+++.|.+.|.+....  .|+..+...++..+..
T Consensus       471 ~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL~l--~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  471 YEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKALAL--KPDNIFISELLKLAIE  534 (611)
T ss_pred             HHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHHhc--CCccHHHHHHHHHHHH
Confidence            999999999988875 678889999988999999999999999988764  5777666666665443

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

Probab=99.55  E-value=8.1e-11  Score=101.32  Aligned_cols=307  Identities=11%  Similarity=-0.005  Sum_probs=204.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCC--CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLF--PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      .++.+.+.|...|.-.|+++.++.+...+......  .-...|..+.+++-..|++++|..+|.+..+....--...+..
T Consensus       268 ~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~G  347 (1018)
T KOG2002|consen  268 ENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVG  347 (1018)
T ss_pred             CCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccc
Confidence            47778888888888888888888888877654311  1233577788888888888888888877776532211334455


Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC----ChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG----HTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      +...+.+.|+.+.+...|+.+...... +..+...+...|...+    ..+.|..++.+.....       +.+...|..
T Consensus       348 lgQm~i~~~dle~s~~~fEkv~k~~p~-~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-------~~d~~a~l~  419 (1018)
T KOG2002|consen  348 LGQMYIKRGDLEESKFCFEKVLKQLPN-NYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-------PVDSEAWLE  419 (1018)
T ss_pred             hhHHHHHhchHHHHHHHHHHHHHhCcc-hHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-------cccHHHHHH
Confidence            777888888888888888888776322 5556666666666654    4566777777766653       556677777


Q ss_pred             HHHHHHhcCChHHHHHHHHHhh----hCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---CCCCCH------HH
Q 040261          169 ITDGLCKEGFVDKAKELFLKMK----DENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---GVQPNV------VT  235 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~------~~  235 (343)
                      +...+....-+.. +.++..+.    ..+..+.+...|.+...+...|+++.|...|......   ...++.      .+
T Consensus       420 laql~e~~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~  498 (1018)
T KOG2002|consen  420 LAQLLEQTDPWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTL  498 (1018)
T ss_pred             HHHHHHhcChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHH
Confidence            7776665444433 66665533    3344566788888888888888888888888877654   112222      22


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK  315 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  315 (343)
                      -..+.......++.+.|...|..+.+.. +--...|..++......+...+|...++...... ..++..+..+...+..
T Consensus       499 ~YNlarl~E~l~~~~~A~e~Yk~Ilkeh-p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-~~np~arsl~G~~~l~  576 (1018)
T KOG2002|consen  499 KYNLARLLEELHDTEVAEEMYKSILKEH-PGYIDAYLRLGCMARDKNNLYEASLLLKDALNID-SSNPNARSLLGNLHLK  576 (1018)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHHHC-chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-cCCcHHHHHHHHHHHh
Confidence            3335666677778888888888887753 2223445555434444567778888888776642 4456666666767777


Q ss_pred             cCChHHHHHHHHHHHhC
Q 040261          316 NKEIEGALSLYSEMLSK  332 (343)
Q Consensus       316 ~~~~~~a~~~~~~~~~~  332 (343)
                      ..++.-|.+-|+...+.
T Consensus       577 k~~~~~a~k~f~~i~~~  593 (1018)
T KOG2002|consen  577 KSEWKPAKKKFETILKK  593 (1018)
T ss_pred             hhhhcccccHHHHHHhh
Confidence            77777777766666554

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

Probab=99.52  E-value=5.1e-11  Score=96.69  Aligned_cols=277  Identities=10%  Similarity=0.033  Sum_probs=220.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      .+......-..-+...+++.+..++++.+.+.. ++....+..-|.++...|+..+-..+-.++.+.-+. ...+|-++.
T Consensus       242 ~~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~-~a~sW~aVg  319 (611)
T KOG1173|consen  242 ENLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPS-KALSWFAVG  319 (611)
T ss_pred             hcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhCCC-CCcchhhHH
Confidence            344555556666778899999999999998864 556667777777888999988888887888877433 677899999


Q ss_pred             HHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHh
Q 040261          130 NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFC  209 (343)
Q Consensus       130 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  209 (343)
                      --|...|+..+|.+.|.+....++       .-...|..+...+.-.|..++|+..+....+.- +-...-+--+.--|.
T Consensus       320 ~YYl~i~k~seARry~SKat~lD~-------~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~-~G~hlP~LYlgmey~  391 (611)
T KOG1173|consen  320 CYYLMIGKYSEARRYFSKATTLDP-------TFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLM-PGCHLPSLYLGMEYM  391 (611)
T ss_pred             HHHHHhcCcHHHHHHHHHHhhcCc-------cccHHHHHHhHHhhhcchHHHHHHHHHHHHHhc-cCCcchHHHHHHHHH
Confidence            999999999999999999988763       335689999999999999999999998876541 112222333445677


Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc----C--CCCCHHHHHHHHHHHhcCCc
Q 040261          210 YANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI----G--VRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       210 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~--~~~~~~~~~~l~~~~~~~~~  283 (343)
                      +.++.+-|...|.+..... +-|+...+.+.-.....+.+.+|..+|+.....    +  ...-..+++.|..+|.+.+.
T Consensus       392 ~t~n~kLAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~  470 (611)
T KOG1173|consen  392 RTNNLKLAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNK  470 (611)
T ss_pred             HhccHHHHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhh
Confidence            8899999999999988762 556778888888878889999999999887732    1  11245678999999999999


Q ss_pred             hHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCccc
Q 040261          284 VNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVT  340 (343)
Q Consensus       284 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~t  340 (343)
                      +++|+..+++..... +.+..++.++.-.|...|+++.|...|.+.+  .+.||..+
T Consensus       471 ~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~  524 (611)
T KOG1173|consen  471 YEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIF  524 (611)
T ss_pred             HHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHH
Confidence            999999999988763 5688999999999999999999999999988  66787643

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

Probab=99.52  E-value=8.3e-10  Score=91.50  Aligned_cols=264  Identities=11%  Similarity=0.003  Sum_probs=164.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040261           55 YNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR  134 (343)
Q Consensus        55 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  134 (343)
                      |..-...|.+.+.++-|..+|...++-- +.+...|......--..|..++...++++....-.+ ....|......+..
T Consensus       519 w~~da~~~~k~~~~~carAVya~alqvf-p~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pk-ae~lwlM~ake~w~  596 (913)
T KOG0495|consen  519 WLDDAQSCEKRPAIECARAVYAHALQVF-PCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPK-AEILWLMYAKEKWK  596 (913)
T ss_pred             HhhhHHHHHhcchHHHHHHHHHHHHhhc-cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHh
Confidence            3333344444444444444554444431 223444444444444445555556666665554222 34445555555666


Q ss_pred             cCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcH
Q 040261          135 TGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDW  214 (343)
Q Consensus       135 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  214 (343)
                      .|+...|..++.+..+..       +.+...|..-+.......+++.|..+|.+....+  |+...|.--+...--.+..
T Consensus       597 agdv~~ar~il~~af~~~-------pnseeiwlaavKle~en~e~eraR~llakar~~s--gTeRv~mKs~~~er~ld~~  667 (913)
T KOG0495|consen  597 AGDVPAARVILDQAFEAN-------PNSEEIWLAAVKLEFENDELERARDLLAKARSIS--GTERVWMKSANLERYLDNV  667 (913)
T ss_pred             cCCcHHHHHHHHHHHHhC-------CCcHHHHHHHHHHhhccccHHHHHHHHHHHhccC--CcchhhHHHhHHHHHhhhH
Confidence            677777777777766654       3355666666777777777777777777666543  4555555555555556677


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          215 NEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       215 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      ++|.+++++.++. ++.-...|..+.+.+.+.++.+.|...|..-.+. ++-....|..|...=-+.|.+-+|..++++.
T Consensus       668 eeA~rllEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildra  745 (913)
T KOG0495|consen  668 EEALRLLEEALKS-FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRA  745 (913)
T ss_pred             HHHHHHHHHHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            7777777777665 2333556666677777777777777766554443 2444556677776667778888888888887


Q ss_pred             HhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          295 ESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       295 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .-.+ +.+...|...++.-.+.|..++|..+..+.++.
T Consensus       746 rlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe  782 (913)
T KOG0495|consen  746 RLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQE  782 (913)
T ss_pred             HhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7665 457788888888888999988888777776654

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

Probab=99.50  E-value=4.8e-12  Score=107.59  Aligned_cols=260  Identities=17%  Similarity=0.202  Sum_probs=163.6

Q ss_pred             HHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           38 SLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        38 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      .++-.+...|+.|+..+|..+|.-|+..|+.+.|- +|.-|.-...+.+...|+.++.+..+.++.+.+.          
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            45667788899999999999999999999999998 9998888777888899999999988888887776          


Q ss_pred             CCCCHHHHHHHHHHHHhcCChHH---HHHHHHHHHccCCCCCcccc------------CCcchHHHHHHHHHhcCChHHH
Q 040261          118 CKPDVFTYTTLINGLCRTGHTIV---ALNLFEEMANGNGEFGVVCK------------PDAITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       118 ~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~------------~~~~~~~~l~~~~~~~~~~~~a  182 (343)
                       .|...+|..|..+|...||...   +.+.+..+...-...+...+            .....-...+....-.|.++.+
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaql  158 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQL  158 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHH
Confidence             5788899999999999998754   33322222222111110000            0000111222223334455555


Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccC-cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYAN-DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      ++++..+....... +  +..+++-+.... .+++...+.+...+   .|+..+|..++.+....|+.+.|..++.+|.+
T Consensus       159 lkll~~~Pvsa~~~-p--~~vfLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a~l~~alaag~~d~Ak~ll~emke  232 (1088)
T KOG4318|consen  159 LKLLAKVPVSAWNA-P--FQVFLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHAVLKRALAAGDVDGAKNLLYEMKE  232 (1088)
T ss_pred             HHHHhhCCcccccc-h--HHHHHHHhccCCchHHHHHHHHHHhhc---CCChHHHHHHHHHHHhcCchhhHHHHHHHHHH
Confidence            55554443221100 0  111233333222 23333333333322   46777777777777777777777777777777


Q ss_pred             cCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          262 IGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       262 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                      .|++.+..-|..|+-+   .++..-+..+++.|.+.|+.|+..|+...+..+..+|.
T Consensus       233 ~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  233 KGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             cCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            7777666666666544   66666777777777777777777777766666666544

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

Probab=99.48  E-value=1.5e-09  Score=86.78  Aligned_cols=321  Identities=16%  Similarity=0.176  Sum_probs=197.0

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL-YTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      +||++......  .+...|-..+..-.++.++..|..+|++.+..  -|-+ ..|...+.+--..|++..|.++|++..+
T Consensus        94 Sv~ERALdvd~--r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~ymEE~LgNi~gaRqiferW~~  169 (677)
T KOG1915|consen   94 SVFERALDVDY--RNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIYMEEMLGNIAGARQIFERWME  169 (677)
T ss_pred             HHHHHHHhccc--ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHHHHHHhcccHHHHHHHHHHHc
Confidence            36777776664  47777888888888888888999998888763  2333 3566666666677888888899888876


Q ss_pred             cCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCC----
Q 040261           81 SCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFG----  156 (343)
Q Consensus        81 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----  156 (343)
                      -  +|+...|++.++.=.+...++.|..+|++..-.  .|+..+|......=.+.|....+..+++...+.-++..    
T Consensus       170 w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~  245 (677)
T KOG1915|consen  170 W--EPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEI  245 (677)
T ss_pred             C--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHH
Confidence            4  788888999888888888888888888887754  57777777777776777777766666666554322100    


Q ss_pred             -----------------------------c-----------------------------------------cccCCcchH
Q 040261          157 -----------------------------V-----------------------------------------VCKPDAITY  166 (343)
Q Consensus       157 -----------------------------~-----------------------------------------~~~~~~~~~  166 (343)
                                                   +                                         ..+.|-.+|
T Consensus       246 lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~nYDsW  325 (677)
T KOG1915|consen  246 LFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPYNYDSW  325 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCCCchHH
Confidence                                         0                                         001122223


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCCCCCh--hhHHHHH--------HHHhccCcHHHHHHHHHHHHH----------
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENINPDV--VTYTSLI--------RGFCYANDWNEAKCLFIEMMD----------  226 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~--------~~~~~~~~~~~a~~~~~~~~~----------  226 (343)
                      --.++.-...|+.+...++|++.... ++|-.  ..|...+        -.-....+.+.+.++++..++          
T Consensus       326 fdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~lIPHkkFtFa  404 (677)
T KOG1915|consen  326 FDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDLIPHKKFTFA  404 (677)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcCcccchHH
Confidence            33444444556666666666665543 23311  0111111        001122334444444433322          


Q ss_pred             --------------------------cCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 040261          227 --------------------------QGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL  280 (343)
Q Consensus       227 --------------------------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  280 (343)
                                                .|..|...+|...|..-.+.++++.+..++++.++.+ +.+..+|......=..
T Consensus       405 KiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~-Pe~c~~W~kyaElE~~  483 (677)
T KOG1915|consen  405 KIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFS-PENCYAWSKYAELETS  483 (677)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-hHhhHHHHHHHHHHHH
Confidence                                      1234455555555555556667777777777777665 5566666666666666


Q ss_pred             CCchHHHHHHHHHHHhCCC-CccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          281 TGRVNRAKELFVSMESNGC-MRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       281 ~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .|+.+.|..+|+-..++.. ......|...|+.-...|.++.|..+|+++++.
T Consensus       484 LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  484 LGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             hhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence            7777777777777666421 112334555555556677888888888887765

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

Probab=99.46  E-value=4.7e-10  Score=81.10  Aligned_cols=206  Identities=13%  Similarity=0.025  Sum_probs=149.5

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      +...+.-.|.+.|+...|..-+++.++..+. +..++..+...|.+.|+.+.|.+.|++..+..       +.+..+.|.
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-------p~~GdVLNN  108 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLA-------PNNGDVLNN  108 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-------CCccchhhh
Confidence            4455667778888888888888888877433 56677788888888888888888888888764       456677788


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCC-CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDEN-INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG  247 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  247 (343)
                      ....+|..|++++|...|++..... ..-...+|..+.-+..+.|+++.|...+++.++.. +-...+...+.....+.|
T Consensus       109 YG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~  187 (250)
T COG3063         109 YGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAG  187 (250)
T ss_pred             hhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcc
Confidence            8888888888888888888876642 12235667777777788888888888888887763 333556667777777888


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHH
Q 040261          248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSY  306 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  306 (343)
                      ++..|..+++.....+ .++....-..|+.-...|+.+.+.+.=..+.+.  .|...-+
T Consensus       188 ~y~~Ar~~~~~~~~~~-~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~--fP~s~e~  243 (250)
T COG3063         188 DYAPARLYLERYQQRG-GAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL--FPYSEEY  243 (250)
T ss_pred             cchHHHHHHHHHHhcc-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHH
Confidence            8888888888877766 377777777777777778877777766666654  3444433

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

Probab=99.46  E-value=1.1e-09  Score=85.97  Aligned_cols=288  Identities=16%  Similarity=0.053  Sum_probs=216.5

Q ss_pred             cCChhHHHHHHHHhHh-CCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc-HHHHHHHHHHHhhcCcHHHHH
Q 040261           30 NKHYDTVLSLFKRLNS-IGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD-AVTFTSLIKGLCAESRIMEAA  107 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~  107 (343)
                      .++...|...+-.+.. ..++.|......+..++...|+.++|...|++....+  |+ ........-.+.+.|+.++..
T Consensus       209 ~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d--py~i~~MD~Ya~LL~~eg~~e~~~  286 (564)
T KOG1174|consen  209 NFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN--PDNVEAMDLYAVLLGQEGGCEQDS  286 (564)
T ss_pred             hcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC--hhhhhhHHHHHHHHHhccCHhhHH
Confidence            3444444444443332 2345677788899999999999999999999987653  33 333333444556788888888


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHH
Q 040261          108 ALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFL  187 (343)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  187 (343)
                      .+...+.... +.+...|..-+..+...++++.|+.+-++.++.+       +.+...+..-...+...+++++|.-.|+
T Consensus       287 ~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~-------~r~~~alilKG~lL~~~~R~~~A~IaFR  358 (564)
T KOG1174|consen  287 ALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE-------PRNHEALILKGRLLIALERHTQAVIAFR  358 (564)
T ss_pred             HHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC-------cccchHHHhccHHHHhccchHHHHHHHH
Confidence            8887776542 1244455556666777889999999999998875       4556677777788899999999999999


Q ss_pred             HhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHH-hCCChhHHHHHHHHHHHcCCC
Q 040261          188 KMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM-NELC-KNGKMDEASRLLELMIQIGVR  265 (343)
Q Consensus       188 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~~-~~~~~~~a~~~~~~~~~~~~~  265 (343)
                      ...... |-+...|.-++.+|...|.+.+|..+-+...+. ++.+..+...+. ..+. ...--++|.++++...+.. +
T Consensus       359 ~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~-P  435 (564)
T KOG1174|consen  359 TAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKIN-P  435 (564)
T ss_pred             HHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccC-C
Confidence            887653 346889999999999999999999888777665 345666666553 3332 3344678999998887763 3


Q ss_pred             CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          266 PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       266 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .-....+.+...+...|..+.+..++++....  .||....+.|.+.+...+.+++|+..|...+..
T Consensus       436 ~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~  500 (564)
T KOG1174|consen  436 IYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQ  500 (564)
T ss_pred             ccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            33567778888999999999999999998875  689999999999999999999999999888744

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

Probab=99.45  E-value=3.6e-10  Score=81.66  Aligned_cols=193  Identities=14%  Similarity=0.052  Sum_probs=88.8

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH  137 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  137 (343)
                      +.-.|...|+...|..-+++.++..+. +..+|..+...|.+.|+.+.|.+.|++..+..+. +..+.|.....+|..|+
T Consensus        41 Lal~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~-~GdVLNNYG~FLC~qg~  118 (250)
T COG3063          41 LALGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLAPN-NGDVLNNYGAFLCAQGR  118 (250)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCC-ccchhhhhhHHHHhCCC
Confidence            334444555555555555555544311 3444444444555555555555555554444322 33444444444555555


Q ss_pred             hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHH
Q 040261          138 TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  217 (343)
                      +++|...|++......     ......+|..+.-+..+.|+.+.|...|++..+... -...+...+.......|++-.|
T Consensus       119 ~~eA~q~F~~Al~~P~-----Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp-~~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         119 PEEAMQQFERALADPA-----YGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDP-QFPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             hHHHHHHHHHHHhCCC-----CCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCc-CCChHHHHHHHHHHhcccchHH
Confidence            5555555555444321     122234444444445555555555555555444321 1233344444444455555555


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          218 KCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      ...++.....+. ++..+.-..|+.....|+.+.+-++=..+
T Consensus       193 r~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL  233 (250)
T COG3063         193 RLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQL  233 (250)
T ss_pred             HHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            555555444432 44444444444444455554444443333

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

Probab=99.45  E-value=4.9e-09  Score=86.44  Aligned_cols=307  Identities=11%  Similarity=-0.003  Sum_probs=194.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCC-CCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGL-FPDL-YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      ...-.|..+...+...|+.+.+...+....+... .++. .........+...|++++|.+.+++..+..+. +...+..
T Consensus         4 ~~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~   82 (355)
T cd05804           4 DFALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPR-DLLALKL   82 (355)
T ss_pred             ccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHH
Confidence            4566788888888888999988777777654321 1222 22233344567789999999999999886432 4444442


Q ss_pred             ---HHHHHhhcCcHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           93 ---LIKGLCAESRIMEAAALFTKLRAFGCKPD-VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        93 ---l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                         ........+....+.+.++..  ....|+ ......+...+...|++++|...+++..+..       +.+...+..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-------p~~~~~~~~  153 (355)
T cd05804          83 HLGAFGLGDFSGMRDHVARVLPLW--APENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-------PDDAWAVHA  153 (355)
T ss_pred             hHHHHHhcccccCchhHHHHHhcc--CcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-------CCCcHHHHH
Confidence               111112234555555555541  112233 3444566778899999999999999999875       455677888


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCC-CCCh--hhHHHHHHHHhccCcHHHHHHHHHHHHHcCC-CCCHHHH-H--HHHH
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENI-NPDV--VTYTSLIRGFCYANDWNEAKCLFIEMMDQGV-QPNVVTF-N--VIMN  241 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~-~--~l~~  241 (343)
                      +..++...|++++|...+++...... .|+.  ..|..+...+...|++++|..++++...... .+..... +  .++.
T Consensus       154 la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~  233 (355)
T cd05804         154 VAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLW  233 (355)
T ss_pred             HHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHH
Confidence            89999999999999999999876532 1222  3455778889999999999999999865432 1222211 1  2333


Q ss_pred             HHHhCCChhHHHHHHHHHHHc---CC--CCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCC------c--cHHHHHH
Q 040261          242 ELCKNGKMDEASRLLELMIQI---GV--RPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM------R--DVFSYGI  308 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~---~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~--~~~~~~~  308 (343)
                      .+...|....+.++ +.+...   ..  ............++...|+.+.|..+++.+......      .  .......
T Consensus       234 ~~~~~g~~~~~~~w-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l  312 (355)
T cd05804         234 RLELAGHVDVGDRW-EDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLA  312 (355)
T ss_pred             HHHhcCCCChHHHH-HHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHH
Confidence            34445544444433 222111   10  111122235667788999999999999988763211      1  1122222


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhC
Q 040261          309 LINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       309 l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ...++...|++++|.+.+......
T Consensus       313 ~A~~~~~~g~~~~A~~~L~~al~~  336 (355)
T cd05804         313 EALYAFAEGNYATALELLGPVRDD  336 (355)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            334467899999999999888754

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.44  E-value=5.3e-10  Score=88.86  Aligned_cols=195  Identities=15%  Similarity=0.023  Sum_probs=90.8

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      .|..+...+...|++++|...|++..+..+. +...|..+...+...|++++|...|++..+..       +.+..++..
T Consensus        66 ~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-------P~~~~a~~~  137 (296)
T PRK11189         66 LHYERGVLYDSLGLRALARNDFSQALALRPD-MADAYNYLGIYLTQAGNFDAAYEAFDSVLELD-------PTYNYAYLN  137 (296)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHH
Confidence            3444555555556666666555555554332 44555555555666666666666666555543       223445555


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  248 (343)
                      +..++...|++++|.+.|+...+..  |+..........+...+++++|...+....... .|+...+ .  ......|+
T Consensus       138 lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~-~~~~~~~-~--~~~~~lg~  211 (296)
T PRK11189        138 RGIALYYGGRYELAQDDLLAFYQDD--PNDPYRALWLYLAESKLDPKQAKENLKQRYEKL-DKEQWGW-N--IVEFYLGK  211 (296)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC-CccccHH-H--HHHHHccC
Confidence            5555555566666666665555432  222111111122233445556655554433221 2221111 1  11222333


Q ss_pred             hhHHHHHHHHHHHc---CC---CCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          249 MDEASRLLELMIQI---GV---RPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       249 ~~~a~~~~~~~~~~---~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      ...+ ..+..+.+.   ..   +.....|..+...+.+.|++++|...|++..+.+
T Consensus       212 ~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        212 ISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             CCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            3332 233333211   00   1123455556666666666666666666665543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.44  E-value=1.4e-10  Score=96.25  Aligned_cols=244  Identities=18%  Similarity=0.115  Sum_probs=170.9

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHc-----C-CCccHH-HHHHHHHHHhhcCcHHHHHHHHHHHHhc-----CC-
Q 040261           52 LYTYNILINCFCKMGRVSPGFVVLGRILRS-----C-FTPDAV-TFTSLIKGLCAESRIMEAAALFTKLRAF-----GC-  118 (343)
Q Consensus        52 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-  118 (343)
                      ..+...+...|...|+++.|..++++.++.     | ..|... ..+.+...|...+++.+|..+|+++...     |- 
T Consensus       199 ~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~  278 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGED  278 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCC
Confidence            346667889999999999999999998764     2 123332 3445777888999999999999988653     21 


Q ss_pred             CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc-chHHHHHHHHHhcCChHHHHHHHHHhhhC---C
Q 040261          119 KP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA-ITYSTITDGLCKEGFVDKAKELFLKMKDE---N  193 (343)
Q Consensus       119 ~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~  193 (343)
                      .| -..+++.|..+|.+.|++++|...++...+..........+.. ..++.+...+...+++++|..++....+.   -
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence            12 2346778888999999999998888776543211000012222 34566677788889999998888765432   1


Q ss_pred             CCC----ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC----C--CC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          194 INP----DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG----V--QP-NVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       194 ~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~--~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      +.+    -..+++.+...|...|++++|.++++.++...    .  .+ ....++.+...|.+.+.+..|.++|.+....
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i  438 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDI  438 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHH
Confidence            111    24678888888899999999999888876541    1  12 2456677888888888888888888776543


Q ss_pred             ----CC--CCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          263 ----GV--RPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       263 ----~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                          |.  +-...+|..|...|.+.|++++|.++.+.+.
T Consensus       439 ~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  439 MKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence                21  2224678888888889999999888887765

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.44  E-value=5.5e-11  Score=98.67  Aligned_cols=247  Identities=19%  Similarity=0.167  Sum_probs=180.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhC-----CC-CCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHHc-----C
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSI-----GL-FPDLY-TYNILINCFCKMGRVSPGFVVLGRILRS-----C   82 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~   82 (343)
                      .-..+...+...|...|+++.|.++++...+.     |. .|... ..+.+...|...+++.+|..+|+++...     |
T Consensus       197 ~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G  276 (508)
T KOG1840|consen  197 ERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFG  276 (508)
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcC
Confidence            34556777999999999999999999987663     21 23333 3444778899999999999999998753     2


Q ss_pred             C-Cc-cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc-----CCC-CCH-HHHHHHHHHHHhcCChHHHHHHHHHHHccCC
Q 040261           83 F-TP-DAVTFTSLIKGLCAESRIMEAAALFTKLRAF-----GCK-PDV-FTYTTLINGLCRTGHTIVALNLFEEMANGNG  153 (343)
Q Consensus        83 ~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  153 (343)
                      . .| -..+++.|..+|.+.|++++|...+++..+.     |.. |.. ..++.+...+...+++++|..+++...+...
T Consensus       277 ~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~  356 (508)
T KOG1840|consen  277 EDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYL  356 (508)
T ss_pred             CCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHH
Confidence            1 12 2456788888999999999998888776532     211 222 2456677889999999999999887655432


Q ss_pred             CCCcccc-CCcchHHHHHHHHHhcCChHHHHHHHHHhhhC-----C--CCCChhhHHHHHHHHhccCcHHHHHHHHHHHH
Q 040261          154 EFGVVCK-PDAITYSTITDGLCKEGFVDKAKELFLKMKDE-----N--INPDVVTYTSLIRGFCYANDWNEAKCLFIEMM  225 (343)
Q Consensus       154 ~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  225 (343)
                      ....... .-..+++.|...|.+.|++++|.++++++...     +  ..-....++.+...|.+.+++.+|..+|.+..
T Consensus       357 ~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~  436 (508)
T KOG1840|consen  357 DAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAK  436 (508)
T ss_pred             hhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHH
Confidence            1000011 22468899999999999999999999987543     1  11224567888899999999999988887654


Q ss_pred             Hc----CC-CCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          226 DQ----GV-QPN-VVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       226 ~~----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      ..    |. .|+ ..+|..|...|...|+++.|.++.+.+..
T Consensus       437 ~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  437 DIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            32    21 233 57889999999999999999999988764

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.43  E-value=8.5e-10  Score=87.69  Aligned_cols=219  Identities=12%  Similarity=0.037  Sum_probs=138.9

Q ss_pred             cCChhHHHHHHHHhHhCC-CCCC--HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHH
Q 040261           30 NKHYDTVLSLFKRLNSIG-LFPD--LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEA  106 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  106 (343)
                      .++.+.++.-+.+++... ..|+  ...|..+...+...|+.+.|...|++..+..+ .+...|+.+...+...|++++|
T Consensus        39 ~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P-~~~~a~~~lg~~~~~~g~~~~A  117 (296)
T PRK11189         39 TLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRP-DMADAYNYLGIYLTQAGNFDAA  117 (296)
T ss_pred             chHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHCCCHHHH
Confidence            445566777777766432 1122  34577777778888888888888888887643 3577788888888888888888


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHH
Q 040261          107 AALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELF  186 (343)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  186 (343)
                      ...|++..+..+. +..++..+..++...|++++|.+.+++..+..        |+..........+...++.++|...|
T Consensus       118 ~~~~~~Al~l~P~-~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--------P~~~~~~~~~~l~~~~~~~~~A~~~l  188 (296)
T PRK11189        118 YEAFDSVLELDPT-YNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--------PNDPYRALWLYLAESKLDPKQAKENL  188 (296)
T ss_pred             HHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--------CCCHHHHHHHHHHHccCCHHHHHHHH
Confidence            8888888876433 45667777777888888888888888887754        32222222233344567788888888


Q ss_pred             HHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---CC--C-CCHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          187 LKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---GV--Q-PNVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       187 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~--~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      ++..... .|+...+ .+...  ..|+...+ ..+..+.+.   .+  . .....|..+...+.+.|++++|...|++..
T Consensus       189 ~~~~~~~-~~~~~~~-~~~~~--~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al  263 (296)
T PRK11189        189 KQRYEKL-DKEQWGW-NIVEF--YLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLAL  263 (296)
T ss_pred             HHHHhhC-CccccHH-HHHHH--HccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            6654332 2222222 22222  23443333 233333321   10  1 123567778888888888888888888888


Q ss_pred             HcC
Q 040261          261 QIG  263 (343)
Q Consensus       261 ~~~  263 (343)
                      +.+
T Consensus       264 ~~~  266 (296)
T PRK11189        264 ANN  266 (296)
T ss_pred             HhC
Confidence            765

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

Probab=99.42  E-value=1.8e-10  Score=92.08  Aligned_cols=153  Identities=13%  Similarity=0.039  Sum_probs=75.1

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      -.|+...|.+-|+..+..... +...|..+..+|....+.++....|.+..+.+.. |+.+|..-.....-.+++++|..
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~-~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~-n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPA-FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPE-NPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcc-cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCC-CCchhHhHHHHHHHHHHHHHHHH
Confidence            345555555555555543311 1222444444555555555555555555544322 44445444444444555555555


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040261          109 LFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK  188 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  188 (343)
                      -|++.++..+. +...|..+.-+..+.+.++++...|++....       +|.-+.+|+....++...++++.|.+.|+.
T Consensus       416 DF~Kai~L~pe-~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-------FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~  487 (606)
T KOG0547|consen  416 DFQKAISLDPE-NAYAYIQLCCALYRQHKIAESMKTFEEAKKK-------FPNCPEVYNLFAEILTDQQQFDKAVKQYDK  487 (606)
T ss_pred             HHHHHhhcChh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------CCCCchHHHHHHHHHhhHHhHHHHHHHHHH
Confidence            55555544322 3334444444445555555555555555554       234445555555555555555555555555


Q ss_pred             hhh
Q 040261          189 MKD  191 (343)
Q Consensus       189 ~~~  191 (343)
                      ...
T Consensus       488 ai~  490 (606)
T KOG0547|consen  488 AIE  490 (606)
T ss_pred             HHh
Confidence            433

>PF13041 PPR_2: PPR repeat family

Probab=99.41  E-value=1e-12  Score=73.74  Aligned_cols=49  Identities=43%  Similarity=0.814  Sum_probs=33.3

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFC   63 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   63 (343)
                      ||..+||.++.+|++.|++++|.++|++|.+.|++||..+|+.++++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4566666666666666666666666666666666666666666666665

>PF13041 PPR_2: PPR repeat family

Probab=99.40  E-value=1.2e-12  Score=73.45  Aligned_cols=49  Identities=49%  Similarity=0.959  Sum_probs=31.7

Q ss_pred             ccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040261           85 PDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC  133 (343)
Q Consensus        85 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  133 (343)
                      ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.++++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            5566666666666666666666666666666666666666666666654

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

Probab=99.37  E-value=6.8e-09  Score=87.44  Aligned_cols=262  Identities=13%  Similarity=0.101  Sum_probs=185.7

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc--
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRT--  135 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--  135 (343)
                      ....+...|++++|++.++.-... +.............+.+.|+.++|..+|..+++.++. +..-|..+..+..-.  
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPd-n~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPD-NYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHhhhcc
Confidence            345567889999999999886554 3334666777889999999999999999999999643 455555565555222  


Q ss_pred             ---CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCCh-HHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          136 ---GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFV-DKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       136 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                         .+.+....+++++....        |...+...+.-.+.....+ ..+...+..+...|+|+   +|+.+-..|...
T Consensus        88 ~~~~~~~~~~~~y~~l~~~y--------p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~  156 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKY--------PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDP  156 (517)
T ss_pred             cccccHHHHHHHHHHHHHhC--------ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcCh
Confidence               25677888999887764        3333333333222222223 34455666677778643   566666666655


Q ss_pred             CcHHHHHHHHHHHHHc----C----------CCCCH--HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          212 NDWNEAKCLFIEMMDQ----G----------VQPNV--VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM  275 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~----~----------~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  275 (343)
                      ....-...++......    +          -+|+.  .++..+.+.|-..|++++|+.++++.+++. +..+..|..-.
T Consensus       157 ~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~Ka  235 (517)
T PF12569_consen  157 EKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKA  235 (517)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHH
Confidence            5555555666555432    1          13444  344666788899999999999999999985 44478899999


Q ss_pred             HHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 040261          276 DGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       276 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  334 (343)
                      +.+-+.|++.+|.+.++...... .-|...-+-.+..+.+.|+.++|.+++......+.
T Consensus       236 rilKh~G~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~  293 (517)
T PF12569_consen  236 RILKHAGDLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDV  293 (517)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCC
Confidence            99999999999999999999864 23455555566778899999999999988876654

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 [], [].

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

Probab=99.37  E-value=7.5e-09  Score=81.39  Aligned_cols=273  Identities=14%  Similarity=0.043  Sum_probs=208.0

Q ss_pred             cCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHH
Q 040261           10 MHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAV   88 (343)
Q Consensus        10 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~   88 (343)
                      ....|.|+.....+..++...|+.++|+..|++....+  |+ ..........+.+.|+.+....+...+.... .....
T Consensus       225 ~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d--py~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~  301 (564)
T KOG1174|consen  225 NTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN--PDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTAS  301 (564)
T ss_pred             hccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC--hhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchh
Confidence            33445788999999999999999999999999987643  43 2333333444567888888888887777642 23444


Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      .|-.-+.......+++.|+.+-++.++.+.. +...+..-...+...+++++|.-.|+......       |-+..+|..
T Consensus       302 ~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r-~~~alilKG~lL~~~~R~~~A~IaFR~Aq~La-------p~rL~~Y~G  373 (564)
T KOG1174|consen  302 HWFVHAQLLYDEKKFERALNFVEKCIDSEPR-NHEALILKGRLLIALERHTQAVIAFRTAQMLA-------PYRLEIYRG  373 (564)
T ss_pred             hhhhhhhhhhhhhhHHHHHHHHHHHhccCcc-cchHHHhccHHHHhccchHHHHHHHHHHHhcc-------hhhHHHHHH
Confidence            5555555566778999999999998887533 55666666788899999999999999988864       567899999


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHH-HHH-hccCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHh
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLI-RGF-CYANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCK  245 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~-~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~  245 (343)
                      |+..|...|...+|.-.-....+. ++-+..+.+.+. ..| ....--++|.++++...+.  .|+ ....+.+...+..
T Consensus       374 L~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~--~P~Y~~AV~~~AEL~~~  450 (564)
T KOG1174|consen  374 LFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKI--NPIYTPAVNLIAELCQV  450 (564)
T ss_pred             HHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhcc--CCccHHHHHHHHHHHHh
Confidence            999999999999998776654443 233556665552 222 2233457888888887765  555 5566778888999


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      .|..+.++.++++....  .||....+.|.+.+...+.+.+|.+.|....+.+
T Consensus       451 Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d  501 (564)
T KOG1174|consen  451 EGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD  501 (564)
T ss_pred             hCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            99999999999998775  7899999999999999999999999999888763

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

Probab=99.34  E-value=4.2e-08  Score=78.71  Aligned_cols=300  Identities=12%  Similarity=0.090  Sum_probs=224.5

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      ...|-...+--..+++++.|..+|++.+... ..+...|...+.+-.+...+..|..++++.+..-+.. ...|...+..
T Consensus        73 ~~~WikYaqwEesq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRV-dqlWyKY~ym  150 (677)
T KOG1915|consen   73 MQVWIKYAQWEESQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRV-DQLWYKYIYM  150 (677)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchH-HHHHHHHHHH
Confidence            3344444444456778899999999998765 4677888889999899999999999999998863332 3345555555


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE  176 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  176 (343)
                      =-..|+...|.++|++..+-  .|+..+|.+.++.=.+.+.++.|..++++..-        ++|+..+|....+.-.+.
T Consensus       151 EE~LgNi~gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~--------~HP~v~~wikyarFE~k~  220 (677)
T KOG1915|consen  151 EEMLGNIAGARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVL--------VHPKVSNWIKYARFEEKH  220 (677)
T ss_pred             HHHhcccHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--------ecccHHHHHHHHHHHHhc
Confidence            55679999999999998876  89999999999999999999999999999987        679999999999999999


Q ss_pred             CChHHHHHHHHHhhhC-C-CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCChhHH
Q 040261          177 GFVDKAKELFLKMKDE-N-INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN--VVTFNVIMNELCKNGKMDEA  252 (343)
Q Consensus       177 ~~~~~a~~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a  252 (343)
                      |+...+..+|+...+. | -..+...+.+...--.++..++.|..+++-.++. ++.+  ...|..+...--+-|+....
T Consensus       221 g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gI  299 (677)
T KOG1915|consen  221 GNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGI  299 (677)
T ss_pred             CcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhh
Confidence            9999999999987664 1 0112344555555556678899999999998887 3333  44555555554556765554


Q ss_pred             HHH--------HHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH--HHHHHHH-----HHH---H
Q 040261          253 SRL--------LELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV--FSYGILI-----NGY---C  314 (343)
Q Consensus       253 ~~~--------~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~-----~~~---~  314 (343)
                      ...        ++.+++.+ +-|-.+|-..++.-...|+.+...+++++.... ++|-.  ..|...|     -+|   .
T Consensus       300 Ed~Iv~KRk~qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEl  377 (677)
T KOG1915|consen  300 EDAIVGKRKFQYEKEVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEEL  377 (677)
T ss_pred             HHHHhhhhhhHHHHHHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHH
Confidence            433        33444444 667889999999889999999999999999886 34422  2232222     122   3


Q ss_pred             hcCChHHHHHHHHHHHh
Q 040261          315 KNKEIEGALSLYSEMLS  331 (343)
Q Consensus       315 ~~~~~~~a~~~~~~~~~  331 (343)
                      ...+.+.+.++|+..++
T Consensus       378 e~ed~ertr~vyq~~l~  394 (677)
T KOG1915|consen  378 EAEDVERTRQVYQACLD  394 (677)
T ss_pred             HhhhHHHHHHHHHHHHh
Confidence            46788999999998886

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.28  E-value=1.2e-07  Score=73.13  Aligned_cols=305  Identities=12%  Similarity=0.058  Sum_probs=223.4

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH-HHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT-FTS   92 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~   92 (343)
                      |.++.-..-+...+...|++..|+.-|...++.+ +.+-.++..-...|...|+-..|+.-+.+.++.  .||-.. -..
T Consensus        35 ~advekhlElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQ  111 (504)
T KOG0624|consen   35 PADVEKHLELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQ  111 (504)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHH
Confidence            3456666778888999999999999999888743 222334445556788899999999999998875  566332 223


Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhcCCCCCH--HH------------HHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcc
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAFGCKPDV--FT------------YTTLINGLCRTGHTIVALNLFEEMANGNGEFGVV  158 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  158 (343)
                      -...+.+.|.+++|..-|+...+....-..  ..            ....+..+.-.|+...|+.....+.+..      
T Consensus       112 Rg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~------  185 (504)
T KOG0624|consen  112 RGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ------  185 (504)
T ss_pred             hchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC------
Confidence            345678899999999999999887432111  11            2233445667899999999999998874      


Q ss_pred             ccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHH---
Q 040261          159 CKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVT---  235 (343)
Q Consensus       159 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---  235 (343)
                       +-+...+..-..+|...|++..|+.=++...+.. ..+..++--+-..+...|+.+.++..+++.++.  .|+...   
T Consensus       186 -~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~  261 (504)
T KOG0624|consen  186 -PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFP  261 (504)
T ss_pred             -cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHH
Confidence             5678888888999999999999998888876653 235667777778888999999999999988875  455322   


Q ss_pred             -HHHH---------HHHHHhCCChhHHHHHHHHHHHcCCCCC---HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc
Q 040261          236 -FNVI---------MNELCKNGKMDEASRLLELMIQIGVRPD---ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD  302 (343)
Q Consensus       236 -~~~l---------~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  302 (343)
                       |-.+         +......+++.++..-.+...+......   ...+..+-.++...+++.+|++...+....  .|+
T Consensus       262 ~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~  339 (504)
T KOG0624|consen  262 FYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPD  339 (504)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--Cch
Confidence             2111         1223456777778777777776532211   233455666777889999999999999875  354


Q ss_pred             -HHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          303 -VFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       303 -~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                       ..++.--..+|.-...++.|+.-|+...+.+
T Consensus       340 dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n  371 (504)
T KOG0624|consen  340 DVQVLCDRAEAYLGDEMYDDAIHDYEKALELN  371 (504)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC
Confidence             7788888889999999999999999887653

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

Probab=99.26  E-value=7.2e-08  Score=79.54  Aligned_cols=269  Identities=13%  Similarity=-0.007  Sum_probs=166.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHHcCCCcc-HHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK----MGRVSPGFVVLGRILRSCFTPD-AVTFTSL   93 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l   93 (343)
                      ........+...|++++|..++++..+.. +.+...+.. ...+..    .+....+.+.+...  ....|+ ......+
T Consensus        45 ~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~  120 (355)
T cd05804          45 RAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPLW--APENPDYWYLLGML  120 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHH-hHHHHHhcccccCchhHHHHHhcc--CcCCCCcHHHHHHH
Confidence            34444566778999999999999988754 334444442 222333    34455555555441  112233 3344456


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc--chHHHHHH
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA--ITYSTITD  171 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~~  171 (343)
                      ...+...|++++|.+.+++..+.... +...+..+..++...|++++|...+++.....+.     .++.  ..|..+..
T Consensus       121 a~~~~~~G~~~~A~~~~~~al~~~p~-~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~-----~~~~~~~~~~~la~  194 (355)
T cd05804         121 AFGLEEAGQYDRAEEAARRALELNPD-DAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC-----SSMLRGHNWWHLAL  194 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCCC-CcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC-----CcchhHHHHHHHHH
Confidence            67888999999999999999988543 5667888899999999999999999998876421     1222  34557888


Q ss_pred             HHHhcCChHHHHHHHHHhhhCCC-CCChhhH-H--HHHHHHhccCcHHHHHHH--H-HHHHHcCC-CCCHHHHHHHHHHH
Q 040261          172 GLCKEGFVDKAKELFLKMKDENI-NPDVVTY-T--SLIRGFCYANDWNEAKCL--F-IEMMDQGV-QPNVVTFNVIMNEL  243 (343)
Q Consensus       172 ~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~-~--~l~~~~~~~~~~~~a~~~--~-~~~~~~~~-~~~~~~~~~l~~~~  243 (343)
                      .+...|++++|..++++...... .+..... +  .++..+...|....+.+.  + ........ ............++
T Consensus       195 ~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~  274 (355)
T cd05804         195 FYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALAL  274 (355)
T ss_pred             HHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHH
Confidence            99999999999999999854322 1111111 1  222233333432222222  1 11111100 11112223566777


Q ss_pred             HhCCChhHHHHHHHHHHHcCCC------C--CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          244 CKNGKMDEASRLLELMIQIGVR------P--DASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~------~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...|+.+.|..+++.+......      .  ..........++...|+.++|.+.+......
T Consensus       275 ~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~  336 (355)
T cd05804         275 AGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDD  336 (355)
T ss_pred             hcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            8899999999999988764312      0  1122222333456889999999999877653

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=99.25  E-value=1.2e-09  Score=85.70  Aligned_cols=251  Identities=17%  Similarity=0.128  Sum_probs=143.2

Q ss_pred             HHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHH
Q 040261           25 GCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIM  104 (343)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  104 (343)
                      +.+.-.|++..++.-.+ .....-..+......+.+++...|+.+.+   +..+.... .|.......+...+...++-+
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~v---l~ei~~~~-~~~l~av~~la~y~~~~~~~e   83 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSV---LSEIKKSS-SPELQAVRLLAEYLSSPSDKE   83 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHH---HHHS-TTS-SCCCHHHHHHHHHHCTSTTHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHH---HHHhccCC-ChhHHHHHHHHHHHhCccchH
Confidence            33445677777776555 22222122334455566777777775543   33333332 556655555555554434455


Q ss_pred             HHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          105 EAAALFTKLRAFGCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       105 ~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                      .++.-+++....+... +..........+...|++++|++++...            .+.......+.++.+.++++.|.
T Consensus        84 ~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------------~~lE~~al~Vqi~L~~~R~dlA~  151 (290)
T PF04733_consen   84 SALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------------GSLELLALAVQILLKMNRPDLAE  151 (290)
T ss_dssp             CHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------------TCHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------------CcccHHHHHHHHHHHcCCHHHHH
Confidence            5555554443333222 2222223334556677888887766542            23456666777788888888888


Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          184 ELFLKMKDENINPDVVTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      +.++.|.+.+   +..+...+..++..    .+.+.+|..+|+++.+. ..++..+.+.+..+....|++++|..++.+.
T Consensus       152 k~l~~~~~~~---eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~a  227 (290)
T PF04733_consen  152 KELKNMQQID---EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEA  227 (290)
T ss_dssp             HHHHHHHCCS---CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHhcC---CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            8888877643   33344444444332    33577888888887654 4567777777788888888888888888777


Q ss_pred             HHcCCCCCHHHHHHHHHHHhcCCch-HHHHHHHHHHHhC
Q 040261          260 IQIGVRPDASVYNTLMDGFCLTGRV-NRAKELFVSMESN  297 (343)
Q Consensus       260 ~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  297 (343)
                      .+.+ +-++.+...++.+....|+. +.+.+.+.++...
T Consensus       228 l~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  228 LEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             CCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            6654 44566666677777777766 5666777777653

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.25  E-value=1.1e-08  Score=77.13  Aligned_cols=195  Identities=13%  Similarity=0.142  Sum_probs=128.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH-HHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS-LIKGL   97 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~   97 (343)
                      -|...+..+.+..++..|++++....+.. +.+......+..+|....++..|...++++-..  .|...-|.. -...+
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSL   88 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSL   88 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHH
Confidence            37777888888999999999998877654 336777888889999999999999999998765  344443432 34556


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHH--HHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFT--YTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+.+.+..|+++...|.+.   ++...  ...-.......+++..+..++++....+         +..+.+.......+
T Consensus        89 Y~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---------~Ad~~in~gCllyk  156 (459)
T KOG4340|consen   89 YKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---------EADGQINLGCLLYK  156 (459)
T ss_pred             HHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---------ccchhccchheeec
Confidence            6778888999988887653   12111  1111222345667777777777665332         33444444555567


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCC
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGV  229 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  229 (343)
                      .|+++.|.+-|....+-+.--....|+..+ ++.+.+++..|++...+++++|+
T Consensus       157 egqyEaAvqkFqaAlqvsGyqpllAYniAL-aHy~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  157 EGQYEAAVQKFQAALQVSGYQPLLAYNLAL-AHYSSRQYASALKHISEIIERGI  209 (459)
T ss_pred             cccHHHHHHHHHHHHhhcCCCchhHHHHHH-HHHhhhhHHHHHHHHHHHHHhhh
Confidence            777777777777766543222355566554 44566777777777777776654

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

Probab=99.24  E-value=4.5e-07  Score=75.66  Aligned_cols=100  Identities=9%  Similarity=0.089  Sum_probs=71.0

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCC-----------
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPD---VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGV-----------  229 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------  229 (343)
                      ..|..+.+.|-..|+.+.|..+|++..+...+--   ..+|......-.++.+++.|+++++......-           
T Consensus       388 ~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~  467 (835)
T KOG2047|consen  388 TLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSE  467 (835)
T ss_pred             hHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCC
Confidence            4577888889999999999999999887543322   35566666777788889999998887653211           


Q ss_pred             CC------CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          230 QP------NVVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       230 ~~------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      ++      +...|...+..-...|-++....+++++++..
T Consensus       468 pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLr  507 (835)
T KOG2047|consen  468 PVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLR  507 (835)
T ss_pred             cHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHh
Confidence            11      23455556666667788888888888887654

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

Probab=99.23  E-value=1.4e-09  Score=85.33  Aligned_cols=251  Identities=13%  Similarity=0.049  Sum_probs=166.8

Q ss_pred             HHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH
Q 040261           60 NCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI  139 (343)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  139 (343)
                      +-+.-.|++..++.-.+ ......+.+......+.+++...|+++.++   .++.... .|.......+...+...++-+
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~e   83 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDKE   83 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccchH
Confidence            34455688888876555 222222233445556778888889877654   3333333 566666666665554445555


Q ss_pred             HHHHHHHHHHccCCCCCcccc-CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHH
Q 040261          140 VALNLFEEMANGNGEFGVVCK-PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAK  218 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  218 (343)
                      .+..-++......      .. .+.........++...|++++|++++...      .+.......+.++.+.++++.|.
T Consensus        84 ~~l~~l~~~~~~~------~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~  151 (290)
T PF04733_consen   84 SALEELKELLADQ------AGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAE  151 (290)
T ss_dssp             CHHHHHHHCCCTS---------CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHhc------cccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHH
Confidence            5555555443332      12 22233333445677889999999888653      35677788899999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          219 CLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      +.++.|.+.+  .| .+...+..++..    .+.+.+|..+|+++.+. ..+++.+.+.+..+....|++++|.+++.+.
T Consensus       152 k~l~~~~~~~--eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~a  227 (290)
T PF04733_consen  152 KELKNMQQID--ED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEA  227 (290)
T ss_dssp             HHHHHHHCCS--CC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHhcC--Cc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            9999998753  33 444445555443    34699999999998765 4678899999999999999999999999998


Q ss_pred             HhCCCCccHHHHHHHHHHHHhcCCh-HHHHHHHHHHHhC
Q 040261          295 ESNGCMRDVFSYGILINGYCKNKEI-EGALSLYSEMLSK  332 (343)
Q Consensus       295 ~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  332 (343)
                      ...+ +.++.+...++.+....|+. +.+.+.+.++...
T Consensus       228 l~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  228 LEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             CCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            7764 44677777888888888887 6677888887754

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.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.22  E-value=3.8e-07  Score=77.50  Aligned_cols=98  Identities=12%  Similarity=0.066  Sum_probs=77.5

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHH--HHHHHHhCCCCccHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKE--LFVSMESNGCMRDVFSYGILIN  311 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~l~~  311 (343)
                      ..|......+...|..++|...|......+ +-++....++...+.+.|+..-|..  ++..+.+.+ +.+...|..+..
T Consensus       685 ~~~~~~G~~~~~~~~~~EA~~af~~Al~ld-P~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~  762 (799)
T KOG4162|consen  685 SVYYLRGLLLEVKGQLEEAKEAFLVALALD-PDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGE  762 (799)
T ss_pred             HHHHHhhHHHHHHHhhHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHH
Confidence            344444455566677788888887777664 4456788899999999998887777  999998875 558899999999


Q ss_pred             HHHhcCChHHHHHHHHHHHhCC
Q 040261          312 GYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       312 ~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      .+.+.|+.++|.+.|.......
T Consensus       763 v~k~~Gd~~~Aaecf~aa~qLe  784 (799)
T KOG4162|consen  763 VFKKLGDSKQAAECFQAALQLE  784 (799)
T ss_pred             HHHHccchHHHHHHHHHHHhhc
Confidence            9999999999999999887653

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

Probab=99.22  E-value=9.9e-09  Score=84.01  Aligned_cols=225  Identities=17%  Similarity=0.039  Sum_probs=131.8

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      ..-+.+.|++.+|.-+|+..+... |-+...|..|.......++-..|+..+.+.++..+. |......|.-.|...|.-
T Consensus       292 G~~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q  369 (579)
T KOG1125|consen  292 GCNLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQ  369 (579)
T ss_pred             HHHHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhH
Confidence            344556777777777777776654 445667777777777777777777777777765422 566666677777777777


Q ss_pred             HHHHHHHHHHHhcCCCC--------CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261          104 MEAAALFTKLRAFGCKP--------DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+|++.++..+...++-        +...-..  ..+.....+....++|-.+....+     ..+|+.+...|.-.|.-
T Consensus       370 ~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~-----~~~DpdvQ~~LGVLy~l  442 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLP-----TKIDPDVQSGLGVLYNL  442 (579)
T ss_pred             HHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCC-----CCCChhHHhhhHHHHhc
Confidence            77777777665442110        0000000  011111222333344444433321     23566666666666666


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChhHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      .|++++|.+.|+.+.... |-|...||.|...++...+.++|+..|.+.++.  .|+ .++...|.-.|...|.+++|..
T Consensus       443 s~efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  443 SGEFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVK  519 (579)
T ss_pred             chHHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHH
Confidence            777777777776666543 235666677776666666677777777766664  444 3344446666666777777666


Q ss_pred             HHHHHH
Q 040261          255 LLELMI  260 (343)
Q Consensus       255 ~~~~~~  260 (343)
                      .|-.++
T Consensus       520 hlL~AL  525 (579)
T KOG1125|consen  520 HLLEAL  525 (579)
T ss_pred             HHHHHH
Confidence            665544

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

Probab=99.16  E-value=7.4e-08  Score=86.73  Aligned_cols=234  Identities=11%  Similarity=0.072  Sum_probs=152.4

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc-CCC---ccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHH
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRS-CFT---PDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTY  125 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  125 (343)
                      .+...|...|....+.++.+.|.++.++++.. ++.   --...|.++++.-...|.-+...++|++..+.  .-....|
T Consensus      1456 NSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V~ 1533 (1710)
T KOG1070|consen 1456 NSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTVH 1533 (1710)
T ss_pred             CcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHHH
Confidence            34456777777777777788888777777653 111   12345666666666667777777777777765  2123456


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCC-ChhhHHHH
Q 040261          126 TTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINP-DVVTYTSL  204 (343)
Q Consensus       126 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l  204 (343)
                      ..|...|.+.+..++|.++++.|.+.-       ......|...+..+.+.++-++|..++.+..+.-.+- -.....-.
T Consensus      1534 ~~L~~iy~k~ek~~~A~ell~~m~KKF-------~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~Iskf 1606 (1710)
T KOG1070|consen 1534 LKLLGIYEKSEKNDEADELLRLMLKKF-------GQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKF 1606 (1710)
T ss_pred             HHHHHHHHHhhcchhHHHHHHHHHHHh-------cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHH
Confidence            677777888888888888888887763       3456777777777777777778887777766542110 12334445


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCH--HHHHHHHHHHhcCC
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDA--SVYNTLMDGFCLTG  282 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~  282 (343)
                      +..-.+.|+.+.+..+|+..+... +-....|+..+..-.++|+.+.+..+|++++..++.|-.  ..|.-.+..=.+.|
T Consensus      1607 AqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~G 1685 (1710)
T KOG1070|consen 1607 AQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHG 1685 (1710)
T ss_pred             HHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcC
Confidence            555567788888888887777652 334567777788777888888888888888777665542  34555554444556


Q ss_pred             chHHHHHHHHH
Q 040261          283 RVNRAKELFVS  293 (343)
Q Consensus       283 ~~~~a~~~~~~  293 (343)
                      +-..++.+=.+
T Consensus      1686 de~~vE~VKar 1696 (1710)
T KOG1070|consen 1686 DEKNVEYVKAR 1696 (1710)
T ss_pred             chhhHHHHHHH
Confidence            55544444333

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

Probab=99.15  E-value=1.1e-06  Score=73.37  Aligned_cols=169  Identities=13%  Similarity=0.091  Sum_probs=91.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...|..+.-.+....++++|+..|......+ +.|...+.-+.-.-++.++++........+.+.. +..-..|..+.
T Consensus        73 ~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~A  150 (700)
T KOG1156|consen   73 KSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFA  150 (700)
T ss_pred             ccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHH
Confidence            355667777777766777777777777766654 4455566665555566666666666655555542 12344566666


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcC-CCCCHHHHHHHH------HHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFG-CKPDVFTYTTLI------NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      .++.-.|+...|..++++..+.. ..|+...+....      ......|..++|++.+......-       ......-.
T Consensus       151 vs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i-------~Dkla~~e  223 (700)
T KOG1156|consen  151 VAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQI-------VDKLAFEE  223 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHH-------HHHHHHhh
Confidence            67777788888888887776653 234544443222      12233444444444443332211       11111122


Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                      .-...+.+.+++++|..++..+...
T Consensus       224 ~ka~l~~kl~~lEeA~~~y~~Ll~r  248 (700)
T KOG1156|consen  224 TKADLLMKLGQLEEAVKVYRRLLER  248 (700)
T ss_pred             hHHHHHHHHhhHHhHHHHHHHHHhh
Confidence            2334455555555555555555554

>PLN02789 farnesyltranstransferase

Probab=99.13  E-value=5.4e-07  Score=71.82  Aligned_cols=216  Identities=9%  Similarity=0.056  Sum_probs=150.8

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG-RVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      .++..+-..+...++.++|+.+.+++++.. +-+..+|+....++...| ++++++..++++.+.+.+ +..+|+.....
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~  115 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHH
Confidence            455566677777889999999999999855 334456777766777777 579999999999987644 66677766655


Q ss_pred             HhhcCcH--HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           97 LCAESRI--MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        97 ~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      +.+.|+.  ++++.+++++.+...+ +..+|....-++...|+++++++.++++.+.+       +.+..+|+....++.
T Consensus       116 l~~l~~~~~~~el~~~~kal~~dpk-Ny~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d-------~~N~sAW~~R~~vl~  187 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILSLDAK-NYHAWSHRQWVLRTLGGWEDELEYCHQLLEED-------VRNNSAWNQRYFVIT  187 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHC-------CCchhHHHHHHHHHH
Confidence            5566653  6788999999988655 78899999999999999999999999999986       456677777666655


Q ss_pred             hc---CCh----HHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc----CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          175 KE---GFV----DKAKELFLKMKDENINPDVVTYTSLIRGFCYA----NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       175 ~~---~~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      +.   |..    ++.+....++.... +-+...|+.+...+...    +...+|...+.+..+.+ +.+......|+..|
T Consensus       188 ~~~~l~~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~  265 (320)
T PLN02789        188 RSPLLGGLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLL  265 (320)
T ss_pred             hccccccccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHH
Confidence            44   222    35555555555543 33566676666666552    23445666666655532 33455566666666


Q ss_pred             Hh
Q 040261          244 CK  245 (343)
Q Consensus       244 ~~  245 (343)
                      +.
T Consensus       266 ~~  267 (320)
T PLN02789        266 CE  267 (320)
T ss_pred             Hh
Confidence            53

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

Probab=99.13  E-value=3.7e-08  Score=80.75  Aligned_cols=258  Identities=12%  Similarity=0.097  Sum_probs=187.9

Q ss_pred             HHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHH
Q 040261           61 CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIV  140 (343)
Q Consensus        61 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  140 (343)
                      -+.+.|++.+|.-.|+..++.++. +...|..|.......++-..|+..+.+..+..+. +..+.-.|.-.|...|.-..
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqdP~-haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQDPQ-HAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhChH-HHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhHHH
Confidence            356789999999999999988644 7889999999999999999999999999988544 67788888889999999999


Q ss_pred             HHHHHHHHHccCCCCCccccC--CcchHHHHHHHHHhcCChHHHHHHHHHh-hhCCCCCChhhHHHHHHHHhccCcHHHH
Q 040261          141 ALNLFEEMANGNGEFGVVCKP--DAITYSTITDGLCKEGFVDKAKELFLKM-KDENINPDVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~a  217 (343)
                      |++.++..............+  +...-..  .............++|-.+ ...+..+|+.....|.-.|.-.|++++|
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdra  449 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRA  449 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHH
Confidence            999999887654221110000  0000000  1111222233444555444 4445457888899999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC-HHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          218 KCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD-ASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      .+.|+.++... +-|...||.|...++...+.++|+..|.++.+.  +|+ +.+.-.|.-+|...|.+++|.+.|-....
T Consensus       450 iDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  450 VDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLEALS  526 (579)
T ss_pred             HHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence            99999999863 445789999999999999999999999999986  454 34555566789999999999998876543


Q ss_pred             C---------CCCccHHHHHHHHHHHHhcCChHHHHHH
Q 040261          297 N---------GCMRDVFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       297 ~---------~~~~~~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      .         +..++...|..|=.++...++.|-+.+.
T Consensus       527 mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  527 MQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             hhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence            2         1122345777777777777777755443

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

Probab=99.12  E-value=2.2e-07  Score=83.89  Aligned_cols=239  Identities=13%  Similarity=0.079  Sum_probs=186.9

Q ss_pred             HHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc-CCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261           74 VLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF-GCKP---DVFTYTTLINGLCRTGHTIVALNLFEEMA  149 (343)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  149 (343)
                      -|+++.... +-+...|-..|....+.++.++|.++.++.... ++.-   -...|.++++.-...|.-+...++|+++.
T Consensus      1446 Dferlvrss-PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAc 1524 (1710)
T KOG1070|consen 1446 DFERLVRSS-PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERAC 1524 (1710)
T ss_pred             HHHHHHhcC-CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHH
Confidence            344444442 224667888999999999999999999998754 1111   13467888888888888899999999998


Q ss_pred             ccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCC
Q 040261          150 NGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGV  229 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  229 (343)
                      +..        ..-..|..|...|.+.+..++|.++++.|.+.- .-....|...+..+.++++-+.|..++.+.++.  
T Consensus      1525 qyc--------d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~-- 1593 (1710)
T KOG1070|consen 1525 QYC--------DAYTVHLKLLGIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQNEAEAARELLKRALKS-- 1593 (1710)
T ss_pred             Hhc--------chHHHHHHHHHHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--
Confidence            864        235688999999999999999999999998762 246788999999999999999999999999876  


Q ss_pred             CCC---HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH--H
Q 040261          230 QPN---VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV--F  304 (343)
Q Consensus       230 ~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~  304 (343)
                      -|.   .......++.-.+.|+.+++..+|+...... +.....|+.+++.=.++|+.+.++.+|+++...++.|-.  .
T Consensus      1594 lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKf 1672 (1710)
T KOG1070|consen 1594 LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKF 1672 (1710)
T ss_pred             cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHH
Confidence            333   3445556667778999999999999988764 556789999999999999999999999999998876643  3


Q ss_pred             HHHHHHHHHHhcCChHHHHHH
Q 040261          305 SYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      .|...+..=...|+-+.+..+
T Consensus      1673 ffKkwLeyEk~~Gde~~vE~V 1693 (1710)
T KOG1070|consen 1673 FFKKWLEYEKSHGDEKNVEYV 1693 (1710)
T ss_pred             HHHHHHHHHHhcCchhhHHHH
Confidence            555556555566775554443

>PLN02789 farnesyltranstransferase

Probab=99.12  E-value=3.6e-07  Score=72.80  Aligned_cols=213  Identities=9%  Similarity=0.017  Sum_probs=148.0

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC-cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040261           56 NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES-RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR  134 (343)
Q Consensus        56 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  134 (343)
                      ..+-..+...++.++|+..++++++..+. +..+|+....++...| ++++++..++++.+.+.+ +..+|+.....+.+
T Consensus        41 ~~~ra~l~~~e~serAL~lt~~aI~lnP~-~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l~~  118 (320)
T PLN02789         41 DYFRAVYASDERSPRALDLTADVIRLNPG-NYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLAEK  118 (320)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHHHH
Confidence            33344455567888899999998886433 4556766666666666 578999999999887655 55667766555666


Q ss_pred             cCCh--HHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc-
Q 040261          135 TGHT--IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA-  211 (343)
Q Consensus       135 ~~~~--~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  211 (343)
                      .|+.  ++++.+++++.+.+       +.+..+|+....++.+.|+++++++.++++.+.+.. +...|+.....+.+. 
T Consensus       119 l~~~~~~~el~~~~kal~~d-------pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~  190 (320)
T PLN02789        119 LGPDAANKELEFTRKILSLD-------AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSP  190 (320)
T ss_pred             cCchhhHHHHHHHHHHHHhC-------cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhcc
Confidence            6653  67788888888775       567788888888888899999999999999887643 566666665554443 


Q ss_pred             --Cc----HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC----CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 040261          212 --ND----WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN----GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL  280 (343)
Q Consensus       212 --~~----~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  280 (343)
                        |.    .++.......++... +-+...|+.+...+...    +...+|...+.+..+.+ +.+......|+..|+.
T Consensus       191 ~l~~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        191 LLGGLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             ccccccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence              22    245666666666653 44577777777777663    34456777777766654 4466677777777765

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.10  E-value=6.1e-07  Score=69.62  Aligned_cols=98  Identities=16%  Similarity=0.230  Sum_probs=62.3

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHH-HHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHH-HHHHHHHHhc
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVRPDASVY-NTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSY-GILINGYCKN  316 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~  316 (343)
                      +.++.+..|++.+|+++|-.+....++ |..+| ..|.++|.+.+.++.|..++-++..   +.+..+. ..+..-|.+.
T Consensus       399 ~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t---~~e~fsLLqlIAn~CYk~  474 (557)
T KOG3785|consen  399 LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNT---PSERFSLLQLIANDCYKA  474 (557)
T ss_pred             HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCC---chhHHHHHHHHHHHHHHH
Confidence            456666778888888888766544333 34444 4456688888888888777655543   2233333 3334567788


Q ss_pred             CChHHHHHHHHHHHhCCCCCCccccC
Q 040261          317 KEIEGALSLYSEMLSKGIRPTVVTYN  342 (343)
Q Consensus       317 ~~~~~a~~~~~~~~~~~~~p~~~t~~  342 (343)
                      +++--|.+.|+.+...  .|+...|.
T Consensus       475 ~eFyyaaKAFd~lE~l--DP~pEnWe  498 (557)
T KOG3785|consen  475 NEFYYAAKAFDELEIL--DPTPENWE  498 (557)
T ss_pred             HHHHHHHHhhhHHHcc--CCCccccC
Confidence            8888888888887744  56655553

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.06  E-value=1.5e-06  Score=71.07  Aligned_cols=124  Identities=19%  Similarity=0.146  Sum_probs=88.3

Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCHHH-------------------------HHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGVQPNVVT-------------------------FNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------------------------~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      ++.+.++++.+...+.+.+.....|+...                         ...-...+.+.|++..|+..|.+++.
T Consensus       307 a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIk  386 (539)
T KOG0548|consen  307 AYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIK  386 (539)
T ss_pred             hhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHh
Confidence            45556677777777777655433333211                         11114456678899999999998888


Q ss_pred             cCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          262 IGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       262 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .. +-|...|..-.-+|.+.|.+..|++-.+...+.. ++....|..-..++....+|+.|.+.|.+.++.
T Consensus       387 r~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~-p~~~kgy~RKg~al~~mk~ydkAleay~eale~  455 (539)
T KOG0548|consen  387 RD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIELD-PNFIKAYLRKGAALRAMKEYDKALEAYQEALEL  455 (539)
T ss_pred             cC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            76 6678888888888999999998888888777763 334556666667777778888888888888755

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

Probab=99.04  E-value=8.4e-07  Score=74.09  Aligned_cols=264  Identities=14%  Similarity=0.117  Sum_probs=156.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      ..|...+.+| ..+++...+.+.+.+.+. .+-...+.....-.+...|+.++|........+..+. +.+.|+.+.-.+
T Consensus         9 ~lF~~~lk~y-E~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~-S~vCwHv~gl~~   85 (700)
T KOG1156|consen    9 ALFRRALKCY-ETKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLK-SHVCWHVLGLLQ   85 (700)
T ss_pred             HHHHHHHHHH-HHHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCcc-cchhHHHHHHHH
Confidence            3444444444 556777777777666552 2223344444444556677778887777777665433 666777777777


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      -...++++|++.|......+.. |...+.-+.-.-++.|+++.......++.+..       +.....|..+..++.-.|
T Consensus        86 R~dK~Y~eaiKcy~nAl~~~~d-N~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-------~~~ra~w~~~Avs~~L~g  157 (700)
T KOG1156|consen   86 RSDKKYDEAIKCYRNALKIEKD-NLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-------PSQRASWIGFAVAQHLLG  157 (700)
T ss_pred             hhhhhHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-------hhhHHHHHHHHHHHHHHH
Confidence            6777788888888887776543 56666666656667777777777777766653       334556777777777778


Q ss_pred             ChHHHHHHHHHhhhCC-CCCChhhHHHHH------HHHhccCcHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhCCCh
Q 040261          178 FVDKAKELFLKMKDEN-INPDVVTYTSLI------RGFCYANDWNEAKCLFIEMMDQGVQPNVVTF-NVIMNELCKNGKM  249 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~-~~~~~~~~~~l~------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~  249 (343)
                      ++..|..+++...+.. -.|+...+....      ......|..++|.+.+..-...  ..|...+ ..-...+.+.+++
T Consensus       158 ~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~l  235 (700)
T KOG1156|consen  158 EYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQL  235 (700)
T ss_pred             HHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhH
Confidence            8888888777765543 234554444332      2334556666666666554332  2222222 2344556677888


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHH-HHHHHHhcCCchHHHH-HHHHHHHh
Q 040261          250 DEASRLLELMIQIGVRPDASVYN-TLMDGFCLTGRVNRAK-ELFVSMES  296 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~-~~~~~~~~  296 (343)
                      ++|..++..++..+  ||..-|. .+..++.+-.+.-++. .+|....+
T Consensus       236 EeA~~~y~~Ll~rn--Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~  282 (700)
T KOG1156|consen  236 EEAVKVYRRLLERN--PDNLDYYEGLEKALGKIKDMLEALKALYAILSE  282 (700)
T ss_pred             HhHHHHHHHHHhhC--chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhh
Confidence            88888888777763  4444333 3333443232333333 55555544

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.03  E-value=2.1e-06  Score=80.01  Aligned_cols=315  Identities=12%  Similarity=0.005  Sum_probs=199.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCC--C----CCCH--HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH---
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIG--L----FPDL--YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA---   87 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~----~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---   87 (343)
                      ........+...|+++++..+++.....-  .    .+..  .....+...+...|+++.|...++.........+.   
T Consensus       411 l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  490 (903)
T PRK04841        411 LVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSR  490 (903)
T ss_pred             hHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHH
Confidence            34455666678899999999998765421  0    1111  12223334566889999999999988763212121   


Q ss_pred             -HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCC-----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccc-c
Q 040261           88 -VTFTSLIKGLCAESRIMEAAALFTKLRAFGC-----KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVC-K  160 (343)
Q Consensus        88 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~  160 (343)
                       ...+.+...+...|++++|...+++.....-     .....+...+...+...|+++.|...+++........+... .
T Consensus       491 ~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~  570 (903)
T PRK04841        491 IVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLP  570 (903)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccc
Confidence             2345566667788999999999988764311     11123445667778899999999999888765421110000 1


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhC--CCCC--ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC--CCCCHH
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDE--NINP--DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG--VQPNVV  234 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~  234 (343)
                      .....+..+...+...|++++|...+.+....  ...+  ....+..+...+...|++++|...+.......  ......
T Consensus       571 ~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~  650 (903)
T PRK04841        571 MHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSD  650 (903)
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHh
Confidence            11223445566777889999999998886542  1111  23344556667788999999999998875531  111110


Q ss_pred             --HH--HHHHHHHHhCCChhHHHHHHHHHHHcCCCCC---HHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCc-c
Q 040261          235 --TF--NVIMNELCKNGKMDEASRLLELMIQIGVRPD---ASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMR-D  302 (343)
Q Consensus       235 --~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~  302 (343)
                        ..  ...+..+...|+.+.|..++...........   ...+..+..++...|+.++|...+++....    |..+ .
T Consensus       651 ~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~  730 (903)
T PRK04841        651 WIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDL  730 (903)
T ss_pred             HhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHH
Confidence              10  1122444568899999998877544221111   112345677788999999999999887653    3222 2


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          303 VFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       303 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      ..+...+..++.+.|+.++|...+.+.....
T Consensus       731 a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        731 NRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            3456667788999999999999999988654

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=99.03  E-value=1.1e-07  Score=73.48  Aligned_cols=187  Identities=11%  Similarity=-0.045  Sum_probs=116.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH---HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH--HH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL---YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA--VT   89 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~   89 (343)
                      .....+..++..+.+.|++++|...|+++.... +.+.   .++..+..++...|++++|...++++.+..+....  .+
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            456778888888889999999999999887643 2222   46677788888899999999999998876432111  13


Q ss_pred             HHHHHHHHhhc--------CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC
Q 040261           90 FTSLIKGLCAE--------SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        90 ~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      +..+..++.+.        |++++|.+.++++.+..+. +...+..+.....    ..      ...             
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~----~~------~~~-------------  165 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDY----LR------NRL-------------  165 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHH----HH------HHH-------------
Confidence            44445555543        6788888888888876332 2222211111100    00      000             


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC--CCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENI--NPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                       ......+...+.+.|++++|...++.......  +.....+..+..++...|++++|..+++.+...
T Consensus       166 -~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       166 -AGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             -HHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             00112445566777777777777777665421  223566677777777777777777777766554

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).

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

Probab=99.00  E-value=9.8e-08  Score=80.53  Aligned_cols=216  Identities=16%  Similarity=0.115  Sum_probs=169.0

Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTI  169 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  169 (343)
                      -..+...+...|-...|..+++++.         .|..++.+|...|+..+|..+..+..++        +|++..|..+
T Consensus       401 q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--------~~d~~lyc~L  463 (777)
T KOG1128|consen  401 QRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--------DPDPRLYCLL  463 (777)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--------CCcchhHHHh
Confidence            3445667777888888988888765         4667888999999999999999888873        5888999999


Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCh
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM  249 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  249 (343)
                      ........-+++|.++.+.....       .-..+.....+.++++++.+.++.-.+.. +....+|-.+..+..+.+++
T Consensus       464 GDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~  535 (777)
T KOG1128|consen  464 GDVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKE  535 (777)
T ss_pred             hhhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhh
Confidence            88888777788888888775432       11122222345788999999998877763 44567787888888889999


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          250 DEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      +.|.+.|....... +-+...|+.+-.+|.+.++-.+|...+.+..+-+ ..+...|...+....+.|.+++|++.+.++
T Consensus       536 q~av~aF~rcvtL~-Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rl  613 (777)
T KOG1128|consen  536 QAAVKAFHRCVTLE-PDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRL  613 (777)
T ss_pred             HHHHHHHHHHhhcC-CCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHH
Confidence            99999998888764 4557789999999999999999999999888876 556677777777888889999999999888


Q ss_pred             HhC
Q 040261          330 LSK  332 (343)
Q Consensus       330 ~~~  332 (343)
                      ...
T Consensus       614 l~~  616 (777)
T KOG1128|consen  614 LDL  616 (777)
T ss_pred             HHh
Confidence            654

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.99  E-value=8.8e-07  Score=67.14  Aligned_cols=262  Identities=13%  Similarity=0.148  Sum_probs=166.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHH-HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNI-LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      .+......|..+|....++..|-..++++...  .|...-|.. -.+++.+.+.+..|+.+...|...   ++...-..-
T Consensus        42 ~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~---~~L~~~~lq  116 (459)
T KOG4340|consen   42 RSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSLYKACIYADALRVAFLLLDN---PALHSRVLQ  116 (459)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCC---HHHHHHHHH
Confidence            47888999999999999999999999998774  365555544 346777889999999998887642   222111111


Q ss_pred             HH--HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHH
Q 040261           94 IK--GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITD  171 (343)
Q Consensus        94 ~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  171 (343)
                      +.  .....+++..+..++++....|   +..+.+...-...+.|+++.|.+-|+...+-++     . .....|+..+ 
T Consensus       117 LqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEaAvqkFqaAlqvsG-----y-qpllAYniAL-  186 (459)
T KOG4340|consen  117 LQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEAAVQKFQAALQVSG-----Y-QPLLAYNLAL-  186 (459)
T ss_pred             HHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccccHHHHHHHHHHHHhhcC-----C-CchhHHHHHH-
Confidence            22  2334577777777777766442   344445555556778888888888888877664     2 2344555444 


Q ss_pred             HHHhcCChHHHHHHHHHhhhCCCCC-------------Ch---------------hhHHHHHHHHhccCcHHHHHHHHHH
Q 040261          172 GLCKEGFVDKAKELFLKMKDENINP-------------DV---------------VTYTSLIRGFCYANDWNEAKCLFIE  223 (343)
Q Consensus       172 ~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~---------------~~~~~l~~~~~~~~~~~~a~~~~~~  223 (343)
                      +..+.++++.|++...++.++|++.             |.               ..+|.-...+.+.++++.|.+-+-.
T Consensus       187 aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtD  266 (459)
T KOG4340|consen  187 AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTD  266 (459)
T ss_pred             HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhc
Confidence            3445678888888888877765431             11               1133333445667777777777766


Q ss_pred             HHHc-CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHH
Q 040261          224 MMDQ-GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVS  293 (343)
Q Consensus       224 ~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  293 (343)
                      |.-+ ....|+.|...+.-.- ..+++....+-+.-+.+.+ +....||..++-.|++..-++.|-+++.+
T Consensus       267 mPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~n-PfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  267 MPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQN-PFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             CCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcC-CCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            6422 1234555554443221 2344555555555555554 44567888888888888888877777654

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

Probab=98.98  E-value=1e-06  Score=78.37  Aligned_cols=173  Identities=9%  Similarity=0.082  Sum_probs=115.8

Q ss_pred             CCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           11 HPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL-YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        11 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      .-.|.+...+..|+..+...+++++|.++.+...+..  |+. ..|..+...+.+.++.+.+..+               
T Consensus        25 ~~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~--P~~i~~yy~~G~l~~q~~~~~~~~lv---------------   87 (906)
T PRK14720         25 NYSLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH--KKSISALYISGILSLSRRPLNDSNLL---------------   87 (906)
T ss_pred             cCCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC--CcceehHHHHHHHHHhhcchhhhhhh---------------
Confidence            3445778889999999999999999999998766643  443 3444444456666664443333               


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTI  169 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  169 (343)
                        .++.......++.-+..++..+.+.+  -+..++..+..+|-+.|+.+++..+++++.+.+       +.++.+.|.+
T Consensus        88 --~~l~~~~~~~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-------~~n~~aLNn~  156 (906)
T PRK14720         88 --NLIDSFSQNLKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-------RDNPEIVKKL  156 (906)
T ss_pred             --hhhhhcccccchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-------cccHHHHHHH
Confidence              33444444455544445555555542  244577788888888888888888888888876       5677888888


Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      ...|... +.++|.+++.+....               +...+++..+..+|..+...
T Consensus       157 AY~~ae~-dL~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~  198 (906)
T PRK14720        157 ATSYEEE-DKEKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHY  198 (906)
T ss_pred             HHHHHHh-hHHHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhc
Confidence            8888888 888888888776653               34445556666666665554

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

Probab=98.97  E-value=3.7e-07  Score=67.76  Aligned_cols=149  Identities=11%  Similarity=0.149  Sum_probs=111.8

Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCh
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM  249 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  249 (343)
                      +..|...|+++......+.+..    |.        ..+...++.+++...++...+.. +.+...|..+...|...|++
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~----~~--------~~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~   89 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLAD----PL--------HQFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDY   89 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhC----cc--------ccccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCH
Confidence            3567888888887555433222    10        01223566777877787777764 66788888899999999999


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHH-HhcCCc--hHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHH
Q 040261          250 DEASRLLELMIQIGVRPDASVYNTLMDG-FCLTGR--VNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLY  326 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  326 (343)
                      ++|...+++..+.. +.+...+..+..+ +...|+  .++|.+++++..+.. +.+...+..+...+.+.|++++|+..|
T Consensus        90 ~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~  167 (198)
T PRK10370         90 DNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELW  167 (198)
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999998875 5577788888776 466676  589999999988874 346778888888899999999999999


Q ss_pred             HHHHhCC
Q 040261          327 SEMLSKG  333 (343)
Q Consensus       327 ~~~~~~~  333 (343)
                      +++++..
T Consensus       168 ~~aL~l~  174 (198)
T PRK10370        168 QKVLDLN  174 (198)
T ss_pred             HHHHhhC
Confidence            9988663

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.96  E-value=7.4e-06  Score=63.53  Aligned_cols=310  Identities=12%  Similarity=0.068  Sum_probs=214.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHH-HHHHHHHHhcCCcchHHHHHHHHHHcCCCccH------
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTY-NILINCFCKMGRVSPGFVVLGRILRSCFTPDA------   87 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------   87 (343)
                      .+-.++..-...|...|+..-|+.=+.+.++  .+||...- ..-...+.+.|.++.|..-|+..++.....+.      
T Consensus        70 ~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~ARiQRg~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqs  147 (504)
T KOG0624|consen   70 NNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMAARIQRGVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQS  147 (504)
T ss_pred             hhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHHHHHHhchhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHH
Confidence            4555566667888899999999999988887  45775432 22345678999999999999999886432111      


Q ss_pred             ------H--HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccc
Q 040261           88 ------V--TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        88 ------~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                            .  .....+..+.-.|+...|+.....+.+.. +.|...+..-..+|...|++..|+.-++...+..       
T Consensus       148 kl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs-------  219 (504)
T KOG0624|consen  148 KLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLS-------  219 (504)
T ss_pred             HHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcc-------
Confidence                  1  12234455667789999999999998863 3477778888899999999999998888887754       


Q ss_pred             cCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhh----HHHH---------HHHHhccCcHHHHHHHHHHHHH
Q 040261          160 KPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVT----YTSL---------IRGFCYANDWNEAKCLFIEMMD  226 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~l---------~~~~~~~~~~~~a~~~~~~~~~  226 (343)
                      ..+...+-.+-..+...|+.+.++...++-.+.+  ||...    |..+         +......++|.++..-.+...+
T Consensus       220 ~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKld--pdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk  297 (504)
T KOG0624|consen  220 QDNTEGHYKISQLLYTVGDAENSLKEIRECLKLD--PDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLK  297 (504)
T ss_pred             ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccC--cchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence            3456667777788888999999998888877653  55422    2211         1233456777788887777777


Q ss_pred             cCCCCCH---HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH
Q 040261          227 QGVQPNV---VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV  303 (343)
Q Consensus       227 ~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  303 (343)
                      .......   ..+..+-.++...+++.+|++...+..+.. +.|..++..-..+|.-...++.|..-|+...+.+.. +.
T Consensus       298 ~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d-~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n~s-n~  375 (504)
T KOG0624|consen  298 NEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDID-PDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELNES-NT  375 (504)
T ss_pred             cCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcC-chHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcc-cH
Confidence            6322122   234455566777889999999999988864 445888888889999999999999999888776421 21


Q ss_pred             HHHHHH-----------------HHHHHhcCChHHHHHHHHHHHhCCCCCCcc
Q 040261          304 FSYGIL-----------------INGYCKNKEIEGALSLYSEMLSKGIRPTVV  339 (343)
Q Consensus       304 ~~~~~l-----------------~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~  339 (343)
                      ..-..+                 |-+-.++-.-.+..+.|++|-. .+.||..
T Consensus       376 ~~reGle~Akrlkkqs~kRDYYKILGVkRnAsKqEI~KAYRKlAq-kWHPDNF  427 (504)
T KOG0624|consen  376 RAREGLERAKRLKKQSGKRDYYKILGVKRNASKQEITKAYRKLAQ-KWHPDNF  427 (504)
T ss_pred             HHHHHHHHHHHHHHHhccchHHHHhhhcccccHHHHHHHHHHHHH-hcCCccc
Confidence            111111                 1112233345667777888754 4677754

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

Probab=98.95  E-value=2.7e-07  Score=68.52  Aligned_cols=121  Identities=16%  Similarity=0.141  Sum_probs=54.6

Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG  247 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  247 (343)
                      ..+....+.|++..|...+.+..... ++|...|+.+..+|.+.|++++|..-+.+..+.. .-+...++.+.-.+.-.|
T Consensus       105 ~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~g  182 (257)
T COG5010         105 AQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRG  182 (257)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcC
Confidence            34444444455555555544444332 3344445555445555555555554444444431 122333444444444445


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      +++.|..++......+ +-|..+-..+.......|++++|..+.
T Consensus       183 d~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         183 DLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             CHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            5555555544444432 223334444444444445555444443

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

Probab=98.95  E-value=1.1e-05  Score=67.76  Aligned_cols=92  Identities=15%  Similarity=0.124  Sum_probs=48.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHh-CCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNS-IGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      .|-..+..+.++|+.......|++.+. ..+......|...+......+-++.+..++++.++-    ++..-+-.+..+
T Consensus       104 Iwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~L  179 (835)
T KOG2047|consen  104 IWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEYL  179 (835)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHHH
Confidence            344444555556666666666665443 122222335555555555556666666666666543    222244455555


Q ss_pred             hhcCcHHHHHHHHHHHH
Q 040261           98 CAESRIMEAAALFTKLR  114 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~  114 (343)
                      +..+++++|.+.+....
T Consensus       180 ~~~d~~~eaa~~la~vl  196 (835)
T KOG2047|consen  180 AKSDRLDEAAQRLATVL  196 (835)
T ss_pred             HhccchHHHHHHHHHhc
Confidence            56666666665555543

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

Probab=98.94  E-value=7.4e-07  Score=66.28  Aligned_cols=159  Identities=13%  Similarity=0.070  Sum_probs=99.2

Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHH
Q 040261           91 TSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTIT  170 (343)
Q Consensus        91 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  170 (343)
                      ..+-..+...|+-+....+........ ..|.......+....+.|++..|...+.+.....       ++|...|+.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~-~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-------p~d~~~~~~lg  141 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAY-PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-------PTDWEAWNLLG  141 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccC-cccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-------CCChhhhhHHH
Confidence            445555666666666666655544332 2244455556666777777777777777776654       56667777777


Q ss_pred             HHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChh
Q 040261          171 DGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMD  250 (343)
Q Consensus       171 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  250 (343)
                      -+|.+.|+.+.|..-|.+..+.. +-++..++.+.-.+.-.|+++.|..++......+ .-+..+-..+..+....|+++
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~  219 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFR  219 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChH
Confidence            77777777777777777666542 2245556666666666777777777777666653 334555556666666777777


Q ss_pred             HHHHHHHHH
Q 040261          251 EASRLLELM  259 (343)
Q Consensus       251 ~a~~~~~~~  259 (343)
                      .|..+...-
T Consensus       220 ~A~~i~~~e  228 (257)
T COG5010         220 EAEDIAVQE  228 (257)
T ss_pred             HHHhhcccc
Confidence            776665443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.93  E-value=6.9e-07  Score=68.99  Aligned_cols=60  Identities=13%  Similarity=-0.029  Sum_probs=39.2

Q ss_pred             HHHHHHhcCCchHHHHHHHHHHHhCCC--CccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          273 TLMDGFCLTGRVNRAKELFVSMESNGC--MRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       273 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .+...+.+.|++++|...++.+.+...  +.....+..+..++...|++++|...++.+..+
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            344556777777777777777765421  123456667777777777777777777776544

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).

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.93  E-value=3e-06  Score=72.29  Aligned_cols=283  Identities=14%  Similarity=0.070  Sum_probs=176.3

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.+++..+.++.  |+.+...+.--|+..++.+.|.+..++..+.+-..+...|..+.-.+...+++..|+.+.+.....
T Consensus       465 qale~av~~d~~--dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E  542 (799)
T KOG4162|consen  465 QALEEAVQFDPT--DPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEE  542 (799)
T ss_pred             HHHHHHHhcCCC--CchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            345555555554  445555566667777788888888888777654567778888887788888888888887776653


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc---------------------C-------CCCCHHHHHHHHHHHH
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF---------------------G-------CKPDVFTYTTLINGLC  133 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------------------~-------~~~~~~~~~~l~~~~~  133 (343)
                      - ..|-.....-+..-...++.++++.....+...                     |       ..-...++..+.....
T Consensus       543 ~-~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a  621 (799)
T KOG4162|consen  543 F-GDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVA  621 (799)
T ss_pred             h-hhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHH
Confidence            1 111111111111112234444444333332211                     0       0000111111111111


Q ss_pred             hcCChHHHHHHHHHHHccCCCCCccccCC------cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHH
Q 040261          134 RTGHTIVALNLFEEMANGNGEFGVVCKPD------AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG  207 (343)
Q Consensus       134 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  207 (343)
                      ..+........+......       ..|+      ...|......+.+.+..++|...+.+..... +.....|......
T Consensus       622 ~~~~~~~se~~Lp~s~~~-------~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~-~l~~~~~~~~G~~  693 (799)
T KOG4162|consen  622 SQLKSAGSELKLPSSTVL-------PGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKID-PLSASVYYLRGLL  693 (799)
T ss_pred             hhhhhcccccccCccccc-------CCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcc-hhhHHHHHHhhHH
Confidence            000000000000000000       0111      1234555677888899999998888876653 3456777777788


Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH--HHHHHHHcCCCCCHHHHHHHHHHHhcCCchH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR--LLELMIQIGVRPDASVYNTLMDGFCLTGRVN  285 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  285 (343)
                      +...|.+++|...|......+ +-+.....++...+.+.|+..-|..  ++..+.+.+ +.+...|-.+...+.+.|+.+
T Consensus       694 ~~~~~~~~EA~~af~~Al~ld-P~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~v~k~~Gd~~  771 (799)
T KOG4162|consen  694 LEVKGQLEEAKEAFLVALALD-PDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGEVFKKLGDSK  771 (799)
T ss_pred             HHHHHhhHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHccchH
Confidence            888999999999999888763 3346788899999999999888888  999999987 778999999999999999999


Q ss_pred             HHHHHHHHHHhC
Q 040261          286 RAKELFVSMESN  297 (343)
Q Consensus       286 ~a~~~~~~~~~~  297 (343)
                      +|.+.|....+.
T Consensus       772 ~Aaecf~aa~qL  783 (799)
T KOG4162|consen  772 QAAECFQAALQL  783 (799)
T ss_pred             HHHHHHHHHHhh
Confidence            999999987764

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.92  E-value=6.9e-06  Score=76.61  Aligned_cols=304  Identities=13%  Similarity=-0.007  Sum_probs=180.7

Q ss_pred             HhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC------Ccc--HHHHHHHHHHHhh
Q 040261           28 AKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF------TPD--AVTFTSLIKGLCA   99 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~--~~~~~~l~~~~~~   99 (343)
                      ...|++..+...++.+.......+..........+...|+++++..++......-.      .+.  ......+...+..
T Consensus       385 ~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  464 (903)
T PRK04841        385 FNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAIN  464 (903)
T ss_pred             HhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHh
Confidence            34455555555554432111111122223344455677889999888887754311      111  1122223345567


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDV----FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .|++++|...+++..+.-...+.    .....+...+...|+++.|...+++........+. ......+...+...+..
T Consensus       465 ~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~-~~~~~~~~~~la~~~~~  543 (903)
T PRK04841        465 DGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDV-YHYALWSLLQQSEILFA  543 (903)
T ss_pred             CCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcc-hHHHHHHHHHHHHHHHH
Confidence            89999999999987763211121    23455666778899999999999887754321100 01112345566777889


Q ss_pred             cCChHHHHHHHHHhhhC----CCC--C-ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC--CCC--CHHHHHHHHHHHH
Q 040261          176 EGFVDKAKELFLKMKDE----NIN--P-DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG--VQP--NVVTFNVIMNELC  244 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~l~~~~~  244 (343)
                      .|+++.|...+++....    +..  + ....+..+...+...|++++|...+.+.....  ..+  ....+..+...+.
T Consensus       544 ~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~  623 (903)
T PRK04841        544 QGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISL  623 (903)
T ss_pred             CCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHH
Confidence            99999999998876442    211  1 12334455566777899999999988876531  112  2334445666788


Q ss_pred             hCCChhHHHHHHHHHHHcCC--CCCHH--H--HHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc---HHHHHHHHHHHHh
Q 040261          245 KNGKMDEASRLLELMIQIGV--RPDAS--V--YNTLMDGFCLTGRVNRAKELFVSMESNGCMRD---VFSYGILINGYCK  315 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~--~~~~~--~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~  315 (343)
                      ..|+++.|...++.+.....  .....  .  ....+..+...|+.+.|...+...........   ...+..+..++..
T Consensus       624 ~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~  703 (903)
T PRK04841        624 ARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQIL  703 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHH
Confidence            89999999999988755311  11111  0  01122444568899999998877554221111   1123456777889


Q ss_pred             cCChHHHHHHHHHHHhC
Q 040261          316 NKEIEGALSLYSEMLSK  332 (343)
Q Consensus       316 ~~~~~~a~~~~~~~~~~  332 (343)
                      .|++++|...+++....
T Consensus       704 ~g~~~~A~~~l~~al~~  720 (903)
T PRK04841        704 LGQFDEAEIILEELNEN  720 (903)
T ss_pred             cCCHHHHHHHHHHHHHH
Confidence            99999999999888653

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

Probab=98.92  E-value=7.7e-06  Score=61.12  Aligned_cols=256  Identities=15%  Similarity=0.095  Sum_probs=168.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      .+.|+  ++-+.-.|++..++..-......  +.+...-..+.++|...|++....   ..+.... .|.......+...
T Consensus        10 d~LF~--iRn~fY~Gnyq~~ine~~~~~~~--~~~~e~d~y~~raylAlg~~~~~~---~eI~~~~-~~~lqAvr~~a~~   81 (299)
T KOG3081|consen   10 DELFN--IRNYFYLGNYQQCINEAEKFSSS--KTDVELDVYMYRAYLALGQYQIVI---SEIKEGK-ATPLQAVRLLAEY   81 (299)
T ss_pred             hhHHH--HHHHHHhhHHHHHHHHHHhhccc--cchhHHHHHHHHHHHHcccccccc---ccccccc-CChHHHHHHHHHH
Confidence            44454  34445578888887776654432  234444455667777777765433   2333222 3344444444444


Q ss_pred             HhhcCcHHHH-HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           97 LCAESRIMEA-AALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        97 ~~~~~~~~~a-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      ....++.+.- .++.+.+.......+......-...|.+.+++++|++......            +..+...=..++.+
T Consensus        82 ~~~e~~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------------~lE~~Al~VqI~lk  149 (299)
T KOG3081|consen   82 LELESNKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------------NLEAAALNVQILLK  149 (299)
T ss_pred             hhCcchhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------------hHHHHHHHHHHHHH
Confidence            4444444443 3455555555444343444445567899999999999887722            23344444566778


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDE  251 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  251 (343)
                      ..+.+.|...+++|.+-   .+..+.+.|..++.+    .+...+|.-+|++|.++ ..|+..+.+....++...|++++
T Consensus       150 ~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~ee  225 (299)
T KOG3081|consen  150 MHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEE  225 (299)
T ss_pred             HHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHH
Confidence            88999999999999875   367778877777654    45689999999999886 58899999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc-hHHHHHHHHHHHhC
Q 040261          252 ASRLLELMIQIGVRPDASVYNTLMDGFCLTGR-VNRAKELFVSMESN  297 (343)
Q Consensus       252 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~  297 (343)
                      |..+++++.... ..++.+...++.+-...|. .+...+.+..++..
T Consensus       226 Ae~lL~eaL~kd-~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  226 AESLLEEALDKD-AKDPETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             HHHHHHHHHhcc-CCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            999999998876 4456666666655555554 45556666777654

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.91  E-value=2.1e-06  Score=75.51  Aligned_cols=135  Identities=13%  Similarity=0.095  Sum_probs=83.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL  128 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  128 (343)
                      +.+...+..|..+..+.|..++|..+++...+..+. +......+...+.+.+++++|+..+++.....+. +......+
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd-~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~-~~~~~~~~  160 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPD-SSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSS-SAREILLE  160 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCC-CHHHHHHH
Confidence            344556666666666666666666666666665321 3455555666666666666666666666665433 44555566


Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                      ..++.+.|++++|..+|+++...+       +.+..++..+..++.+.|+.++|...|++..+.
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~-------p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQH-------PEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcC-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            666666666666666666666532       334566666666666666666666666666554

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

Probab=98.90  E-value=1.2e-06  Score=65.08  Aligned_cols=120  Identities=10%  Similarity=0.168  Sum_probs=78.7

Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HhCCC--hhHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL-CKNGK--MDEA  252 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~--~~~a  252 (343)
                      .++.+++...++...+.+ +.+...|..+...|...|++++|...+++..+.. +.+...+..+..++ ...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            455566666666655543 3466677777777777777777777777777653 33455666666543 45555  4777


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          253 SRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      .+++++..+.+ +-+...+..+...+...|++++|...|+++.+..
T Consensus       130 ~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~  174 (198)
T PRK10370        130 REMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLDLN  174 (198)
T ss_pred             HHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            77777777765 4456666777777777777777777777776653

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

Probab=98.90  E-value=2.3e-05  Score=65.20  Aligned_cols=171  Identities=15%  Similarity=0.111  Sum_probs=91.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCc-cHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTP-DAVTFTSLI   94 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~   94 (343)
                      +..++..-+-++.+.+++++|+.+.+.-..  ...+..-+..-..+..+.+..++|+..++     |..+ +..+...-.
T Consensus        45 d~~a~~cKvValIq~~ky~~ALk~ikk~~~--~~~~~~~~fEKAYc~Yrlnk~Dealk~~~-----~~~~~~~~ll~L~A  117 (652)
T KOG2376|consen   45 DEDAIRCKVVALIQLDKYEDALKLIKKNGA--LLVINSFFFEKAYCEYRLNKLDEALKTLK-----GLDRLDDKLLELRA  117 (652)
T ss_pred             cHhhHhhhHhhhhhhhHHHHHHHHHHhcch--hhhcchhhHHHHHHHHHcccHHHHHHHHh-----cccccchHHHHHHH
Confidence            444555555555555666655544332110  00011111112223345555566655555     1222 233555666


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCC---------------------------CHHHHHHH---HHHHHhcCChHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKP---------------------------DVFTYTTL---INGLCRTGHTIVALNL  144 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~---------------------------~~~~~~~l---~~~~~~~~~~~~a~~~  144 (343)
                      ..+.+.|++++|+.+|+.+.+.+.+-                           ...+|..+   ...+...|++.+|+++
T Consensus       118 QvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~el  197 (652)
T KOG2376|consen  118 QVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDSYELLYNTACILIENGKYNQAIEL  197 (652)
T ss_pred             HHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcchHHHHHHHHHHHHhcccHHHHHHH
Confidence            77888999999999999886543220                           01122222   2345678999999999


Q ss_pred             HHHHHccCCCCCcc--cc-CCc-----chHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          145 FEEMANGNGEFGVV--CK-PDA-----ITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       145 ~~~~~~~~~~~~~~--~~-~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                      ++.....+...-..  .. .+.     .+-.-+...+...|+.++|..++....+.+
T Consensus       198 L~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  198 LEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRN  254 (652)
T ss_pred             HHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc
Confidence            99882211100000  00 000     122345566778999999999998887664

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

Probab=98.89  E-value=2e-05  Score=65.56  Aligned_cols=312  Identities=15%  Similarity=0.128  Sum_probs=182.7

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      ..-+=+..+.+.|++++|....+++...+ +.+...+..-+-++.+.+++++|+.+.+.-...  ..+...+-.-..+..
T Consensus        14 ~l~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Y   90 (652)
T KOG2376|consen   14 ALLTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEY   90 (652)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHH
Confidence            34445667778899999999999998866 556778888888999999999998655432211  111111112234445


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCC----------------c----c
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFG----------------V----V  158 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----------------~----~  158 (343)
                      +.+..++|+..++-....    +..+...-.+.+.+.+++++|+.+|+.+.+++.+..                .    .
T Consensus        91 rlnk~Dealk~~~~~~~~----~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~  166 (652)
T KOG2376|consen   91 RLNKLDEALKTLKGLDRL----DDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQS  166 (652)
T ss_pred             HcccHHHHHHHHhccccc----chHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHh
Confidence            779999999998833322    344666777889999999999999999976653210                0    0


Q ss_pred             cc-CCcchHHHH---HHHHHhcCChHHHHHHHHHhhhC-------CCCC------Ch-hhHHHHHHHHhccCcHHHHHHH
Q 040261          159 CK-PDAITYSTI---TDGLCKEGFVDKAKELFLKMKDE-------NINP------DV-VTYTSLIRGFCYANDWNEAKCL  220 (343)
Q Consensus       159 ~~-~~~~~~~~l---~~~~~~~~~~~~a~~~~~~~~~~-------~~~~------~~-~~~~~l~~~~~~~~~~~~a~~~  220 (343)
                      .+ ....+|..+   ...+...|++.+|+++++...+.       +-.-      .. ..--.+...+-..|+-++|..+
T Consensus       167 v~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~i  246 (652)
T KOG2376|consen  167 VPEVPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSI  246 (652)
T ss_pred             ccCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHH
Confidence            00 012234333   34456789999999999887221       1000      01 1122344556778999999999


Q ss_pred             HHHHHHcCCCCCHHHH----HHHHHHHHhCCChh-------------HHHHHHHHH------------------------
Q 040261          221 FIEMMDQGVQPNVVTF----NVIMNELCKNGKMD-------------EASRLLELM------------------------  259 (343)
Q Consensus       221 ~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~~-------------~a~~~~~~~------------------------  259 (343)
                      +...++.. .+|....    |.|+..-....-++             -+..+...+                        
T Consensus       247 y~~~i~~~-~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q  325 (652)
T KOG2376|consen  247 YVDIIKRN-PADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQ  325 (652)
T ss_pred             HHHHHHhc-CCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence            99998875 3443222    22221111000011             000000000                        


Q ss_pred             -----HHc-CCCCCHHHHHHHHHHHhc-C-CchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHH----
Q 040261          260 -----IQI-GVRPDASVYNTLMDGFCL-T-GRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS----  327 (343)
Q Consensus       260 -----~~~-~~~~~~~~~~~l~~~~~~-~-~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----  327 (343)
                           ... +..|. ..+..++..+.+ . ....++..++....+.............+......|+++.|++++.    
T Consensus       326 ~r~~~a~lp~~~p~-~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~  404 (652)
T KOG2376|consen  326 VRELSASLPGMSPE-SLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLE  404 (652)
T ss_pred             HHHHHHhCCccCch-HHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence                 000 11222 233334333322 2 2366677777766665322234455666777889999999999999    


Q ss_pred             ----HHHhCCCCCCcc
Q 040261          328 ----EMLSKGIRPTVV  339 (343)
Q Consensus       328 ----~~~~~~~~p~~~  339 (343)
                          .+.+.+..|-.+
T Consensus       405 ~~~ss~~~~~~~P~~V  420 (652)
T KOG2376|consen  405 SWKSSILEAKHLPGTV  420 (652)
T ss_pred             hhhhhhhhhccChhHH
Confidence                666656555544

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

Probab=98.87  E-value=4e-07  Score=76.96  Aligned_cols=220  Identities=15%  Similarity=0.081  Sum_probs=159.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      |--..-..+...+.+.|-...|+.+|+++.         .|.-.+.+|...|+..+|..+..+-.+.  +|++..|..+.
T Consensus       396 p~Wq~q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LG  464 (777)
T KOG1128|consen  396 PIWQLQRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLG  464 (777)
T ss_pred             CcchHHHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhh
Confidence            444445567778888888888888888753         4556777888888888888888777763  67888888888


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      +......-+++|.++.+.....       +-..+.....+.++++++.+.|+.-.+..       +....+|-.+..+..
T Consensus       465 Dv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-------plq~~~wf~~G~~AL  530 (777)
T KOG1128|consen  465 DVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-------PLQLGTWFGLGCAAL  530 (777)
T ss_pred             hhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-------ccchhHHHhccHHHH
Confidence            8776666677777777664332       22223333344678888888888777654       445677777788888


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      +.++++.|.+.|....... +.+...||.+-.+|.+.++-.+|...+.+..+.+ .-+...|...+....+.|.+++|.+
T Consensus       531 qlek~q~av~aF~rcvtL~-Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~  608 (777)
T KOG1128|consen  531 QLEKEQAAVKAFHRCVTLE-PDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIK  608 (777)
T ss_pred             HHhhhHHHHHHHHHHhhcC-CCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHH
Confidence            8888888888887776642 3356778888888888888888888888888776 4456666667777778888888888


Q ss_pred             HHHHHHH
Q 040261          255 LLELMIQ  261 (343)
Q Consensus       255 ~~~~~~~  261 (343)
                      .+.++..
T Consensus       609 A~~rll~  615 (777)
T KOG1128|consen  609 AYHRLLD  615 (777)
T ss_pred             HHHHHHH
Confidence            8877765

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.87  E-value=2.3e-07  Score=65.20  Aligned_cols=97  Identities=9%  Similarity=-0.095  Sum_probs=74.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      .+..+...+.+.|++++|...|+...... +.+...|..+..++...|++++|...|++..... +.+...+..+..++.
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            45566777788888888888888877755 4567777888888888888888888888888764 336777777888888


Q ss_pred             hcCcHHHHHHHHHHHHhcC
Q 040261           99 AESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~  117 (343)
                      ..|++++|...|+...+..
T Consensus       104 ~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359        104 MMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HcCCHHHHHHHHHHHHHhC
Confidence            8888888888888877763

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.87  E-value=1.8e-06  Score=75.91  Aligned_cols=219  Identities=10%  Similarity=0.085  Sum_probs=154.1

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHH-HHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAA-LFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI  164 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  164 (343)
                      ++.....+=.+.+.-|..++|-+ ++.+..            .++....+.....+++.-+..+...       .+.+..
T Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~   87 (694)
T PRK15179         27 GPTILDLLEAALAEPGESEEAGRELLQQAR------------QVLERHAAVHKPAAALPELLDYVRR-------YPHTEL   87 (694)
T ss_pred             CcHHHhHHHHHhcCcccchhHHHHHHHHHH------------HHHHHhhhhcchHhhHHHHHHHHHh-------ccccHH
Confidence            33344444445556666666533 333322            2233333333334444444444443       355688


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040261          165 TYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC  244 (343)
Q Consensus       165 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  244 (343)
                      .+..|..+..+.|.+++|..+++...+.. +-+......+...+.+.+++++|....++..... +-+......+..++.
T Consensus        88 ~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~a~~l~  165 (694)
T PRK15179         88 FQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLEAKSWD  165 (694)
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHHHHHHH
Confidence            99999999999999999999999998864 2346677788889999999999999999999874 445667778888999


Q ss_pred             hCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHH
Q 040261          245 KNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                      +.|++++|..+|+++...+ +-+..++..+..++...|+.++|...|++..+.. .+....|+.++.      +...-..
T Consensus       166 ~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~-~~~~~~~~~~~~------~~~~~~~  237 (694)
T PRK15179        166 EIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI-GDGARKLTRRLV------DLNADLA  237 (694)
T ss_pred             HhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh-CcchHHHHHHHH------HHHHHHH
Confidence            9999999999999999843 4557899999999999999999999999988753 344555555443      3344455


Q ss_pred             HHHHHHhCC
Q 040261          325 LYSEMLSKG  333 (343)
Q Consensus       325 ~~~~~~~~~  333 (343)
                      .++++...+
T Consensus       238 ~~~~~~~~~  246 (694)
T PRK15179        238 ALRRLGVEG  246 (694)
T ss_pred             HHHHcCccc
Confidence            666665443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.85  E-value=6.1e-06  Score=61.19  Aligned_cols=187  Identities=13%  Similarity=0.132  Sum_probs=92.6

Q ss_pred             CcHHHHHHHHHHHHhc---C-CCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261          101 SRIMEAAALFTKLRAF---G-CKPDVF-TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus       101 ~~~~~a~~~~~~~~~~---~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+.++.++++.++...   | ..++.. .+..++-+....|+.+.|...++++...-       |.+..+-..-.-.+-.
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-------p~S~RV~~lkam~lEa   98 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF-------PGSKRVGKLKAMLLEA   98 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-------CCChhHHHHHHHHHHH
Confidence            3445555555554422   2 222322 23334444455556666666666655542       2222222222233344


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      .|++++|+++++.+.+.+ +.|..++-.-+...-..|..-+|++-+....+. +..|...|..+...|...|++++|.-.
T Consensus        99 ~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fC  176 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFC  176 (289)
T ss_pred             hhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHH
Confidence            566666666666665554 334444444444444455555555555555554 345566666666666666666666666


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhcCC---chHHHHHHHHHHHhC
Q 040261          256 LELMIQIGVRPDASVYNTLMDGFCLTG---RVNRAKELFVSMESN  297 (343)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~  297 (343)
                      +++++-.. |.++..+..+...+...|   +...+.+.+.+..+.
T Consensus       177 lEE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  177 LEELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            66665543 334444444444433332   344555555555553

>PF12854 PPR_1: PPR repeat

Probab=98.83  E-value=5.9e-09  Score=52.45  Aligned_cols=32  Identities=47%  Similarity=1.019  Sum_probs=19.1

Q ss_pred             CCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          298 GCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       298 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      |+.||..+|++++.+|++.|+.++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            45566666666666666666666666666555

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

Probab=98.83  E-value=9.5e-06  Score=60.64  Aligned_cols=250  Identities=12%  Similarity=0.036  Sum_probs=162.3

Q ss_pred             HHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH
Q 040261           60 NCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI  139 (343)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  139 (343)
                      +-+.-.|++..++..-.......  -+...-.-+.++|...|.+.....   ++... -.|....+..+......-++.+
T Consensus        16 Rn~fY~Gnyq~~ine~~~~~~~~--~~~e~d~y~~raylAlg~~~~~~~---eI~~~-~~~~lqAvr~~a~~~~~e~~~~   89 (299)
T KOG3081|consen   16 RNYFYLGNYQQCINEAEKFSSSK--TDVELDVYMYRAYLALGQYQIVIS---EIKEG-KATPLQAVRLLAEYLELESNKK   89 (299)
T ss_pred             HHHHHhhHHHHHHHHHHhhcccc--chhHHHHHHHHHHHHccccccccc---ccccc-cCChHHHHHHHHHHhhCcchhH
Confidence            34455677777766655544332  233333345567777776654433   22222 2445555555555444455544


Q ss_pred             HHHHH-HHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHH
Q 040261          140 VALNL-FEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAK  218 (343)
Q Consensus       140 ~a~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  218 (343)
                      .-+.- .+.+....      ...+......-...|.+.|++++|++......      +......=+..+.+..+.+-|.
T Consensus        90 ~~~~~l~E~~a~~~------~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~  157 (299)
T KOG3081|consen   90 SILASLYELVADST------DGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAE  157 (299)
T ss_pred             HHHHHHHHHHHhhc------cchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHH
Confidence            43333 33333322      12222333444567899999999999987722      3444444456677888999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          219 CLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      ..++.|.+..   +..+.+.|..++.+    .+....|.-+|++|.+. .+|+..+.+....++...|++++|..+++..
T Consensus       158 ~~lk~mq~id---ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~ea  233 (299)
T KOG3081|consen  158 KELKKMQQID---EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEA  233 (299)
T ss_pred             HHHHHHHccc---hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHH
Confidence            9999998753   67778878777764    35688999999999875 4889999999999999999999999999999


Q ss_pred             HhCCCCccHHHHHHHHHHHHhcCCh-HHHHHHHHHHHhC
Q 040261          295 ESNGCMRDVFSYGILINGYCKNKEI-EGALSLYSEMLSK  332 (343)
Q Consensus       295 ~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  332 (343)
                      .... ..++.+...++.+-...|.. +-..+.+.++...
T Consensus       234 L~kd-~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  234 LDKD-AKDPETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             Hhcc-CCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            8874 34666666666665555654 4445666666543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.80  E-value=8.8e-07  Score=62.24  Aligned_cols=95  Identities=8%  Similarity=-0.061  Sum_probs=70.8

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL  280 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  280 (343)
                      +......+...|++++|...|+...... +.+...+..+..++...|++++|...|+++.+.+ +.+...+..+..++..
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~  104 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKM  104 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHH
Confidence            4455666777788888888888777663 4456777777777888888888888888887765 5567777777777788


Q ss_pred             CCchHHHHHHHHHHHhC
Q 040261          281 TGRVNRAKELFVSMESN  297 (343)
Q Consensus       281 ~~~~~~a~~~~~~~~~~  297 (343)
                      .|++++|...|+...+.
T Consensus       105 ~g~~~eAi~~~~~Al~~  121 (144)
T PRK15359        105 MGEPGLAREAFQTAIKM  121 (144)
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            88888888888877765

>PF12854 PPR_1: PPR repeat

Probab=98.78  E-value=1.1e-08  Score=51.52  Aligned_cols=31  Identities=42%  Similarity=0.802  Sum_probs=13.2

Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHH
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKL  113 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  113 (343)
                      +.||..+|+.++.+|++.|++++|.++|++|
T Consensus         3 ~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    3 CEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            3344444444444444444444444444433

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

Probab=98.78  E-value=5.6e-05  Score=62.37  Aligned_cols=132  Identities=14%  Similarity=0.158  Sum_probs=102.0

Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP-NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD  276 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  276 (343)
                      ..+|...+..-.+....+.|..+|.++.+.+..+ +..+.++++..++ .+|.+-|.++|+.-.+.- .-++.--...+.
T Consensus       366 tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf-~d~p~yv~~Yld  443 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKF-GDSPEYVLKYLD  443 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhc-CCChHHHHHHHH
Confidence            4567777777778888899999999999887776 5677777777765 678888999998766541 233444566777


Q ss_pred             HHhcCCchHHHHHHHHHHHhCCCCcc--HHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          277 GFCLTGRVNRAKELFVSMESNGCMRD--VFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       277 ~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      .+...++-..+..+|++....++.++  ...|..++.-=..-|+...+.++-+++..
T Consensus       444 fL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  444 FLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            78888898999999999988755554  47899999888888999988888777654

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.76  E-value=2.8e-05  Score=63.92  Aligned_cols=215  Identities=13%  Similarity=0.059  Sum_probs=133.3

Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      ++..+..++..|++-+....+..  -+..-++....+|...|.+..+...-+...+.++........=...+..+..+|.
T Consensus       232 naaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~  309 (539)
T KOG0548|consen  232 NAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYT  309 (539)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhh
Confidence            33333444444555554444442  2333344445555556655555555544444432110000000111222334677


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhH-------------------------HHHHHHHhccCcHHHHHHHHHHHHHcCC
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTY-------------------------TSLIRGFCYANDWNEAKCLFIEMMDQGV  229 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~-------------------------~~l~~~~~~~~~~~~a~~~~~~~~~~~~  229 (343)
                      +.++++.++..|.+.......|+...=                         ..-...+.+.|++..|...+.++++.. 
T Consensus       310 k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-  388 (539)
T KOG0548|consen  310 KREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-  388 (539)
T ss_pred             hHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-
Confidence            788899999999887665444433221                         111345678899999999999999985 


Q ss_pred             CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHH
Q 040261          230 QPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGIL  309 (343)
Q Consensus       230 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  309 (343)
                      +-|...|..-.-+|.+.|.+..|+.-.+..++.+ ++....|..=..++....++++|.+.|.+..+..  |+..-+..-
T Consensus       389 P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~-p~~~kgy~RKg~al~~mk~ydkAleay~eale~d--p~~~e~~~~  465 (539)
T KOG0548|consen  389 PEDARLYSNRAACYLKLGEYPEALKDAKKCIELD-PNFIKAYLRKGAALRAMKEYDKALEAYQEALELD--PSNAEAIDG  465 (539)
T ss_pred             CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--chhHHHHHH
Confidence            6678899999999999999999999988888875 4555666666666777789999999999998864  554444433


Q ss_pred             HHHHHh
Q 040261          310 INGYCK  315 (343)
Q Consensus       310 ~~~~~~  315 (343)
                      +.-|..
T Consensus       466 ~~rc~~  471 (539)
T KOG0548|consen  466 YRRCVE  471 (539)
T ss_pred             HHHHHH
Confidence            333333

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

Probab=98.75  E-value=6.5e-06  Score=73.50  Aligned_cols=232  Identities=9%  Similarity=0.046  Sum_probs=152.7

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc-HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD-AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      +...+..|+..+...+++++|.++.+...+..  |+ ...|..+...+.+.++..++..+                 .++
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~--P~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~~l   90 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEH--KKSISALYISGILSLSRRPLNDSNLL-----------------NLI   90 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC--CcceehHHHHHHHHHhhcchhhhhhh-----------------hhh
Confidence            45678888888888899999999988777653  33 33333333455566664444333                 333


Q ss_pred             HHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHh
Q 040261          130 NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFC  209 (343)
Q Consensus       130 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  209 (343)
                      .......++..+..+...+...        ..+..++..+..+|-+.|+.++|..+++++.+.. +-++...|.+...|.
T Consensus        91 ~~~~~~~~~~~ve~~~~~i~~~--------~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~a  161 (906)
T PRK14720         91 DSFSQNLKWAIVEHICDKILLY--------GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYE  161 (906)
T ss_pred             hhcccccchhHHHHHHHHHHhh--------hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHH
Confidence            3444444554444444455543        2345688889999999999999999999999987 558899999999999


Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-----hCCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHhcCCc
Q 040261          210 YANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC-----KNGKMDEASRLLELMIQI-GVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       210 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      .. +.++|..++.+....-+  +..-|+.+...+.     ...+.+.-..+.+.+... +..--..++-.+...|...++
T Consensus       162 e~-dL~KA~~m~~KAV~~~i--~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~  238 (906)
T PRK14720        162 EE-DKEKAITYLKKAIYRFI--KKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALED  238 (906)
T ss_pred             Hh-hHHHHHHHHHHHHHHHH--hhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhh
Confidence            99 99999999988876511  1111222222111     122333344444444333 323334556666677888899


Q ss_pred             hHHHHHHHHHHHhCCCCccHHHHHHHHHHHH
Q 040261          284 VNRAKELFVSMESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       284 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  314 (343)
                      ++++..+++.+.+.. +.|.....-++.+|.
T Consensus       239 ~~~~i~iLK~iL~~~-~~n~~a~~~l~~~y~  268 (906)
T PRK14720        239 WDEVIYILKKILEHD-NKNNKAREELIRFYK  268 (906)
T ss_pred             hhHHHHHHHHHHhcC-CcchhhHHHHHHHHH
Confidence            999999999999874 346667777777776

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

Probab=98.75  E-value=7.7e-07  Score=62.16  Aligned_cols=109  Identities=14%  Similarity=0.066  Sum_probs=76.5

Q ss_pred             HHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261            4 FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus         4 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      |+......|.  +......+...+.+.|++++|.+.|+.+...+ +.+...+..+..++...|++++|..+++...+.+ 
T Consensus         6 ~~~~l~~~p~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-   81 (135)
T TIGR02552         6 LKDLLGLDSE--QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-   81 (135)
T ss_pred             HHHHHcCChh--hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence            4444444443  55666677777777888888888887776654 4466677777777777788888888887776654 


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      +.+...+..+...+...|++++|.+.++...+.
T Consensus        82 p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        82 PDDPRPYFHAAECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            335666666777777778888888888777765

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

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.73  E-value=2.2e-05  Score=61.25  Aligned_cols=185  Identities=10%  Similarity=0.103  Sum_probs=117.4

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      +.-+....++..|+.+++--...+-.....+-.-+..++.+.|++++|...+.-+.... .++...+..+.-++.-.|.+
T Consensus        29 Ledfls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y  107 (557)
T KOG3785|consen   29 LEDFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQY  107 (557)
T ss_pred             HHHHHhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHH
Confidence            45566778888999888766543322111233334566778899999999998887753 56677777777777777888


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                      .+|..+..+..+     ++.....++....+.++-++-..+.+.+...           ..--.++.+.....-.+++|+
T Consensus       108 ~eA~~~~~ka~k-----~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----------~EdqLSLAsvhYmR~HYQeAI  171 (557)
T KOG3785|consen  108 IEAKSIAEKAPK-----TPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----------LEDQLSLASVHYMRMHYQEAI  171 (557)
T ss_pred             HHHHHHHhhCCC-----ChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----------HHHHHhHHHHHHHHHHHHHHH
Confidence            888877655432     4444555666667777776666665555432           223344455555555677888


Q ss_pred             HHHHHhhhCCCCCChhhHHHH-HHHHhccCcHHHHHHHHHHHHHc
Q 040261          184 ELFLKMKDENINPDVVTYTSL-IRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      ++++.....+  |+-...|.- .-+|.+..-++-+.++++-..+.
T Consensus       172 dvYkrvL~dn--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q  214 (557)
T KOG3785|consen  172 DVYKRVLQDN--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ  214 (557)
T ss_pred             HHHHHHHhcC--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh
Confidence            8888877653  444444433 33556666677777777766665

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.71  E-value=3.8e-05  Score=57.12  Aligned_cols=188  Identities=13%  Similarity=0.088  Sum_probs=115.1

Q ss_pred             cCChhHHHHHHHHhHh---CC-CCCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHH
Q 040261           30 NKHYDTVLSLFKRLNS---IG-LFPDLY-TYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIM  104 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~---~~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  104 (343)
                      ..+.++.++++..+..   .| ..++.. .|..++-+....|+.+.|...++.+..+- +-+..+-..-.-.+-..|+++
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHhhchh
Confidence            3456777777777653   23 334544 35556666677778888888887776653 212222111112233357778


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHH
Q 040261          105 EAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKE  184 (343)
Q Consensus       105 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  184 (343)
                      +|+++|+.+.+.++ .|..++..-+...-..|+.-+|++-+....+.       +..|...|.-+...|...|++++|.-
T Consensus       104 ~A~e~y~~lL~ddp-t~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-------F~~D~EAW~eLaeiY~~~~~f~kA~f  175 (289)
T KOG3060|consen  104 EAIEYYESLLEDDP-TDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-------FMNDQEAWHELAEIYLSEGDFEKAAF  175 (289)
T ss_pred             hHHHHHHHHhccCc-chhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-------hcCcHHHHHHHHHHHHhHhHHHHHHH
Confidence            88888888877752 25556666666666677777777777777665       46677788888888888888888888


Q ss_pred             HHHHhhhCCCCCChhhHHHHHHHHhc---cCcHHHHHHHHHHHHHc
Q 040261          185 LFLKMKDENINPDVVTYTSLIRGFCY---ANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       185 ~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~  227 (343)
                      .++++.-.. |.++..+..+...+..   ..+.+.+.+++.+.++.
T Consensus       176 ClEE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  176 CLEELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            887776643 2234444444444333   23455666777666654

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

Probab=98.66  E-value=3.1e-06  Score=59.06  Aligned_cols=111  Identities=14%  Similarity=0.057  Sum_probs=91.4

Q ss_pred             HHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCC
Q 040261           39 LFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGC  118 (343)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  118 (343)
                      .+++..+.. +.+......+...+...|++++|.+.++.+...+ +.+...+..+..++...|++++|...+++..+.+.
T Consensus         5 ~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p   82 (135)
T TIGR02552         5 TLKDLLGLD-SEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDP   82 (135)
T ss_pred             hHHHHHcCC-hhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            455555533 2344567778888899999999999999998865 34778888899999999999999999999888753


Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261          119 KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       119 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      . +...+..+..++...|+++.|...++...+..
T Consensus        83 ~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  115 (135)
T TIGR02552        83 D-DPRPYFHAAECLLALGEPESALKALDLAIEIC  115 (135)
T ss_pred             C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            3 67778888899999999999999999998864

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=98.64  E-value=6.4e-05  Score=61.29  Aligned_cols=209  Identities=12%  Similarity=0.024  Sum_probs=137.7

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCC--CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIG--LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      +..=.-..++.++...-+.+...+  -.|+...+...+........-..+..++.+..+.  .-...-|. ..-.+...|
T Consensus       244 ~THPlp~~RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~--~~~aa~YG-~A~~~~~~~  320 (484)
T COG4783         244 LTHPLPEERIADLRNRAEQSPPYNKLDSPDFQLARARIRAKYEALPNQQAADLLAKRSKR--GGLAAQYG-RALQTYLAG  320 (484)
T ss_pred             hcCCCchhHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhccccccchHHHHHHHhCc--cchHHHHH-HHHHHHHhc
Confidence            333344456666666666665432  2355556666666554444434444443333221  11222333 334445678


Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHH
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDK  181 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  181 (343)
                      ++++|+..++.+...-+ -|...+......+...++.++|.+.++.+....       +........+..++.+.|++.+
T Consensus       321 ~~d~A~~~l~~L~~~~P-~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~-------P~~~~l~~~~a~all~~g~~~e  392 (484)
T COG4783         321 QYDEALKLLQPLIAAQP-DNPYYLELAGDILLEANKAKEAIERLKKALALD-------PNSPLLQLNLAQALLKGGKPQE  392 (484)
T ss_pred             ccchHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-------CCccHHHHHHHHHHHhcCChHH
Confidence            88999999988887633 255666677788888999999999999888864       2335667777888889999999


Q ss_pred             HHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          182 AKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       182 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      |+.+++...... +-|+..|..|.++|...|+..++..-..+..                  ...|++++|...+....+
T Consensus       393 ai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~------------------~~~G~~~~A~~~l~~A~~  453 (484)
T COG4783         393 AIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEGY------------------ALAGRLEQAIIFLMRASQ  453 (484)
T ss_pred             HHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHHH------------------HhCCCHHHHHHHHHHHHH
Confidence            999888877664 5578889999999988888888776665543                  235777777777777666


Q ss_pred             c
Q 040261          262 I  262 (343)
Q Consensus       262 ~  262 (343)
                      .
T Consensus       454 ~  454 (484)
T COG4783         454 Q  454 (484)
T ss_pred             h
Confidence            5

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

Probab=98.64  E-value=0.00011  Score=59.92  Aligned_cols=239  Identities=14%  Similarity=0.076  Sum_probs=155.7

Q ss_pred             HHHHHhcCC-hhHHHHHHHHhH---hCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC--CCccHHHHHHHHHHH
Q 040261           24 FGCLAKNKH-YDTVLSLFKRLN---SIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGL   97 (343)
Q Consensus        24 ~~~~~~~~~-~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~   97 (343)
                      +..+.+.|. .....+.|+++.   ..+-.|+....+.=+    -..++..+...-+.+...+  -.|+...+...+.+.
T Consensus       209 i~~L~raGydp~gM~~ff~rl~~~~~~~~~~p~yl~THPl----p~~RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~  284 (484)
T COG4783         209 ITTLVRAGYDPQGMPEFFERLADQLRYGGQPPEYLLTHPL----PEERIADLRNRAEQSPPYNKLDSPDFQLARARIRAK  284 (484)
T ss_pred             HHHHHHcCCCchhHHHHHHHHHHHHhcCCCCChHHhcCCC----chhHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHH
Confidence            445556663 455667777776   333344433211100    1112222333333333211  234555566666655


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      .....-..+..++.+..+.  . .....-.....+...|+++.|++.++.+....       |.|+.........+.+.+
T Consensus       285 ~~~~~~~~~~~~~~~~~~~--~-~~aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~-------P~N~~~~~~~~~i~~~~n  354 (484)
T COG4783         285 YEALPNQQAADLLAKRSKR--G-GLAAQYGRALQTYLAGQYDEALKLLQPLIAAQ-------PDNPYYLELAGDILLEAN  354 (484)
T ss_pred             hccccccchHHHHHHHhCc--c-chHHHHHHHHHHHHhcccchHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcC
Confidence            4443333343333333321  1 22233334445677899999999999998874       456666677778999999


Q ss_pred             ChHHHHHHHHHhhhCCCCCC-hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHH
Q 040261          178 FVDKAKELFLKMKDENINPD-VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  256 (343)
                      +.++|.+.++++....  |+ ....-.+..++.+.|++.+|..+++...... +-+...|..|.++|...|+..++....
T Consensus       355 k~~~A~e~~~kal~l~--P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~  431 (484)
T COG4783         355 KAKEAIERLKKALALD--PNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLAR  431 (484)
T ss_pred             ChHHHHHHHHHHHhcC--CCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHH
Confidence            9999999999998864  44 5666778899999999999999999998874 678899999999999999999999888


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          257 ELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       257 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+.....                  |+++.|...+....+.
T Consensus       432 AE~~~~~------------------G~~~~A~~~l~~A~~~  454 (484)
T COG4783         432 AEGYALA------------------GRLEQAIIFLMRASQQ  454 (484)
T ss_pred             HHHHHhC------------------CCHHHHHHHHHHHHHh
Confidence            7765542                  5666666666666554

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

Probab=98.58  E-value=0.0001  Score=65.48  Aligned_cols=83  Identities=16%  Similarity=0.139  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      ..|..+..+-.+.|...+|++-|-+.      -|+..|..+++...+.|.+++-.+++....+..        ..+..-+
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~--------~E~~id~ 1170 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKV--------REPYIDS 1170 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhh--------cCccchH
Confidence            34445555555555555554443221      134445555555555555555555554444432        1222334


Q ss_pred             HHHHHHHhcCChHHHHH
Q 040261          168 TITDGLCKEGFVDKAKE  184 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~  184 (343)
                      .++.+|++.++..+..+
T Consensus      1171 eLi~AyAkt~rl~elE~ 1187 (1666)
T KOG0985|consen 1171 ELIFAYAKTNRLTELEE 1187 (1666)
T ss_pred             HHHHHHHHhchHHHHHH
Confidence            44555555555444433

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.57  E-value=1.6e-05  Score=68.04  Aligned_cols=108  Identities=16%  Similarity=0.203  Sum_probs=59.6

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV  284 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  284 (343)
                      +.+......|.+|+.+++.++.+.  ....-|..+...|+..|+++.|.++|-+.         ..++..|..|.+.|+|
T Consensus       739 ieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccH
Confidence            344455566677777777666553  22334556666777777777777766543         1344456667777777


Q ss_pred             HHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHH
Q 040261          285 NRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       285 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      ..|.++-.+...  .......|..-..-.-++|++.+|.++
T Consensus       808 ~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeql  846 (1636)
T KOG3616|consen  808 EDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQL  846 (1636)
T ss_pred             HHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhhe
Confidence            777666555432  122334444444444444544444443

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

Probab=98.56  E-value=9.9e-06  Score=57.16  Aligned_cols=126  Identities=14%  Similarity=0.161  Sum_probs=84.1

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC--HHHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN---VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD--ASVYNTL  274 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l  274 (343)
                      .|..++..+ ..++...+...++.+.+.. +.+   ....-.+...+...|++++|...|+.+......|+  ......+
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            344455444 4677777877788777763 222   12233345667788888888888888887652222  2244456


Q ss_pred             HHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          275 MDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       275 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      ...+...|++++|...++.....  ......+....+.|.+.|++++|...|++.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            77788888888888888764433  344556677778888888888888888764

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

Probab=98.56  E-value=6.2e-06  Score=67.30  Aligned_cols=122  Identities=16%  Similarity=0.143  Sum_probs=68.3

Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCC
Q 040261          203 SLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTG  282 (343)
Q Consensus       203 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  282 (343)
                      .++..+...++++.|..+++++.+..  |+  ....+++.+...++..+|.+++++.++.. +-+...+......+.+.+
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcC
Confidence            33444445556666666666665542  33  22335555555555666666666655442 334555555555566666


Q ss_pred             chHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          283 RVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       283 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      +.+.|..+.+++.... +.+..+|..|..+|...|+++.|+..++.+.
T Consensus       249 ~~~lAL~iAk~av~ls-P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  249 KYELALEIAKKAVELS-PSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            6666666666666542 2234466666666666666666666665553

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

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

Probab=98.55  E-value=0.0001  Score=64.10  Aligned_cols=286  Identities=16%  Similarity=0.108  Sum_probs=141.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhC-C--------CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSI-G--------LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD   86 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~--------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~   86 (343)
                      +..+|..+...|.+..+.+-|.-.+-.|... |        -.|+ ..-..........|-+++|+.+|.+-.+.     
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~-----  829 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRY-----  829 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHH-----
Confidence            4456777777777776666665555444321 1        0111 12122222334567777777777766542     


Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCC-----------
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEF-----------  155 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------  155 (343)
                          ..|=..|...|.+++|.++-+.--+..+   ..||.....-+-..++.+.|++.|++......+.           
T Consensus       830 ----DLlNKlyQs~g~w~eA~eiAE~~DRiHL---r~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~  902 (1416)
T KOG3617|consen  830 ----DLLNKLYQSQGMWSEAFEIAETKDRIHL---RNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQI  902 (1416)
T ss_pred             ----HHHHHHHHhcccHHHHHHHHhhccceeh---hhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHH
Confidence                2233445566788888777655332222   2355555566666777887777776542211000           


Q ss_pred             --CccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH
Q 040261          156 --GVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV  233 (343)
Q Consensus       156 --~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  233 (343)
                        ......+...|.......-..|+.+.|+.++.....         |-.+++..+-.|+.++|-++-++-      -|.
T Consensus       903 e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~es------gd~  967 (1416)
T KOG3617|consen  903 EQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEES------GDK  967 (1416)
T ss_pred             HHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHhc------ccH
Confidence              000122445566666666677888888888776543         222333333344444443333221      122


Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHc----------CCC------------CCH-----------HHHHHHHHHHhc
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQI----------GVR------------PDA-----------SVYNTLMDGFCL  280 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----------~~~------------~~~-----------~~~~~l~~~~~~  280 (343)
                      .....+.+.|...|++.+|..+|.++...          +++            .|.           .-+...+..|-+
T Consensus       968 AAcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~g~~~~~AVmLYHk 1047 (1416)
T KOG3617|consen  968 AACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEELGGYAHKAVMLYHK 1047 (1416)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHcchhhhHHHHHHHh
Confidence            33333444444444444444444333210          000            000           011222334556


Q ss_pred             CCchHHHHHHHHH--------HHhC--CCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          281 TGRVNRAKELFVS--------MESN--GCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       281 ~~~~~~a~~~~~~--------~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      +|.+.+|+++--+        ++..  ....|+...+.-.+.+....++++|..++-..
T Consensus      1048 AGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~a 1106 (1416)
T KOG3617|consen 1048 AGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLA 1106 (1416)
T ss_pred             hcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            6666666654311        1111  22346667777777777777888877665433

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.53  E-value=3.3e-05  Score=68.20  Aligned_cols=165  Identities=12%  Similarity=0.020  Sum_probs=116.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC-CccHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF-TPDAVTFTSLI   94 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~   94 (343)
                      -...|..|...|....+...|...|+...+.+ ..+..........|++..+++.|..+.-..-+... ..-...|..+.
T Consensus       491 ~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG  569 (1238)
T KOG1127|consen  491 LAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRG  569 (1238)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhcc
Confidence            45678999999998889999999999988765 45667788888999999999999888433322211 11122334445


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc-chHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA-ITYSTITDGL  173 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~  173 (343)
                      -.|.+.++...|..-|+...+..+. |...|..++.+|.+.|.+..|.++|.+....+        |+. ..--......
T Consensus       570 ~yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr--------P~s~y~~fk~A~~e  640 (1238)
T KOG1127|consen  570 PYYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKASLLR--------PLSKYGRFKEAVME  640 (1238)
T ss_pred             ccccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhHhcC--------cHhHHHHHHHHHHH
Confidence            5567778888888888888776554 77788899999999999999999998887754        322 1111222334


Q ss_pred             HhcCChHHHHHHHHHhh
Q 040261          174 CKEGFVDKAKELFLKMK  190 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~  190 (343)
                      +..|.+.+|...+..+.
T Consensus       641 cd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  641 CDNGKYKEALDALGLII  657 (1238)
T ss_pred             HHhhhHHHHHHHHHHHH
Confidence            55677777777766543

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

Probab=98.53  E-value=5.4e-05  Score=65.74  Aligned_cols=230  Identities=16%  Similarity=0.133  Sum_probs=154.1

Q ss_pred             HHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc-C--------CCccHHHHHHHHHH
Q 040261           26 CLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS-C--------FTPDAVTFTSLIKG   96 (343)
Q Consensus        26 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~--------~~~~~~~~~~l~~~   96 (343)
                      .|...|+.+.|.+-.+.++      +..+|..+.++|.+..+++-|.-.+..|... |        ..++ ..=....-.
T Consensus       737 fyvtiG~MD~AfksI~~Ik------S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvL  809 (1416)
T KOG3617|consen  737 FYVTIGSMDAAFKSIQFIK------SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVL  809 (1416)
T ss_pred             EEEEeccHHHHHHHHHHHh------hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHH
Confidence            4556788888877776554      3568999999999999999888877777532 1        1222 222223334


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE  176 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  176 (343)
                      ....|..++|+.+|.+-.+.         ..|=+.|...|.+++|+++-+.-...        . -..+|......+...
T Consensus       810 AieLgMlEeA~~lYr~ckR~---------DLlNKlyQs~g~w~eA~eiAE~~DRi--------H-Lr~Tyy~yA~~Lear  871 (1416)
T KOG3617|consen  810 AIELGMLEEALILYRQCKRY---------DLLNKLYQSQGMWSEAFEIAETKDRI--------H-LRNTYYNYAKYLEAR  871 (1416)
T ss_pred             HHHHhhHHHHHHHHHHHHHH---------HHHHHHHHhcccHHHHHHHHhhccce--------e-hhhhHHHHHHHHHhh
Confidence            45679999999999987753         34556788899999999876643221        1 134666666777778


Q ss_pred             CChHHHHHHHHHhhh----------CC---------CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH
Q 040261          177 GFVDKAKELFLKMKD----------EN---------INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN  237 (343)
Q Consensus       177 ~~~~~a~~~~~~~~~----------~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  237 (343)
                      ++.+.|++.|++...          ..         -..|...|.-.....-..|+.+.|+.++.....         |-
T Consensus       872 ~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~f  942 (1416)
T KOG3617|consen  872 RDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YF  942 (1416)
T ss_pred             ccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hh
Confidence            888888888876321          11         012344455555555666777777776665443         33


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          238 VIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       238 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      .+++..+-.|+.++|.++-++      .-|....-.|.+.|-..|++.+|..+|.+..
T Consensus       943 s~VrI~C~qGk~~kAa~iA~e------sgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  943 SMVRIKCIQGKTDKAARIAEE------SGDKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             hheeeEeeccCchHHHHHHHh------cccHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            456666677888888777654      2355666678889999999999998887654

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

Probab=98.51  E-value=0.0007  Score=60.53  Aligned_cols=278  Identities=15%  Similarity=0.140  Sum_probs=146.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCC--CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGL--FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      .+++.......++...+-..+.+++++++.-.+.  ..+...-+.++-...+ -+..+..++.+++...+ .|+      
T Consensus       982 ~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyD-a~~------ 1053 (1666)
T KOG0985|consen  982 QDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYD-APD------ 1053 (1666)
T ss_pred             CChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHHHHhccCC-chh------
Confidence            5677777788888888888888888888764221  1122223333333333 23344444444443322 111      


Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhcC---------------------CCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAFG---------------------CKPDVFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~~---------------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      +...+...+-+++|..+|++..-.+                     ---.+..|..+..+-.+.|...+|.+-|-+    
T Consensus      1054 ia~iai~~~LyEEAF~ifkkf~~n~~A~~VLie~i~~ldRA~efAe~~n~p~vWsqlakAQL~~~~v~dAieSyik---- 1129 (1666)
T KOG0985|consen 1054 IAEIAIENQLYEEAFAIFKKFDMNVSAIQVLIENIGSLDRAYEFAERCNEPAVWSQLAKAQLQGGLVKDAIESYIK---- 1129 (1666)
T ss_pred             HHHHHhhhhHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHHHHHhhCChHHHHHHHHHHHhcCchHHHHHHHHh----
Confidence            1222333344455555554421100                     001344566666666666666666554432    


Q ss_pred             CCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC
Q 040261          152 NGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP  231 (343)
Q Consensus       152 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  231 (343)
                              ..|+..|..++....+.|.+++-.+.+....+..-.|..  =+.++-+|++.++..+.++++       .-|
T Consensus      1130 --------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~i--d~eLi~AyAkt~rl~elE~fi-------~gp 1192 (1666)
T KOG0985|consen 1130 --------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYI--DSELIFAYAKTNRLTELEEFI-------AGP 1192 (1666)
T ss_pred             --------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccc--hHHHHHHHHHhchHHHHHHHh-------cCC
Confidence                    124566777777777777777777777665555433332  345666777777666655544       134


Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHH------------------
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVS------------------  293 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~------------------  293 (343)
                      +......+..-|...+.++.|.-+|...         ..|..|...+...|++..|.+.-++                  
T Consensus      1193 N~A~i~~vGdrcf~~~~y~aAkl~y~~v---------SN~a~La~TLV~LgeyQ~AVD~aRKAns~ktWK~VcfaCvd~~ 1263 (1666)
T KOG0985|consen 1193 NVANIQQVGDRCFEEKMYEAAKLLYSNV---------SNFAKLASTLVYLGEYQGAVDAARKANSTKTWKEVCFACVDKE 1263 (1666)
T ss_pred             CchhHHHHhHHHhhhhhhHHHHHHHHHh---------hhHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHhchh
Confidence            5555555555555555555555544332         2333444444444444444333222                  


Q ss_pred             ------HHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          294 ------MESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       294 ------~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                            |....+.....-..-++.-|-..|-+++.+.+++..+
T Consensus      1264 EFrlAQiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1264 EFRLAQICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             hhhHHHhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh
Confidence                  2222222334445566777777777777777776554

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.50  E-value=3e-07  Score=47.03  Aligned_cols=34  Identities=50%  Similarity=0.961  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      +|+.++.+|++.|++++|.++|++|...|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            5778888888888888888888888888887763

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.

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

Probab=98.48  E-value=1.1e-05  Score=65.83  Aligned_cols=126  Identities=18%  Similarity=0.198  Sum_probs=104.1

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      .....++..+...++++.|..+|+++.+..  |+  ....+++.+...++..+|.+++++..+.. +-+...+..-...+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            344566777788899999999999998874  44  45567888888889999999999998763 44666777777889


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      .+.++++.|..+.+++.+.. +-+..+|..|..+|.+.|+++.|+..++.+.
T Consensus       245 l~k~~~~lAL~iAk~av~ls-P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELS-PSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            99999999999999999974 5556799999999999999999998887653

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

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

Probab=98.48  E-value=1.8e-05  Score=55.89  Aligned_cols=128  Identities=12%  Similarity=0.028  Sum_probs=96.9

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH--HHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD---LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA--VTFT   91 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~   91 (343)
                      ...|..++..+ ..++...+...++.+.... +.+   ....-.+...+...|++++|...|+.+......++.  ....
T Consensus        12 ~~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l   89 (145)
T PF09976_consen   12 SALYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARL   89 (145)
T ss_pred             HHHHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHH
Confidence            34566677766 4889999999999988754 223   233444667788999999999999999987633332  2445


Q ss_pred             HHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261           92 SLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEM  148 (343)
Q Consensus        92 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  148 (343)
                      .+...+...|++++|+..++.....  ......+.....++.+.|+.++|...|+..
T Consensus        90 ~LA~~~~~~~~~d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   90 RLARILLQQGQYDEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            5778889999999999999775443  234556778889999999999999999864

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.45  E-value=4.8e-07  Score=45.89  Aligned_cols=33  Identities=30%  Similarity=0.659  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCC
Q 040261          304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRP  336 (343)
Q Consensus       304 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  336 (343)
                      .+|+.++.+|.+.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            467777777777777777777777777777776

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

Probab=98.45  E-value=0.00091  Score=58.85  Aligned_cols=224  Identities=13%  Similarity=0.128  Sum_probs=152.5

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHH--HHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHH
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINC--FCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIM  104 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  104 (343)
                      ....+++..|+.-..++.+..  |+. .|...+.+  +.+.|+.++|..+++.....+.. |..+...+-.+|.+.++.+
T Consensus        19 ~ld~~qfkkal~~~~kllkk~--Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d   94 (932)
T KOG2053|consen   19 LLDSSQFKKALAKLGKLLKKH--PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLD   94 (932)
T ss_pred             HhhhHHHHHHHHHHHHHHHHC--CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhh
Confidence            346788899999998877643  444 23333333  56889999999888887766544 7888888999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC------
Q 040261          105 EAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF------  178 (343)
Q Consensus       105 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~------  178 (343)
                      +|..+|++....  .|+......+..+|.+.+++.+-.+.--++-+.       .+.+...+-++++.+...-.      
T Consensus        95 ~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-------~pk~~yyfWsV~Slilqs~~~~~~~~  165 (932)
T KOG2053|consen   95 EAVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-------FPKRAYYFWSVISLILQSIFSENELL  165 (932)
T ss_pred             HHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------CCcccchHHHHHHHHHHhccCCcccc
Confidence            999999998876  567777788888999988887665555555443       34556666666666553211      


Q ss_pred             ----hHHHHHHHHHhhhCCCCC-ChhhHHHHHHHHhccCcHHHHHHHHH-HHHHcCCCCCHHHHHHHHHHHHhCCChhHH
Q 040261          179 ----VDKAKELFLKMKDENINP-DVVTYTSLIRGFCYANDWNEAKCLFI-EMMDQGVQPNVVTFNVIMNELCKNGKMDEA  252 (343)
Q Consensus       179 ----~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  252 (343)
                          ..-|.+.++.+.+.+.+. +..-...-...+...|.+++|.+++. ...+.-...+...-+.-+..+...+++.+.
T Consensus       166 ~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l  245 (932)
T KOG2053|consen  166 DPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQEL  245 (932)
T ss_pred             cchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHH
Confidence                234556666665543111 11112222334456788999999984 344433333444555667778888999999


Q ss_pred             HHHHHHHHHcC
Q 040261          253 SRLLELMIQIG  263 (343)
Q Consensus       253 ~~~~~~~~~~~  263 (343)
                      .++-.++...|
T Consensus       246 ~~l~~~Ll~k~  256 (932)
T KOG2053|consen  246 FELSSRLLEKG  256 (932)
T ss_pred             HHHHHHHHHhC
Confidence            99998888876

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

Probab=98.45  E-value=0.00069  Score=59.56  Aligned_cols=223  Identities=17%  Similarity=0.165  Sum_probs=151.6

Q ss_pred             HhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH--HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHH
Q 040261           63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG--LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIV  140 (343)
Q Consensus        63 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  140 (343)
                      ...+++.+|.+-.+++.+.  .|+.. |...+.+  ..+.|+.++|..+++.....+.. |..|...+-.+|.+.++.++
T Consensus        20 ld~~qfkkal~~~~kllkk--~Pn~~-~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKK--HPNAL-YAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHH--CCCcH-HHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhH
Confidence            4567889999999998876  34443 3344444  45789999999999988877666 88899999999999999999


Q ss_pred             HHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc-------
Q 040261          141 ALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND-------  213 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------  213 (343)
                      |..+|++.....        |+......+..+|.+.+++.+-.++--++-+. .+-+...+-.+++...+.-.       
T Consensus        96 ~~~~Ye~~~~~~--------P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~  166 (932)
T KOG2053|consen   96 AVHLYERANQKY--------PSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLD  166 (932)
T ss_pred             HHHHHHHHHhhC--------CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCccccc
Confidence            999999999865        55777777778888888776544443333332 23345555555554433211       


Q ss_pred             ---HHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhCCChhHHHHHH-HHHHHcCCCCCHHHHHHHHHHHhcCCchHHHH
Q 040261          214 ---WNEAKCLFIEMMDQG-VQPNVVTFNVIMNELCKNGKMDEASRLL-ELMIQIGVRPDASVYNTLMDGFCLTGRVNRAK  288 (343)
Q Consensus       214 ---~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  288 (343)
                         ..-|.+.++.+.+.+ -.-+..-.-.-...+...|++++|..++ ....+.-.+-+...-+.-+..+...+++.+..
T Consensus       167 ~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~  246 (932)
T KOG2053|consen  167 PILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELF  246 (932)
T ss_pred             chhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHH
Confidence               223555666666553 1112222222334456788899999998 44444433445555566777888889999999


Q ss_pred             HHHHHHHhCC
Q 040261          289 ELFVSMESNG  298 (343)
Q Consensus       289 ~~~~~~~~~~  298 (343)
                      ++..++...|
T Consensus       247 ~l~~~Ll~k~  256 (932)
T KOG2053|consen  247 ELSSRLLEKG  256 (932)
T ss_pred             HHHHHHHHhC
Confidence            9999888876

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.44  E-value=9.4e-05  Score=63.60  Aligned_cols=109  Identities=20%  Similarity=0.308  Sum_probs=70.1

Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHH
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGF  208 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  208 (343)
                      +.+....+++.+|+.+++.+....        ....-|..+...|...|+++.|.++|-+.-         .++-.+..|
T Consensus       739 ieaai~akew~kai~ildniqdqk--------~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my  801 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQK--------TASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMY  801 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhc--------cccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHH
Confidence            344455667777777777776643        334566777788888888888888875432         255567788


Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHH
Q 040261          209 CYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  256 (343)
                      .+.|+|+.|.++-.+...  .......|-.-..-.-+.|++.+|.+++
T Consensus       802 ~k~~kw~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  802 GKAGKWEDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             hccccHHHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            888888888887665532  2333444544444555566666665554

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

Probab=98.41  E-value=1.2e-05  Score=65.94  Aligned_cols=123  Identities=17%  Similarity=0.188  Sum_probs=79.1

Q ss_pred             CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHH
Q 040261          194 INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ--GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVY  271 (343)
Q Consensus       194 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  271 (343)
                      .+.+......++..+....+.+.+..++.+....  ....-..|..++++.|.+.|..+.++.+++.=...|+-||..++
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            3445566666666666666677777776666654  12122334456777777777777777777777777777777777


Q ss_pred             HHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhc
Q 040261          272 NTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKN  316 (343)
Q Consensus       272 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  316 (343)
                      +.|+..+.+.|++..|.++...|..++...++.++..-+.+|.+-
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            777777777777777777777766665555555555555555443

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 [].

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

Probab=98.38  E-value=3.9e-05  Score=63.11  Aligned_cols=121  Identities=15%  Similarity=0.093  Sum_probs=67.9

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCCh
Q 040261          119 KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV  198 (343)
Q Consensus       119 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  198 (343)
                      +.+......+++.+....+.+.+..++.++......    ...-..+..++++.|.+.|..+.++.+++.=...|+-||.
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~----~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~  138 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNC----SYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDN  138 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCccc----ccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCCh
Confidence            334555555566666666666666666665554321    1122334456666666666666666666666666666666


Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      .+++.++..+.+.|++..|.++...|..++...+..++...+.+|
T Consensus       139 ~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~  183 (429)
T PF10037_consen  139 FSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSC  183 (429)
T ss_pred             hhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHH
Confidence            666666666666666666666666665554444444444333333

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 [].

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.38  E-value=3.1e-05  Score=56.47  Aligned_cols=96  Identities=7%  Similarity=0.027  Sum_probs=66.9

Q ss_pred             HHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC--HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261            6 YMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD--LYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus         6 ~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      .+....+.+.....+..+...+...|++++|...|++..+.+..+.  ...+..+..++.+.|++++|...+.+..+...
T Consensus        24 ~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p  103 (172)
T PRK02603         24 KILPINKKAKEAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP  103 (172)
T ss_pred             HHcccccHhhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc
Confidence            3333334444566778888888888999999999988876432222  35777788888888999999988888887542


Q ss_pred             CccHHHHHHHHHHHhhcCc
Q 040261           84 TPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~  102 (343)
                      . +...+..+...+...|+
T Consensus       104 ~-~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603        104 K-QPSALNNIAVIYHKRGE  121 (172)
T ss_pred             c-cHHHHHHHHHHHHHcCC
Confidence            2 45566666667766665

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.36  E-value=9.2e-07  Score=44.81  Aligned_cols=33  Identities=30%  Similarity=0.505  Sum_probs=23.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP   50 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~   50 (343)
                      .+|+.++.+|++.|+++.|.++|+.|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            467777777777777777777777777777665

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.36  E-value=8.2e-07  Score=45.36  Aligned_cols=33  Identities=33%  Similarity=0.562  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD   51 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~   51 (343)
                      +|+.++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            688888888888888888888888888888876

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

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

Probab=98.33  E-value=1.1e-05  Score=51.91  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=50.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCC-CCCHHHHHHHHHHHHhcCC--------cchHHHHHHHHHHcCCCccHHHHHH
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGL-FPDLYTYNILINCFCKMGR--------VSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~--------~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      ..|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..-        .-..+.+|+.|+..++.|+..+|+.
T Consensus        30 ~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYni  109 (120)
T PF08579_consen   30 DNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNI  109 (120)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHH
Confidence            345566666888888888888888887 7788888888877665422        2234555555655556666666665


Q ss_pred             HHHHHh
Q 040261           93 LIKGLC   98 (343)
Q Consensus        93 l~~~~~   98 (343)
                      ++..+.
T Consensus       110 vl~~Ll  115 (120)
T PF08579_consen  110 VLGSLL  115 (120)
T ss_pred             HHHHHH
Confidence            555543

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 [, , ].

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

Probab=98.29  E-value=2.7e-05  Score=50.33  Aligned_cols=94  Identities=23%  Similarity=0.235  Sum_probs=59.3

Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK  315 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  315 (343)
                      +..+...+...|++++|...++.+.+.. +.+...+..+...+...+++++|.+.++...... +.+...+..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHH
Confidence            3345555666677777777777666553 3334556666666666777777777777666543 2334566666667777


Q ss_pred             cCChHHHHHHHHHHHh
Q 040261          316 NKEIEGALSLYSEMLS  331 (343)
Q Consensus       316 ~~~~~~a~~~~~~~~~  331 (343)
                      .|+++.|...+.+...
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            7777777777766654

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

Probab=98.28  E-value=2.7e-05  Score=50.30  Aligned_cols=96  Identities=16%  Similarity=0.150  Sum_probs=64.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      ++..+...+...|++++|...++...+.. +.+...+..+..++...+++++|.+.++....... .+..++..+...+.
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~   79 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHH
Confidence            35566667777788888888887776643 23345666667777777777777777777766542 24456666667777


Q ss_pred             hcCcHHHHHHHHHHHHhc
Q 040261           99 AESRIMEAAALFTKLRAF  116 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~  116 (343)
                      ..|+++.|...+....+.
T Consensus        80 ~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          80 KLGKYEEALEAYEKALEL   97 (100)
T ss_pred             HHHhHHHHHHHHHHHHcc
Confidence            777777777777766543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.28  E-value=6.2e-05  Score=51.10  Aligned_cols=101  Identities=9%  Similarity=-0.058  Sum_probs=77.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCC--CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--ccHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLF--PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PDAVTFTSL   93 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l   93 (343)
                      .++..++..+.+.|++++|...|+.+......  .....+..+..++.+.|+++.|...++.+......  .....+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            46777888888999999999999998764311  11346677888899999999999999998875322  124567777


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCC
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGC  118 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~  118 (343)
                      ..++.+.|+.++|.+.++++.+..+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~~p  107 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKRYP  107 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHCc
Confidence            7888888999999999999888743

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

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

Probab=98.26  E-value=6.5e-05  Score=59.32  Aligned_cols=130  Identities=12%  Similarity=0.159  Sum_probs=72.7

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc-cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          165 TYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY-ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       165 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      +|..++....+.+..+.|..+|.+..+.+ ..+...|......-.. .++.+.|..+|+...+. +..+...|...+..+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            45666666666666677777776666432 2233444444443222 45555567777666665 344555566666666


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCC---HHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPD---ASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...++.+.|..+|++.+.. +.++   ...|...+..=.+.|+.+.+.++.+++.+.
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6666677777777666654 2222   236666666666666666666666666653

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.

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.24  E-value=0.0011  Score=59.13  Aligned_cols=182  Identities=13%  Similarity=0.084  Sum_probs=117.4

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  182 (343)
                      ...++..|-+..+..+. -...|..|...|....+...|.+.|++..+.+       +.+..........|.+..+++.|
T Consensus       474 ~~~al~ali~alrld~~-~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-------atdaeaaaa~adtyae~~~we~a  545 (1238)
T KOG1127|consen  474 SALALHALIRALRLDVS-LAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-------ATDAEAAAASADTYAEESTWEEA  545 (1238)
T ss_pred             HHHHHHHHHHHHhcccc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-------chhhhhHHHHHHHhhccccHHHH
Confidence            55566665555544222 23467777888877778888888888887765       45667777788888888888888


Q ss_pred             HHHHHHhhhCC-CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          183 KELFLKMKDEN-INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       183 ~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      ..+.-...+.. ...-..-|....-.|...++...+..-|+...+.. +.|...|..++.+|...|++..|.++|.++..
T Consensus       546 ~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~  624 (1238)
T KOG1127|consen  546 FEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASL  624 (1238)
T ss_pred             HHHHHHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHh
Confidence            87743322211 00111223334445677778888888888877764 45677888888888888888888888888776


Q ss_pred             cCCCCCHHHHHHHH--HHHhcCCchHHHHHHHHHHHh
Q 040261          262 IGVRPDASVYNTLM--DGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       262 ~~~~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      .  .|+. .|...-  -.-+..|.+.+|+..+.....
T Consensus       625 L--rP~s-~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  625 L--RPLS-KYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             c--CcHh-HHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            5  3332 222222  233556778888777776553

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.22  E-value=7.4e-05  Score=50.71  Aligned_cols=94  Identities=11%  Similarity=0.053  Sum_probs=40.4

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCC--ccHHHHHHHHHHHH
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVR--PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM--RDVFSYGILINGYC  314 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~  314 (343)
                      ++..+.+.|++++|...++.+.+....  .....+..+..++.+.|+++.|...++.+......  .....+..+..++.
T Consensus         8 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~   87 (119)
T TIGR02795         8 AALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQ   87 (119)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHH
Confidence            344444445555555555444443100  01223333444455555555555555544432100  01233444444445


Q ss_pred             hcCChHHHHHHHHHHHhC
Q 040261          315 KNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       315 ~~~~~~~a~~~~~~~~~~  332 (343)
                      +.|++++|.+.++++...
T Consensus        88 ~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        88 ELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HhCChHHHHHHHHHHHHH
Confidence            555555555555555443

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.

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

Probab=98.18  E-value=8.1e-06  Score=51.46  Aligned_cols=81  Identities=16%  Similarity=0.199  Sum_probs=51.1

Q ss_pred             CCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVR-PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                      .|+++.|+.+++++.+.... ++...+..+..+|.+.|++++|..++++ .+.+ +.+......+..+|.+.|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~-~~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD-PSNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH-HCHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC-CCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            46777788888877776421 2344555577778888888888888877 2221 1233444455777788888888887


Q ss_pred             HHHH
Q 040261          325 LYSE  328 (343)
Q Consensus       325 ~~~~  328 (343)
                      ++++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            7765

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.18  E-value=0.00072  Score=52.12  Aligned_cols=184  Identities=11%  Similarity=0.097  Sum_probs=105.7

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH---HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT---FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      +...+-.....+...|++++|.+.|+.+....+.. ...   .-.++.++.+.+++++|...+++..+..+......+..
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~  109 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVL  109 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHH
Confidence            33333344455567889999999999988764332 222   23466778888999999999988887744333333333


Q ss_pred             HHHHHHh--c---------------CC---hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHH
Q 040261          128 LINGLCR--T---------------GH---TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFL  187 (343)
Q Consensus       128 l~~~~~~--~---------------~~---~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  187 (343)
                      .+.+.+.  .               .+   ...|+..|+.+.+..        |++             .-..+|...+.
T Consensus       110 Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~y--------P~S-------------~ya~~A~~rl~  168 (243)
T PRK10866        110 YMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGY--------PNS-------------QYTTDATKRLV  168 (243)
T ss_pred             HHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHC--------cCC-------------hhHHHHHHHHH
Confidence            3333321  1               11   235666677776654        222             12233333333


Q ss_pred             HhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          188 KMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ--GVQPNVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       188 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      .+...   . ...--.+...|.+.|.+..|..-++.+++.  +.+........+..+|...|..++|..+...+.
T Consensus       169 ~l~~~---l-a~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        169 FLKDR---L-AKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHH---H-HHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            33221   0 011113455677777777777777777765  222334555667777878888888777766553

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

Probab=98.16  E-value=0.0001  Score=60.46  Aligned_cols=95  Identities=8%  Similarity=-0.015  Sum_probs=82.0

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc
Q 040261           21 NILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE  100 (343)
Q Consensus        21 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  100 (343)
                      ......+...|++++|++.|+++++.. +.+...|..+..++...|++++|+..+++++.... .+...|..+..++...
T Consensus         6 ~~~a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~~a~~~lg~~~~~l   83 (356)
T PLN03088          6 EDKAKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDP-SLAKAYLRKGTACMKL   83 (356)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHh
Confidence            344667778999999999999999865 45677888899999999999999999999998753 3677888899999999


Q ss_pred             CcHHHHHHHHHHHHhcC
Q 040261          101 SRIMEAAALFTKLRAFG  117 (343)
Q Consensus       101 ~~~~~a~~~~~~~~~~~  117 (343)
                      |++++|...|++..+.+
T Consensus        84 g~~~eA~~~~~~al~l~  100 (356)
T PLN03088         84 EEYQTAKAALEKGASLA  100 (356)
T ss_pred             CCHHHHHHHHHHHHHhC
Confidence            99999999999999874

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.16  E-value=6.4e-05  Score=52.30  Aligned_cols=98  Identities=6%  Similarity=-0.128  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040261           53 YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGL  132 (343)
Q Consensus        53 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  132 (343)
                      ...-.+...+...|++++|..+|+.+....+. +...|..|..++-..|++++|+..|......++. ++..+-.+..++
T Consensus        36 ~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d-dp~~~~~ag~c~  113 (157)
T PRK15363         36 NTLYRYAMQLMEVKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID-APQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHH
Confidence            34444555566777777777777777665422 5566666777777777777777777777776643 666677777777


Q ss_pred             HhcCChHHHHHHHHHHHccC
Q 040261          133 CRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ...|+.+.|.+.|+......
T Consensus       114 L~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHHh
Confidence            77777777777777776664

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

Probab=98.15  E-value=8.7e-06  Score=51.32  Aligned_cols=79  Identities=15%  Similarity=0.252  Sum_probs=30.7

Q ss_pred             CChhHHHHHHHHhHhCCCC-CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHH
Q 040261           31 KHYDTVLSLFKRLNSIGLF-PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAAL  109 (343)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  109 (343)
                      |+++.|+.+++++.+.... ++...+..+..++.+.|++++|..+++. .+.+. .+......+..++.+.|++++|+++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            4445555555554443210 1222333344444455555555544444 11111 1122222334444444555554444


Q ss_pred             HH
Q 040261          110 FT  111 (343)
Q Consensus       110 ~~  111 (343)
                      ++
T Consensus        81 l~   82 (84)
T PF12895_consen   81 LE   82 (84)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

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

Probab=98.14  E-value=2.4e-05  Score=59.74  Aligned_cols=102  Identities=19%  Similarity=0.183  Sum_probs=81.4

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchH
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVN  285 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  285 (343)
                      .-+.+.+++.+|+..|.+.++.. +-|.+.|..-..+|.+.|.++.|++-.+..+..+ +-...+|..|..+|...|+++
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHccCcHH
Confidence            34567889999999999998873 4467777778889999999999999998888865 445678999999999999999


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHH
Q 040261          286 RAKELFVSMESNGCMRDVFSYGILIN  311 (343)
Q Consensus       286 ~a~~~~~~~~~~~~~~~~~~~~~l~~  311 (343)
                      +|.+.|++..+.  .|+-.+|-.=+.
T Consensus       167 ~A~~aykKaLel--dP~Ne~~K~nL~  190 (304)
T KOG0553|consen  167 EAIEAYKKALEL--DPDNESYKSNLK  190 (304)
T ss_pred             HHHHHHHhhhcc--CCCcHHHHHHHH
Confidence            999999988875  576666554443

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

Probab=98.11  E-value=0.00018  Score=58.93  Aligned_cols=86  Identities=17%  Similarity=0.091  Sum_probs=41.7

Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHH
Q 040261          209 CYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAK  288 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  288 (343)
                      ...|++++|+..++++++.. +-+...|..+..++...|++++|+..++++++.. +.+...|..+..+|...|++++|.
T Consensus        13 ~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA~   90 (356)
T PLN03088         13 FVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTAK   90 (356)
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHHH
Confidence            34445555555555554442 2233444444445555555555555555555443 233444444555555555555555


Q ss_pred             HHHHHHHh
Q 040261          289 ELFVSMES  296 (343)
Q Consensus       289 ~~~~~~~~  296 (343)
                      ..|++..+
T Consensus        91 ~~~~~al~   98 (356)
T PLN03088         91 AALEKGAS   98 (356)
T ss_pred             HHHHHHHH
Confidence            55555544

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.11  E-value=0.0002  Score=49.91  Aligned_cols=97  Identities=10%  Similarity=-0.078  Sum_probs=70.3

Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGF  278 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  278 (343)
                      ...-.+..-+...|++++|..+|+.+...+ +-+..-|..|..++-..|++++|+..|..+...+ +-++..+-.+..++
T Consensus        36 ~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~  113 (157)
T PRK15363         36 NTLYRYAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHH
Confidence            344445555667788888888888877764 3345556667777777888888888888887776 45667777777788


Q ss_pred             hcCCchHHHHHHHHHHHhC
Q 040261          279 CLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...|+.+.|.+.|+.....
T Consensus       114 L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            8888888888888776654

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

Probab=98.11  E-value=4.4e-06  Score=41.18  Aligned_cols=29  Identities=45%  Similarity=0.888  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      +|+.++++|.+.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            56666666666666666666666666655

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

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

Probab=98.10  E-value=0.0001  Score=47.66  Aligned_cols=71  Identities=14%  Similarity=0.285  Sum_probs=35.5

Q ss_pred             HhCCChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHhcCC--------chHHHHHHHHHHHhCCCCccHHHHHHHHHHHH
Q 040261          244 CKNGKMDEASRLLELMIQIGV-RPDASVYNTLMDGFCLTG--------RVNRAKELFVSMESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  314 (343)
                      ...+++...-.+|+.+.+.|+ .|+..+|+.++.+.++..        ++-..+.+++.|...+++|+..+|+.++..+.
T Consensus        36 ~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Ll  115 (120)
T PF08579_consen   36 FENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLL  115 (120)
T ss_pred             HhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHH
Confidence            333555555555555555554 445555555554444321        22334455555555555566666655555544

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 [, , ].

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.10  E-value=0.00045  Score=50.37  Aligned_cols=82  Identities=16%  Similarity=0.133  Sum_probs=38.5

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGF  278 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  278 (343)
                      +..+...+...|++++|...+++..+....+.  ...+..+...+.+.|++++|...+++..+.. +.+...+..+...+
T Consensus        38 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~  116 (172)
T PRK02603         38 YYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIAVIY  116 (172)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            44444444555555555555555544321111  2344455555555555555555555555542 22333444444444


Q ss_pred             hcCCc
Q 040261          279 CLTGR  283 (343)
Q Consensus       279 ~~~~~  283 (343)
                      ...|+
T Consensus       117 ~~~g~  121 (172)
T PRK02603        117 HKRGE  121 (172)
T ss_pred             HHcCC
Confidence            44443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=98.09  E-value=0.00049  Score=59.09  Aligned_cols=143  Identities=15%  Similarity=0.150  Sum_probs=100.2

Q ss_pred             CCCCChhhHHHHHHHHhcc-----CcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCC--------ChhHHHHHHHH
Q 040261          193 NINPDVVTYTSLIRGFCYA-----NDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNG--------KMDEASRLLEL  258 (343)
Q Consensus       193 ~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~--------~~~~a~~~~~~  258 (343)
                      ..+.+...|...+++....     ++...|..+|++..+.  .|+ ...+..+..++....        +...+.+..++
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            3456778888888775432     3477899999999987  455 455555544443221        12333444444


Q ss_pred             HHHc-CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCC
Q 040261          259 MIQI-GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPT  337 (343)
Q Consensus       259 ~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  337 (343)
                      .... ..+.+...+..+.-.....|++++|...+++....+  |+...|..+...+...|++++|...+++....  .|.
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P~  485 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RPG  485 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCC
Confidence            3332 124456778777777777899999999999999975  68889999999999999999999999999855  455


Q ss_pred             cccc
Q 040261          338 VVTY  341 (343)
Q Consensus       338 ~~t~  341 (343)
                      ..||
T Consensus       486 ~pt~  489 (517)
T PRK10153        486 ENTL  489 (517)
T ss_pred             CchH
Confidence            4443

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

Probab=98.06  E-value=0.00031  Score=55.52  Aligned_cols=130  Identities=13%  Similarity=0.076  Sum_probs=57.3

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh-cCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR-TGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      +|..+++..-+.+..+.|..+|.+.++.+ ..+...|......-.+ .++.+.|.++|+...+.       .+.+...|.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-------f~~~~~~~~   74 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-------FPSDPDFWL   74 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-------HTT-HHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-------CCCCHHHHH
Confidence            34444455555555555555555554332 1123333333333222 33444455555555544       233444455


Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPD---VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      ..+..+.+.++.+.|..+|++.... ++++   ...|...+..-.+.|+.+.+..+.+++.+.
T Consensus        75 ~Y~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   75 EYLDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            5555555555555555555554443 1111   124555555555555555555555555443

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

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

Probab=98.06  E-value=0.0013  Score=52.18  Aligned_cols=25  Identities=12%  Similarity=0.147  Sum_probs=11.1

Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHH
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMD  226 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~  226 (343)
                      ..+...+.+.|++++|..+|+++..
T Consensus       159 ~~~A~l~~~l~~y~~A~~~~e~~~~  183 (282)
T PF14938_consen  159 LKAADLYARLGRYEEAIEIYEEVAK  183 (282)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            3334444444455555555544443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=98.05  E-value=0.00019  Score=52.11  Aligned_cols=94  Identities=16%  Similarity=0.044  Sum_probs=62.8

Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP--NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM  275 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  275 (343)
                      ...+..+...+...|++++|...++........+  ...++..+...+...|++++|...+++..+.. +.....+..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            4556666777777888888888888887653222  23467777888888888888888888887753 33345555555


Q ss_pred             HHHh-------cCCchHHHHHHHH
Q 040261          276 DGFC-------LTGRVNRAKELFV  292 (343)
Q Consensus       276 ~~~~-------~~~~~~~a~~~~~  292 (343)
                      ..+.       ..|+++.|...++
T Consensus       114 ~i~~~~~~~~~~~g~~~~A~~~~~  137 (168)
T CHL00033        114 VICHYRGEQAIEQGDSEIAEAWFD  137 (168)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHH
Confidence            5555       6666665544444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.05  E-value=0.0031  Score=48.70  Aligned_cols=60  Identities=10%  Similarity=0.015  Sum_probs=40.5

Q ss_pred             HHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHH---HHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           92 SLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTY---TTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        92 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      .....+.+.|++++|.+.|+.+....+.+ ....   -.++.++.+.++++.|...+++..+..
T Consensus        37 ~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~   99 (243)
T PRK10866         37 ATAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN   99 (243)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            34444556788888888888887764332 2222   345667778888888888888887765

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.03  E-value=0.0031  Score=50.80  Aligned_cols=266  Identities=14%  Similarity=0.018  Sum_probs=140.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      .......+.+..++.+|+..+...++.. +.+..-|..-+..+...|+++.|.--.+.-.+.... ......-.-+++..
T Consensus        52 ~k~~gn~~yk~k~Y~nal~~yt~Ai~~~-pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~-~~k~~~r~~~c~~a  129 (486)
T KOG0550|consen   52 AKEEGNAFYKQKTYGNALKNYTFAIDMC-PDNASYYSNRAATLMMLGRFEEALGDARQSVRLKDG-FSKGQLREGQCHLA  129 (486)
T ss_pred             HHhhcchHHHHhhHHHHHHHHHHHHHhC-ccchhhhchhHHHHHHHHhHhhcccchhhheecCCC-ccccccchhhhhhh
Confidence            3334555666677788888888777755 233445555555566666666665444443332100 01111112222222


Q ss_pred             cCcHHHHHHHH---------------HHHHhcCC-CCCHHHHHHH-HHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261          100 ESRIMEAAALF---------------TKLRAFGC-KPDVFTYTTL-INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus       100 ~~~~~~a~~~~---------------~~~~~~~~-~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      .++..+|.+.+               +.+..... +|....+..+ ..++.-.|++++|.+.--...+.+       ..+
T Consensus       130 ~~~~i~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld-------~~n  202 (486)
T KOG0550|consen  130 LSDLIEAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD-------ATN  202 (486)
T ss_pred             hHHHHHHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc-------cch
Confidence            22222222222               22221111 1222333322 345566778888877776666654       122


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHH-------------HHHHHhccCcHHHHHHHHHHHHHc--
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTS-------------LIRGFCYANDWNEAKCLFIEMMDQ--  227 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------------l~~~~~~~~~~~~a~~~~~~~~~~--  227 (343)
                      ....-.-..++.-.++.+.+...|.+....+  |+...-..             -..-..+.|.+..|.+.+.+.+..  
T Consensus       203 ~~al~vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP  280 (486)
T KOG0550|consen  203 AEALYVRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDP  280 (486)
T ss_pred             hHHHHhcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCc
Confidence            2222222233445677788888887776643  33322111             122345678888888888887764  


Q ss_pred             -CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          228 -GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       228 -~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                       +..|+...|.....+..+.|+.++|+.--++....+ +.-...+..-..++...++|++|++-++...+.
T Consensus       281 ~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD-~syikall~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  281 SNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKID-SSYIKALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             cccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence             234556667667777778888888888777776543 111222333334555667788888888776654

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

Probab=98.02  E-value=0.00062  Score=54.04  Aligned_cols=198  Identities=12%  Similarity=0.089  Sum_probs=107.9

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHc----CCC-ccHHHHHHHHHHHhhcCcHHHHHHHHHHHHh----cCCCCC--H
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRS----CFT-PDAVTFTSLIKGLCAESRIMEAAALFTKLRA----FGCKPD--V  122 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~--~  122 (343)
                      .|......|...|++++|.+.|.+....    +-. .-...|.....++.+ .++++|.+.+++..+    .| .++  .
T Consensus        37 ~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~-~~~~~Ai~~~~~A~~~y~~~G-~~~~aA  114 (282)
T PF14938_consen   37 LYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKK-GDPDEAIECYEKAIEIYREAG-RFSQAA  114 (282)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHCT--HHHHH
T ss_pred             HHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh-hCHHHHHHHHHHHHHHHHhcC-cHHHHH
Confidence            3455555566666666666666655431    101 112233334444433 366777766666543    22 112  2


Q ss_pred             HHHHHHHHHHHhc-CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-----C
Q 040261          123 FTYTTLINGLCRT-GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENIN-----P  196 (343)
Q Consensus       123 ~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~  196 (343)
                      ..+..+...|... |+++.|.+.|++........+. ...-..++..+...+.+.|++++|.++|+++......     .
T Consensus       115 ~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~-~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~  193 (282)
T PF14938_consen  115 KCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGS-PHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKY  193 (282)
T ss_dssp             HHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccch
Confidence            3456667778777 8999999999887664311000 1112345677888999999999999999998664322     1


Q ss_pred             Chh-hHHHHHHHHhccCcHHHHHHHHHHHHHcC--CCCC--HHHHHHHHHHHHhCCChhHHHHH
Q 040261          197 DVV-TYTSLIRGFCYANDWNEAKCLFIEMMDQG--VQPN--VVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       197 ~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~--~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      +.. .+-..+-++...|++..|...+++.....  +..+  ......|+.++ +.||.+.....
T Consensus       194 ~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~-~~~D~e~f~~a  256 (282)
T PF14938_consen  194 SAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAY-EEGDVEAFTEA  256 (282)
T ss_dssp             HHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHH-HTT-CCCHHHH
T ss_pred             hHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH-HhCCHHHHHHH
Confidence            121 22333446677788889988888887652  2222  23344455554 34454443333

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=98.01  E-value=0.00021  Score=51.88  Aligned_cols=65  Identities=9%  Similarity=0.013  Sum_probs=30.9

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP--DLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ...|..+...+...|++++|...|++.......+  ...++..+..++...|++++|...+++..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3344445555555555555555555554322111  1124444555555555555555555555443

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

Probab=98.01  E-value=0.0061  Score=50.95  Aligned_cols=176  Identities=11%  Similarity=0.111  Sum_probs=128.8

Q ss_pred             hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCC-ChhhHHHHHHHHhccCcHHH
Q 040261          138 TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINP-DVVTYTSLIRGFCYANDWNE  216 (343)
Q Consensus       138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~  216 (343)
                      .+.....++++....      ...-..+|..++....+..-...|..+|.+..+.+..+ .+...++++..++ .++.+-
T Consensus       347 ~~~~~~~~~~ll~~~------~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~  419 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIE------DIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKET  419 (656)
T ss_pred             hhhhHHHHHHHHhhh------ccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhH
Confidence            555666666666554      22335678889999999999999999999999887666 6777788887766 578899


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          217 AKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       217 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      |.++|+--++. ..-+..--...+..+...++-..+..+|++....+.+++  ..+|..++..=..-|+...+.++-+++
T Consensus       420 AfrIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~  498 (656)
T KOG1914|consen  420 AFRIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRR  498 (656)
T ss_pred             HHHHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            99999987765 233344445677888899999999999999999865554  578999999888999999999988876


Q ss_pred             HhCC---CCccHHHHHHHHHHHHhcCChHH
Q 040261          295 ESNG---CMRDVFSYGILINGYCKNKEIEG  321 (343)
Q Consensus       295 ~~~~---~~~~~~~~~~l~~~~~~~~~~~~  321 (343)
                      ...-   ..+....-..+++-|.-.+.+..
T Consensus       499 ~~af~~~qe~~~~~~~~~v~RY~~~d~~~c  528 (656)
T KOG1914|consen  499 FTAFPADQEYEGNETALFVDRYGILDLYPC  528 (656)
T ss_pred             HHhcchhhcCCCChHHHHHHHHhhcccccc
Confidence            5431   12222233445555655555443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=98.00  E-value=0.00089  Score=44.95  Aligned_cols=111  Identities=17%  Similarity=0.100  Sum_probs=79.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC--HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--ccHHHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD--LYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PDAVTFTSLI   94 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~   94 (343)
                      ....+..++-..|+.++|+.+|++....|....  ...+..+...+...|++++|..++++.....+.  .+......+.
T Consensus         3 ~~~~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~A   82 (120)
T PF12688_consen    3 ALYELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLA   82 (120)
T ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHH
Confidence            345567788889999999999999999886544  346677888899999999999999998875322  1222233344


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC  133 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  133 (343)
                      .++...|+.++|++.+-.....    +...|..-|..|.
T Consensus        83 l~L~~~gr~~eAl~~~l~~la~----~~~~y~ra~~~ya  117 (120)
T PF12688_consen   83 LALYNLGRPKEALEWLLEALAE----TLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            5677889999999888766543    3445655555554

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

Probab=97.99  E-value=1.1e-05  Score=39.74  Aligned_cols=29  Identities=38%  Similarity=0.698  Sum_probs=17.6

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45666666666666666666666665554

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.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.98  E-value=0.00095  Score=57.38  Aligned_cols=135  Identities=12%  Similarity=0.052  Sum_probs=96.6

Q ss_pred             CCChhhHHHHHHHHHhcC-----ChhHHHHHHHHhHhCCCCCC-HHHHHHHHHHHHhcCC--------cchHHHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNK-----HYDTVLSLFKRLNSIGLFPD-LYTYNILINCFCKMGR--------VSPGFVVLGRIL   79 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~--------~~~a~~~~~~~~   79 (343)
                      |.+..+|...+.+.....     +...|..+|++..+..  |+ ...|..+..++.....        ...+.+...+..
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld--P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSE--PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            478889999988865433     3679999999999855  54 4455554444433221        223333333333


Q ss_pred             Hc-CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           80 RS-CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        80 ~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      .. ....+...|..+.-.....|++++|...+++..+.+  |+...|..+...+...|+.++|...+++....+
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~  483 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNLR  483 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            32 123355677777666667899999999999999985  688899999999999999999999999998865

>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=97.96  E-value=0.00022  Score=52.22  Aligned_cols=104  Identities=20%  Similarity=0.274  Sum_probs=66.3

Q ss_pred             CChhhHHHHHHHHHhc-----CChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           15 PPVCSFNILFGCLAKN-----KHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      .+-.+|..++..+.+.     |..+-....+..|.+.|+.-|..+|+.|+..+-+ |.+- -..+|+.+           
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv-p~n~fQ~~-----------  111 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV-PRNFFQAE-----------  111 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc-cccHHHHH-----------
Confidence            4566677777776643     5566666667777777777777777777776654 3322 01111111           


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH  137 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  137 (343)
                          ..-|  -.+-+-|++++++|...|+-||..++..+++.+.+.+.
T Consensus       112 ----F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  112 ----FMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             ----hccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence                1111  12346688888999988988899998888888887665

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

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

Probab=97.95  E-value=0.00035  Score=53.57  Aligned_cols=88  Identities=16%  Similarity=0.112  Sum_probs=40.8

Q ss_pred             HHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHH
Q 040261           26 CLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIME  105 (343)
Q Consensus        26 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  105 (343)
                      -+.+.+++++|+..|.+.++.. +-|...|..-..+|.+.|.++.|++-.+..+..+. ....+|..|..+|...|++++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp-~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDP-HYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcCh-HHHHHHHHHHHHHHccCcHHH
Confidence            3344445555555555554432 22334444444455555555555555444444321 123344445555555555555


Q ss_pred             HHHHHHHHHh
Q 040261          106 AAALFTKLRA  115 (343)
Q Consensus       106 a~~~~~~~~~  115 (343)
                      |++.|++.++
T Consensus       168 A~~aykKaLe  177 (304)
T KOG0553|consen  168 AIEAYKKALE  177 (304)
T ss_pred             HHHHHHhhhc
Confidence            5555544444

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.94  E-value=0.0018  Score=43.51  Aligned_cols=90  Identities=20%  Similarity=0.129  Sum_probs=49.1

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCC---CHHHHHHHHHHHh
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRP---DASVYNTLMDGFC  279 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~  279 (343)
                      ..++-..|+.++|+.++++..+.|....  ...+-.+...+...|++++|..+++...... +.   +......+..++.
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~-p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF-PDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCccccHHHHHHHHHHHH
Confidence            3445556666666666666666654433  2344445556666666666666666665541 11   1222222333555


Q ss_pred             cCCchHHHHHHHHHHH
Q 040261          280 LTGRVNRAKELFVSME  295 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~  295 (343)
                      ..|+.++|.+.+-...
T Consensus        87 ~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   87 NLGRPKEALEWLLEAL  102 (120)
T ss_pred             HCCCHHHHHHHHHHHH
Confidence            6666666666665444

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.94  E-value=0.0025  Score=47.80  Aligned_cols=67  Identities=12%  Similarity=0.083  Sum_probs=40.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCC--CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGL--FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      +...+-.....+.+.|++.+|...|+.+...-.  +-.......++.++.+.|+++.|...+++.++.-
T Consensus         4 ~~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~y   72 (203)
T PF13525_consen    4 TAEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLY   72 (203)
T ss_dssp             -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            344455566666777778888888877765321  1122345556677777777777777777777653

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

Probab=97.90  E-value=0.0001  Score=43.71  Aligned_cols=58  Identities=16%  Similarity=0.149  Sum_probs=39.0

Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +...+.+.|++++|...|+++.+.. +-+...+..+..++...|++++|...|+++++.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3455667777777777777777664 335666777777777777777777777777644

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.89  E-value=0.0021  Score=49.68  Aligned_cols=99  Identities=12%  Similarity=0.066  Sum_probs=44.7

Q ss_pred             ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC---CChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          197 DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN---GKMDEASRLLELMIQIGVRPDASVYNT  273 (343)
Q Consensus       197 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~  273 (343)
                      |...|..|..+|...|+++.|..-|.+..+.. .++...+..+..++...   .+..++..+|+++...+ +-|......
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~l  232 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALSL  232 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHHH
Confidence            44455555555555555555555555544431 23333333333333221   12334445555554443 333444444


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhC
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      |...+...|++.+|...|+.|.+.
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc
Confidence            444455555555555555555443

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.87  E-value=0.0008  Score=51.88  Aligned_cols=99  Identities=16%  Similarity=0.204  Sum_probs=42.3

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc---CcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE---SRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      |...|-.|...|...|+++.|..-|.+..+.. .++...+..+..++...   ....++..+++++...... +..+...
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~-~iral~l  232 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPA-NIRALSL  232 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCc-cHHHHHH
Confidence            44444444444444444444444444444432 22333333333332222   1223444444444444222 3333344


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHcc
Q 040261          128 LINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      +...+...|++.+|...|+.|...
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc
Confidence            444444445555555555444444

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.85  E-value=0.0011  Score=48.69  Aligned_cols=87  Identities=21%  Similarity=0.248  Sum_probs=58.9

Q ss_pred             CChhhHHHHHHHHhc-----cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC----------------ChhHHHH
Q 040261          196 PDVVTYTSLIRGFCY-----ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG----------------KMDEASR  254 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----------------~~~~a~~  254 (343)
                      .+..+|..++..+.+     .|..+=....++.|.+-|+.-|..+|+.|+..+=+..                +-+-|++
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~  124 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAID  124 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHH
Confidence            477888888887754     4667777777888888888888888888888875421                2334556


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhcCC
Q 040261          255 LLELMIQIGVRPDASVYNTLMDGFCLTG  282 (343)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~  282 (343)
                      ++++|...|+-||..++..+++.|.+.+
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhcccc
Confidence            6666666666666666666666554444

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

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

Probab=97.84  E-value=9.9e-05  Score=44.29  Aligned_cols=52  Identities=27%  Similarity=0.339  Sum_probs=29.8

Q ss_pred             hCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          245 KNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      +.|++++|..+|+.+.+.. +-+......+..+|.+.|++++|.++++++...
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4556666666666665553 335555555666666666666666666665554

...

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

Probab=97.83  E-value=6.9e-05  Score=44.98  Aligned_cols=52  Identities=21%  Similarity=0.361  Sum_probs=28.7

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.|++++|+++|+.+.... +.+...+..+..++.+.|++++|.++++++...
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4555666666666655433 234555555556666666666666666655554

...

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

Probab=97.82  E-value=9.9e-05  Score=44.43  Aligned_cols=63  Identities=13%  Similarity=0.179  Sum_probs=32.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG-RVSPGFVVLGRILR   80 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~   80 (343)
                      +.+|..+...+.+.|++++|+..|++..+.. +.+...|..+..++...| ++++|++.+++.++
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            3445555555555555555555555555433 223444555555555555 45555555555444

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.82  E-value=0.0048  Score=49.74  Aligned_cols=265  Identities=13%  Similarity=0.034  Sum_probs=162.9

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH  137 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  137 (343)
                      ....+.+..++..|+..+...++..+. +...|..-+..+...|++++++--.+.-.+.... ........-+++...++
T Consensus        55 ~gn~~yk~k~Y~nal~~yt~Ai~~~pd-~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~-~~k~~~r~~~c~~a~~~  132 (486)
T KOG0550|consen   55 EGNAFYKQKTYGNALKNYTFAIDMCPD-NASYYSNRAATLMMLGRFEEALGDARQSVRLKDG-FSKGQLREGQCHLALSD  132 (486)
T ss_pred             hcchHHHHhhHHHHHHHHHHHHHhCcc-chhhhchhHHHHHHHHhHhhcccchhhheecCCC-ccccccchhhhhhhhHH
Confidence            334556677788888888888887543 5666777777777788888887766555443211 11122223333333333


Q ss_pred             hHHHHHHHH------------HHHccCCCCCccccCCcchHHHH-HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHH
Q 040261          138 TIVALNLFE------------EMANGNGEFGVVCKPDAITYSTI-TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSL  204 (343)
Q Consensus       138 ~~~a~~~~~------------~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  204 (343)
                      ..+|...++            .....-..+.  -+|.-..+..+ ..++.-.|++++|...-..+.+..   ....+...
T Consensus       133 ~i~A~~~~~~~~~~~~anal~~~~~~~~s~s--~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld---~~n~~al~  207 (486)
T KOG0550|consen  133 LIEAEEKLKSKQAYKAANALPTLEKLAPSHS--REPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD---ATNAEALY  207 (486)
T ss_pred             HHHHHHHhhhhhhhHHhhhhhhhhccccccc--CCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc---cchhHHHH
Confidence            333333322            2211110000  11222233322 245667899999988877776653   22233333


Q ss_pred             H--HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH-------------HHHHHHhCCChhHHHHHHHHHHHc---CCCC
Q 040261          205 I--RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV-------------IMNELCKNGKMDEASRLLELMIQI---GVRP  266 (343)
Q Consensus       205 ~--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------------l~~~~~~~~~~~~a~~~~~~~~~~---~~~~  266 (343)
                      +  .++.-.++.+.+...|++.+..+  |+...-..             =..-..+.|++..|...|.+.+..   +.++
T Consensus       208 vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~  285 (486)
T KOG0550|consen  208 VRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKT  285 (486)
T ss_pred             hcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccch
Confidence            3  34445678889999998887753  44322211             123345789999999999999875   3456


Q ss_pred             CHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc-HHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          267 DASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD-VFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       267 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      +...|.....+..+.|+.++|+.-.+...+..  +. ...+..-..++...++|++|.+-+++..+..
T Consensus       286 naklY~nra~v~~rLgrl~eaisdc~~Al~iD--~syikall~ra~c~l~le~~e~AV~d~~~a~q~~  351 (486)
T KOG0550|consen  286 NAKLYGNRALVNIRLGRLREAISDCNEALKID--SSYIKALLRRANCHLALEKWEEAVEDYEKAMQLE  351 (486)
T ss_pred             hHHHHHHhHhhhcccCCchhhhhhhhhhhhcC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            77788888888899999999999999888742  22 2233334456777889999999999887654

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.79  E-value=0.006  Score=43.62  Aligned_cols=102  Identities=15%  Similarity=0.121  Sum_probs=50.1

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-CCh
Q 040261          120 PDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENIN-PDV  198 (343)
Q Consensus       120 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~  198 (343)
                      |+...-..|..++.+.|+..+|...|++....-      ..-|......+..+....+++..|...++++.+.+.. -++
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~------fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~p  160 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGI------FAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSP  160 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccc------cCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCC
Confidence            444444455555555555555555555554433      3344445555555555555555555555555443200 012


Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      .+.-.+.+.+...|.+.+|..-|+.....
T Consensus       161 d~~Ll~aR~laa~g~~a~Aesafe~a~~~  189 (251)
T COG4700         161 DGHLLFARTLAAQGKYADAESAFEVAISY  189 (251)
T ss_pred             CchHHHHHHHHhcCCchhHHHHHHHHHHh
Confidence            22333445555555555555555555543

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.75  E-value=0.0096  Score=44.72  Aligned_cols=47  Identities=19%  Similarity=0.095  Sum_probs=27.1

Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCCCCcc----HHHHHHHHHHHHhcCChHHH
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNGCMRD----VFSYGILINGYCKNKEIEGA  322 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a  322 (343)
                      +...|.+.|.+..|..-++.+.+.-  |+    ......++.+|.+.|..+.+
T Consensus       147 ia~~Y~~~~~y~aA~~r~~~v~~~y--p~t~~~~~al~~l~~~y~~l~~~~~a  197 (203)
T PF13525_consen  147 IARFYYKRGKYKAAIIRFQYVIENY--PDTPAAEEALARLAEAYYKLGLKQAA  197 (203)
T ss_dssp             HHHHHHCTT-HHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHC--CCCchHHHHHHHHHHHHHHhCChHHH
Confidence            4556677777777777777766641  22    23445566667777766643

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

Probab=97.72  E-value=0.00019  Score=42.62  Aligned_cols=57  Identities=16%  Similarity=0.213  Sum_probs=29.7

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ...+.+.|++++|...|+.+.+.. +-+...+..+..++...|++++|...|+++++.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344555555555555555555543 224445555555555555555555555555543

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

Probab=97.70  E-value=0.0018  Score=45.73  Aligned_cols=70  Identities=21%  Similarity=0.320  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh-----CCCCccHHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES-----NGCMRDVFS  305 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~  305 (343)
                      ....++..+...|++++|..+.+.+.... +.+...+..++.+|...|+...|.++|+++.+     .|+.|+..+
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            34455666677778888888887777765 56677777788888888888888777776643     366666654

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

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

Probab=97.70  E-value=0.00043  Score=41.61  Aligned_cols=60  Identities=20%  Similarity=0.167  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcC-ChHHHHHHHHHHH
Q 040261          270 VYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNK-EIEGALSLYSEML  330 (343)
Q Consensus       270 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~  330 (343)
                      .|..+...+...|++++|+..|++..+.. +.+...|..+..+|...| ++++|++.+++.+
T Consensus         5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    5 AWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            34444444444444444444444444432 223344444444444444 3444444444443

...

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.69  E-value=0.0088  Score=42.81  Aligned_cols=158  Identities=13%  Similarity=0.032  Sum_probs=107.5

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH  137 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  137 (343)
                      +..+..+.-+++...+-..+-..  ..|+...-..+..++.+.|+..+|...|++...--..-|......+.++....++
T Consensus        62 ~~~a~~q~ldP~R~~Rea~~~~~--~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~  139 (251)
T COG4700          62 LLMALQQKLDPERHLREATEELA--IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQE  139 (251)
T ss_pred             HHHHHHHhcChhHHHHHHHHHHh--hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhcc
Confidence            34444455555554443333333  2566666677888888899999999999888765556677778888888888999


Q ss_pred             hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHH
Q 040261          138 TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  217 (343)
                      +..|...++.+.+..+.     -.++.....+.+.+...|.+.+|...|+.....-  |+...-......+.+.|+..++
T Consensus       140 ~A~a~~tLe~l~e~~pa-----~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~y--pg~~ar~~Y~e~La~qgr~~ea  212 (251)
T COG4700         140 FAAAQQTLEDLMEYNPA-----FRSPDGHLLFARTLAAQGKYADAESAFEVAISYY--PGPQARIYYAEMLAKQGRLREA  212 (251)
T ss_pred             HHHHHHHHHHHhhcCCc-----cCCCCchHHHHHHHHhcCCchhHHHHHHHHHHhC--CCHHHHHHHHHHHHHhcchhHH
Confidence            99999999888876532     2345566677788888999999999998887753  4444433344445566766655


Q ss_pred             HHHHHHH
Q 040261          218 KCLFIEM  224 (343)
Q Consensus       218 ~~~~~~~  224 (343)
                      ..-+..+
T Consensus       213 ~aq~~~v  219 (251)
T COG4700         213 NAQYVAV  219 (251)
T ss_pred             HHHHHHH
Confidence            5444433

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.69  E-value=0.0034  Score=54.12  Aligned_cols=241  Identities=13%  Similarity=0.047  Sum_probs=142.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc-CCCc--------cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRS-CFTP--------DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK  119 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  119 (343)
                      .|.+..|..+.......-.++.|...|-+.... |++.        +...-.+=+.++  .|++++|+++|-.+.++   
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~drr---  763 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRR---  763 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchh---
Confidence            477788888887777766777777666554331 2110        111111122222  48888998888777654   


Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChh
Q 040261          120 PDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVV  199 (343)
Q Consensus       120 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  199 (343)
                       |     ..+..+.+.|++-.+.++++.--....     -..-..+++.+...+.....|++|.+.+..-..        
T Consensus       764 -D-----LAielr~klgDwfrV~qL~r~g~~d~d-----D~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~--------  824 (1189)
T KOG2041|consen  764 -D-----LAIELRKKLGDWFRVYQLIRNGGSDDD-----DEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD--------  824 (1189)
T ss_pred             -h-----hhHHHHHhhhhHHHHHHHHHccCCCcc-----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--------
Confidence             2     245566777887666655543211110     111235778888888888888888888765432        


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                       ....+.++.+..++++.+.+.+.+     +.+....-.+..++...|.-++|.+.+-+.   + .|.     ..+..|.
T Consensus       825 -~e~~~ecly~le~f~~LE~la~~L-----pe~s~llp~~a~mf~svGMC~qAV~a~Lr~---s-~pk-----aAv~tCv  889 (1189)
T KOG2041|consen  825 -TENQIECLYRLELFGELEVLARTL-----PEDSELLPVMADMFTSVGMCDQAVEAYLRR---S-LPK-----AAVHTCV  889 (1189)
T ss_pred             -hHhHHHHHHHHHhhhhHHHHHHhc-----CcccchHHHHHHHHHhhchHHHHHHHHHhc---c-CcH-----HHHHHHH
Confidence             123456666666666666555443     445666777888888888888888776443   2 222     3456677


Q ss_pred             cCCchHHHHHHHHHHHhCCCCccHHHHH--------------HHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          280 LTGRVNRAKELFVSMESNGCMRDVFSYG--------------ILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~--------------~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ..++|.+|.++.++..-    |...+..              --|..+.+.|++-.|.+++.+|.++
T Consensus       890 ~LnQW~~avelaq~~~l----~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~  952 (1189)
T KOG2041|consen  890 ELNQWGEAVELAQRFQL----PQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAER  952 (1189)
T ss_pred             HHHHHHHHHHHHHhccc----hhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHH
Confidence            77888888877765432    2222111              1233455666666666666666543

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.60  E-value=0.0025  Score=49.58  Aligned_cols=97  Identities=13%  Similarity=0.099  Sum_probs=60.3

Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhCCChhHHHHHHHHHHHcC--CCCCHHHHH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV----VTFNVIMNELCKNGKMDEASRLLELMIQIG--VRPDASVYN  272 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~  272 (343)
                      ..|...+....+.|++++|...|+.+.+.  .|+.    ..+..+..+|...|++++|...|+.+.+.-  -+.....+-
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            34555554445567777777777777765  2332    355566777777777777777777776642  111234444


Q ss_pred             HHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          273 TLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       273 ~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+...+...|+.++|..+++.+.+.
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4555666777777777777777665

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.59  E-value=0.0011  Score=53.36  Aligned_cols=133  Identities=16%  Similarity=0.118  Sum_probs=87.4

Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHH----HcCCC-CCHHHHHHHHHHHHhCCChhHHHHHHHHHHH----cCC-CCCH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMM----DQGVQ-PNVVTFNVIMNELCKNGKMDEASRLLELMIQ----IGV-RPDA  268 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~----~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~  268 (343)
                      ..|..+...|.-.|+++.|+...+.-+    +.|-+ .....+..+..++.-.|+++.|.+.|+....    .|- ....
T Consensus       196 Ra~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEA  275 (639)
T KOG1130|consen  196 RAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEA  275 (639)
T ss_pred             chhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHH
Confidence            446666666777788888887655432    22322 2345677788888889999999988876543    231 1233


Q ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHHh----C-CCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          269 SVYNTLMDGFCLTGRVNRAKELFVSMES----N-GCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       269 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ...-.|...|.-..++++|+..+.+-..    . ...-....+.+|..+|...|..++|+...+.-++
T Consensus       276 QscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  276 QSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHLR  343 (639)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            4555677777777788888887765332    1 1122456778888888888888888877665543

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.56  E-value=0.029  Score=45.24  Aligned_cols=293  Identities=11%  Similarity=0.071  Sum_probs=153.4

Q ss_pred             HHHHHHHHH--hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHH--HHhcCCcchHHHHHHHHHHcCCCccHHH--HHHH
Q 040261           20 FNILFGCLA--KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINC--FCKMGRVSPGFVVLGRILRSCFTPDAVT--FTSL   93 (343)
Q Consensus        20 ~~~l~~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l   93 (343)
                      |..|-..+.  -.|+-..|.++-.+.... +..|......++.+  -.-.|+.+.|.+-|+.|...   |....  ...|
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgL  160 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGL  160 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHH
Confidence            444444443  356666676666554321 23344444444433  33457788888888877652   22221  1222


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc--hHHHHHH
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI--TYSTITD  171 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~~  171 (343)
                      .-..-+.|+.+.|.++-++.-..-.. -...+...+...+..|+++.|+++++.-.....     +.++..  .-..|+.
T Consensus       161 yleAqr~GareaAr~yAe~Aa~~Ap~-l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~v-----ie~~~aeR~rAvLLt  234 (531)
T COG3898         161 YLEAQRLGAREAARHYAERAAEKAPQ-LPWAARATLEARCAAGDWDGALKLVDAQRAAKV-----IEKDVAERSRAVLLT  234 (531)
T ss_pred             HHHHHhcccHHHHHHHHHHHHhhccC-CchHHHHHHHHHHhcCChHHHHHHHHHHHHHHh-----hchhhHHHHHHHHHH
Confidence            22334567777777777666554322 345666777777778888888877776544332     233321  1112221


Q ss_pred             H--H-HhcCChHHHHHHHHHhhhCCCCCChh-hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Q 040261          172 G--L-CKEGFVDKAKELFLKMKDENINPDVV-TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG  247 (343)
Q Consensus       172 ~--~-~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  247 (343)
                      +  . .-..+...|...-.+..+.  .|+.. .--....++.+.|+..++-.+++.+-+....|+  .+    ..|....
T Consensus       235 AkA~s~ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~--ia----~lY~~ar  306 (531)
T COG3898         235 AKAMSLLDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPD--IA----LLYVRAR  306 (531)
T ss_pred             HHHHHHhcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChH--HH----HHHHHhc
Confidence            1  1 1123445555444444332  33321 222334566777777777777777776633333  22    2233322


Q ss_pred             ChhHHHHHHHHHHHc-CCCC-CHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh-cCChHHHHH
Q 040261          248 KMDEASRLLELMIQI-GVRP-DASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK-NKEIEGALS  324 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~-~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~  324 (343)
                      .-+.+..-+++..+. .++| +......+..+-...|++..|..--+.....  .|....|..|.+.-.. .||-.++..
T Consensus       307 ~gdta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~  384 (531)
T COG3898         307 SGDTALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQ  384 (531)
T ss_pred             CCCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHH
Confidence            223333333333321 1233 3455556666677777777777666666553  4666677666665433 377777777


Q ss_pred             HHHHHHhC
Q 040261          325 LYSEMLSK  332 (343)
Q Consensus       325 ~~~~~~~~  332 (343)
                      .+-+..+.
T Consensus       385 wlAqav~A  392 (531)
T COG3898         385 WLAQAVKA  392 (531)
T ss_pred             HHHHHhcC
Confidence            77666544

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.52  E-value=0.0017  Score=52.25  Aligned_cols=270  Identities=14%  Similarity=0.064  Sum_probs=161.4

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHH----HHHHHHHHHHhcCCcchHHHHHHHHHH--c--CCC-ccHHHHHHHH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLY----TYNILINCFCKMGRVSPGFVVLGRILR--S--CFT-PDAVTFTSLI   94 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~--~--~~~-~~~~~~~~l~   94 (343)
                      ..-+++.|+....+.+|+..++.|. .|..    .|..+.++|.-.+++++|+++...=+.  +  |-+ -.......+.
T Consensus        24 GERLck~gdcraGv~ff~aA~qvGT-eDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLG  102 (639)
T KOG1130|consen   24 GERLCKMGDCRAGVDFFKAALQVGT-EDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLG  102 (639)
T ss_pred             HHHHHhccchhhhHHHHHHHHHhcc-hHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhcccccccccc
Confidence            4567899999999999999999883 3333    466677778888889998887653221  1  100 0112223344


Q ss_pred             HHHhhcCcHHHHHHHHHHH----HhcCCC-CCHHHHHHHHHHHHhcCC--------------------hHHHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKL----RAFGCK-PDVFTYTTLINGLCRTGH--------------------TIVALNLFEEMA  149 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~----~~~~~~-~~~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~  149 (343)
                      ..+--.|.+++|+-...+-    ++.|-+ ....++-.+...|...|+                    ++.|.++|..-.
T Consensus       103 NtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL  182 (639)
T KOG1130|consen  103 NTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENL  182 (639)
T ss_pred             chhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHH
Confidence            4444556777765543332    222211 122344455666655442                    233444443322


Q ss_pred             ccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHh----hhCCC-CCChhhHHHHHHHHhccCcHHHHHHHHHHH
Q 040261          150 NGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKM----KDENI-NPDVVTYTSLIRGFCYANDWNEAKCLFIEM  224 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  224 (343)
                      +.....+- -.....+|..|...|.-.|+++.|+...+.-    .+.|- ......+..+..++.-.|+++.|.+.++..
T Consensus       183 ~l~~~lgD-r~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~t  261 (639)
T KOG1130|consen  183 ELSEKLGD-RLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLT  261 (639)
T ss_pred             HHHHHhhh-HHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHH
Confidence            11100000 0122356667777777889999998776542    22221 123456778888999999999999988765


Q ss_pred             HHc----CC-CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc----C-CCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          225 MDQ----GV-QPNVVTFNVIMNELCKNGKMDEASRLLELMIQI----G-VRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       225 ~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      ...    |- .....+...|...|.-..++++|+.++.+-...    + ..-....+-.|..+|...|..++|+.+.+.-
T Consensus       262 l~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~h  341 (639)
T KOG1130|consen  262 LNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELH  341 (639)
T ss_pred             HHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            432    21 223445567888888888999999888765432    1 1123567778888999999999998877654


Q ss_pred             H
Q 040261          295 E  295 (343)
Q Consensus       295 ~  295 (343)
                      .
T Consensus       342 l  342 (639)
T KOG1130|consen  342 L  342 (639)
T ss_pred             H
Confidence            4

>PRK15331 chaperone protein SicA; Provisional

Probab=97.51  E-value=0.0042  Score=43.71  Aligned_cols=94  Identities=9%  Similarity=-0.102  Sum_probs=51.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      ......-+...|++++|..+|+-+...+ +-+..-+..|..++-..+++++|...|......+. -|+..+-....++..
T Consensus        40 iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~  117 (165)
T PRK15331         40 LYAHAYEFYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLL  117 (165)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHH
Confidence            3334444455666666666666655443 23444455555555556666666666665554432 233444445556666


Q ss_pred             cCcHHHHHHHHHHHHh
Q 040261          100 ESRIMEAAALFTKLRA  115 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~  115 (343)
                      .|+.+.|...|+....
T Consensus       118 l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        118 MRKAAKARQCFELVNE  133 (165)
T ss_pred             hCCHHHHHHHHHHHHh
Confidence            6666666666666555

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.49  E-value=0.0047  Score=48.11  Aligned_cols=99  Identities=14%  Similarity=0.031  Sum_probs=55.6

Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPD--VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      |...+....+.|++++|...|+.+.+..+...  ...+..+..+|...|++++|...|+.+....+.    .+.....+.
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~----s~~~~dAl~  221 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPK----SPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC----CcchhHHHH
Confidence            44444444455677777777777666532211  235555666667777777777777776655421    111233344


Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                      .+..++...|+.++|..+|+.+.+.
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4455566666777777766666554

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.47  E-value=0.039  Score=44.53  Aligned_cols=253  Identities=15%  Similarity=0.109  Sum_probs=163.5

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHHH--HHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHH
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLYT--YNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIM  104 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  104 (343)
                      -.-.|+++.|.+-|+.|..   .|....  ...|.-...+.|+.+.|.++-+.....- +.-...+...+...+..|+|+
T Consensus       130 al~eG~~~~Ar~kfeAMl~---dPEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd  205 (531)
T COG3898         130 ALLEGDYEDARKKFEAMLD---DPETRLLGLRGLYLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWD  205 (531)
T ss_pred             HHhcCchHHHHHHHHHHhc---ChHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChH
Confidence            3457999999999999986   333332  2333334457799999999988887653 224678889999999999999


Q ss_pred             HHHHHHHHHHhcC-CCCCHHHH--HHHHHHHH-hcCChHHHHHHHHHHHccCCCCCccccCCcc-hHHHHHHHHHhcCCh
Q 040261          105 EAAALFTKLRAFG-CKPDVFTY--TTLINGLC-RTGHTIVALNLFEEMANGNGEFGVVCKPDAI-TYSTITDGLCKEGFV  179 (343)
Q Consensus       105 ~a~~~~~~~~~~~-~~~~~~~~--~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~  179 (343)
                      .|+++++.-+... +.++..--  ..|+.+-. ..-+.+-+...=.......      +.|+.. .-..-..++.+.|+.
T Consensus       206 ~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~K------L~pdlvPaav~AAralf~d~~~  279 (531)
T COG3898         206 GALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANK------LAPDLVPAAVVAARALFRDGNL  279 (531)
T ss_pred             HHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhh------cCCccchHHHHHHHHHHhccch
Confidence            9999999877653 33343221  12222211 1112222222222222222      445433 233345788999999


Q ss_pred             HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCC-HHHHHHHHHHHHhCCChhHHHHHHH
Q 040261          180 DKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ-GVQPN-VVTFNVIMNELCKNGKMDEASRLLE  257 (343)
Q Consensus       180 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~  257 (343)
                      .++-.+++.+-+....|+.  +.  +..+.+.|+  .+..-+++..+. .++|+ ......+..+....|++..|..--+
T Consensus       280 rKg~~ilE~aWK~ePHP~i--a~--lY~~ar~gd--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Ae  353 (531)
T COG3898         280 RKGSKILETAWKAEPHPDI--AL--LYVRARSGD--TALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAE  353 (531)
T ss_pred             hhhhhHHHHHHhcCCChHH--HH--HHHHhcCCC--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHH
Confidence            9999999999887544443  22  233445554  344444443322 24554 5566677788889999999988877


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHh-cCCchHHHHHHHHHHHhC
Q 040261          258 LMIQIGVRPDASVYNTLMDGFC-LTGRVNRAKELFVSMESN  297 (343)
Q Consensus       258 ~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~  297 (343)
                      ...+.  .|....|..|.+.-. ..||-.++...+.+..+.
T Consensus       354 aa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         354 AAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             HHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            77664  688888888877554 459999999999888875

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.41  E-value=0.039  Score=45.02  Aligned_cols=31  Identities=16%  Similarity=0.145  Sum_probs=17.6

Q ss_pred             ChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          197 DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       197 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      +-..+..++.++.-.|++++|....++|.+.
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            3444455555555566666666666666554

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.36  E-value=0.0014  Score=39.83  Aligned_cols=56  Identities=18%  Similarity=0.288  Sum_probs=33.7

Q ss_pred             HHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           25 GCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ..+.+.+++++|+++++.+...+ |.+...+.....++.+.|++++|.+.++...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34556666666666666666544 334455555666666666666666666666654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.36  E-value=0.0019  Score=39.30  Aligned_cols=54  Identities=17%  Similarity=0.163  Sum_probs=25.2

Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          242 ELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      .+.+.+++++|..++++++..+ +.+...+.....++.+.|++++|.+.+++..+
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3444444555555554444443 33344444444444445555555555544444

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.35  E-value=0.029  Score=48.27  Aligned_cols=87  Identities=11%  Similarity=0.163  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC-----------CHHHHHHHHHHHHhcCCcc--hHHHHHHHHHHcCCCc
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP-----------DLYTYNILINCFCKMGRVS--PGFVVLGRILRSCFTP   85 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~   85 (343)
                      .+..-+..+...|.+++|.++--    .|+..           ++-.++..=.+|.+..+..  +...-++++.++|-.|
T Consensus       558 p~~~~m~q~Ieag~f~ea~~iac----lgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P  633 (1081)
T KOG1538|consen  558 PQSAPMYQYIERGLFKEAYQIAC----LGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKKRGETP  633 (1081)
T ss_pred             cccccchhhhhccchhhhhcccc----cceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCc
Confidence            34455666778888888766521    12111           1222333334444444332  2233344455555555


Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHH
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTK  112 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~  112 (343)
                      +...   +...++-.|.+.+|.++|.+
T Consensus       634 ~~iL---lA~~~Ay~gKF~EAAklFk~  657 (1081)
T KOG1538|consen  634 NDLL---LADVFAYQGKFHEAAKLFKR  657 (1081)
T ss_pred             hHHH---HHHHHHhhhhHHHHHHHHHH
Confidence            5532   33344455666666666644

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

Probab=97.32  E-value=0.06  Score=43.42  Aligned_cols=106  Identities=15%  Similarity=0.161  Sum_probs=60.4

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      +.+..+.-+...|+...|.++-.+.   . .|+..-|...+.+++..+++++...+...      +-++.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F---k-v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF---K-VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHH
Confidence            4444455556666666666654444   1 35666666667777777777666554321      123355666667777


Q ss_pred             cCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHH
Q 040261          280 LTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      +.|+..+|..+..++.          +..-+..|.+.|++.+|.+.
T Consensus       249 ~~~~~~eA~~yI~k~~----------~~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  249 KYGNKKEASKYIPKIP----------DEERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             HCCCHHHHHHHHHhCC----------hHHHHHHHHHCCCHHHHHHH
Confidence            7777777766665521          13345555666666665443

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

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.32  E-value=0.096  Score=45.74  Aligned_cols=119  Identities=11%  Similarity=-0.046  Sum_probs=71.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHh-CCCCCCHHHHHHHH----------HHHHhcCCcchHHHHHHHHHHcCC
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNS-IGLFPDLYTYNILI----------NCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~l~----------~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      |.+..|..+.....+.-.++.|...|-+... .|++    ....+-          ..-.--|++++|.++|-.+.+++ 
T Consensus       690 PHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik----~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD-  764 (1189)
T KOG2041|consen  690 PHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIK----LVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD-  764 (1189)
T ss_pred             CchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchh----HHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh-
Confidence            7788999999999988899999988876643 2321    111111          11223488889988887776542 


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHH
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK--PDVFTYTTLINGLCRTGHTIVALNLFEE  147 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~  147 (343)
                              ..+..+.+.|++-.+.++++.--. +..  .-..+|+.+...+.....+++|.+.+..
T Consensus       765 --------LAielr~klgDwfrV~qL~r~g~~-d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~  821 (1189)
T KOG2041|consen  765 --------LAIELRKKLGDWFRVYQLIRNGGS-DDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSY  821 (1189)
T ss_pred             --------hhHHHHHhhhhHHHHHHHHHccCC-CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence                    234455566777666655543110 000  0123566666666666666666666554

>PRK15331 chaperone protein SicA; Provisional

Probab=97.30  E-value=0.019  Score=40.50  Aligned_cols=91  Identities=12%  Similarity=0.014  Sum_probs=66.9

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV  284 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  284 (343)
                      ..-+...|++++|..+|.-+...+ .-+..-+..|..++-..+++++|...|......+ .-|+..+-....++...|+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d-~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~-~~dp~p~f~agqC~l~l~~~  121 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYD-FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLL-KNDYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc-cCCCCccchHHHHHHHhCCH
Confidence            334567888888888888887764 3345556677777778888888888888776654 33445556667788888888


Q ss_pred             HHHHHHHHHHHhC
Q 040261          285 NRAKELFVSMESN  297 (343)
Q Consensus       285 ~~a~~~~~~~~~~  297 (343)
                      +.|...|.....+
T Consensus       122 ~~A~~~f~~a~~~  134 (165)
T PRK15331        122 AKARQCFELVNER  134 (165)
T ss_pred             HHHHHHHHHHHhC
Confidence            8888888888773

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.28  E-value=0.049  Score=41.50  Aligned_cols=185  Identities=10%  Similarity=0.027  Sum_probs=109.2

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      ..|...+.+.-+..+...        ....+..+-.....+...+.|++-..             .+.+.++....-.|.
T Consensus       134 ~lgnpqesLdRl~~L~~~--------V~~ii~~~e~~~~~ESsv~lW~KRl~-------------~Vmy~~~~~llG~kE  192 (366)
T KOG2796|consen  134 YLGNPQESLDRLHKLKTV--------VSKILANLEQGLAEESSIRLWRKRLG-------------RVMYSMANCLLGMKE  192 (366)
T ss_pred             hcCCcHHHHHHHHHHHHH--------HHHHHHHHHhccchhhHHHHHHHHHH-------------HHHHHHHHHHhcchh
Confidence            345555555444444321        12233333333344556666665432             345566666677777


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH-----HHHHHHHhCCChhHHH
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN-----VIMNELCKNGKMDEAS  253 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-----~l~~~~~~~~~~~~a~  253 (343)
                      +.-....+.+..+...+-++.....+.+.-.+.|+.+.|...|++..+..-..+..+++     .....+.-.+++..|.
T Consensus       193 y~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~  272 (366)
T KOG2796|consen  193 YVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAH  272 (366)
T ss_pred             hhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHH
Confidence            77777777777776655667777777777778888888888887666543233333333     2334455567777777


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHH
Q 040261          254 RLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYG  307 (343)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  307 (343)
                      ..+.+....+ +.++...|.-.-+..-.|+...|.+..+.+.+.  .|...+-+
T Consensus       273 r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~e  323 (366)
T KOG2796|consen  273 RFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHE  323 (366)
T ss_pred             HHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhh
Confidence            7777777664 334444444444445567888888888888775  34444333

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

Probab=97.28  E-value=0.032  Score=39.35  Aligned_cols=71  Identities=21%  Similarity=0.349  Sum_probs=46.0

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH-----cCCCCCHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ-----IGVRPDASVY  271 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  271 (343)
                      ....++..+...|++++|..+.+.+.... +-+...|..++.++...|+...|.+.|+++.+     .|+.|+..+-
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            34556666777788888888888877764 55677788888888888888888888877643     3777776543

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

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.27  E-value=0.074  Score=43.46  Aligned_cols=169  Identities=11%  Similarity=0.082  Sum_probs=109.2

Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCC---CCCChhhHHHHHHHHhc---cCcHHHHHHHHHHHHHcCCCCCHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDEN---INPDVVTYTSLIRGFCY---ANDWNEAKCLFIEMMDQGVQPNVVT  235 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~  235 (343)
                      +..+...++-.|....+++..+++.+.+....   +.-....-....-++.+   .|+.++|..++..+......++..+
T Consensus       140 s~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~  219 (374)
T PF13281_consen  140 SPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDT  219 (374)
T ss_pred             ChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHH
Confidence            34455566777999999999999999987751   11122222334455566   8999999999999766666788889


Q ss_pred             HHHHHHHHHh---------CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc----hHHHHHHH----HHHHhCC
Q 040261          236 FNVIMNELCK---------NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR----VNRAKELF----VSMESNG  298 (343)
Q Consensus       236 ~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----~~~a~~~~----~~~~~~~  298 (343)
                      |..+.+.|-.         ....++|...|.+.-+..  |+...=-.++..+...|.    -.+..++-    ..+.+.|
T Consensus       220 ~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~--~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg  297 (374)
T PF13281_consen  220 LGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEIE--PDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKG  297 (374)
T ss_pred             HHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcCC--ccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhc
Confidence            9888877642         224677888888776653  443221112222222222    22333333    1222233


Q ss_pred             ---CCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          299 ---CMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       299 ---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                         -..+...+.+++.++.-.|++++|.+.+++|...
T Consensus       298 ~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  298 SLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence               2346667788899999999999999999999866

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=97.24  E-value=0.014  Score=48.30  Aligned_cols=66  Identities=15%  Similarity=0.053  Sum_probs=57.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL----YTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      |.+...++.+..+|.+.|++++|+..|++.++.+  |+.    .+|..+..+|...|+.++|++.+++.++.
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALELN--PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            5678899999999999999999999999988854  553    35888999999999999999999999875

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

Probab=97.16  E-value=0.012  Score=39.99  Aligned_cols=96  Identities=14%  Similarity=0.062  Sum_probs=48.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhh
Q 040261          121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVT  200 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  200 (343)
                      |..++..++.++++.|+.+....+++..-.-+...      ...           .+.         .-......|+..+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~------~~~-----------~~~---------~~~~spl~Pt~~l   54 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNG------KKK-----------EGD---------YPPSSPLYPTSRL   54 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCC------ccc-----------cCc---------cCCCCCCCCCHHH
Confidence            34566677777777777777777776553322100      000           000         1122234455555


Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCCHHHHHHHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQ-GVQPNVVTFNVIMNE  242 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~  242 (343)
                      ..+++.+|+..+++..|.++++...+. +++.+...|..|+.-
T Consensus        55 L~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   55 LIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            555555555555555555555555443 444445555555543

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

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

Probab=97.12  E-value=0.00083  Score=41.53  Aligned_cols=68  Identities=22%  Similarity=0.259  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC-CcchHHHHHHHHHhcCChHHHHHHHHHhhh
Q 040261          123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP-DAITYSTITDGLCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       123 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  191 (343)
                      .+++.+...|...|++++|+..+++..+.....+. ..+ ...++..+..++...|++++|++.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            46777888888899999998888887654211110 122 256778888889999999999998887643

...

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

Probab=97.10  E-value=0.015  Score=39.57  Aligned_cols=51  Identities=12%  Similarity=0.083  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC-CCCccHHHHHHHHHHHH
Q 040261          264 VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN-GCMRDVFSYGILINGYC  314 (343)
Q Consensus       264 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~  314 (343)
                      ..|+..+..+++.+|+..+++..|.++.+.+.+. +++.+..+|..|+.-+.
T Consensus        48 l~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   48 LYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4577788888888888888888888888776653 55556777777776543

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

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

Probab=97.08  E-value=0.0034  Score=38.72  Aligned_cols=26  Identities=23%  Similarity=0.319  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      +++.+...|...|++++|+..+++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al   32 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKAL   32 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444444444444444444443

...

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.02  E-value=0.15  Score=42.25  Aligned_cols=297  Identities=12%  Similarity=0.091  Sum_probs=158.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhHhCCCC----CCHHHHHHHHHHHHhc--------CCcchHHHHHHHHH-------Hc
Q 040261           21 NILFGCLAKNKHYDTVLSLFKRLNSIGLF----PDLYTYNILINCFCKM--------GRVSPGFVVLGRIL-------RS   81 (343)
Q Consensus        21 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~-------~~   81 (343)
                      +..++++...|++.++..+++++...=.+    .+..+|+.++-.++++        ...+-+.++++.+.       ..
T Consensus       132 ~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~  211 (549)
T PF07079_consen  132 EIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAF  211 (549)
T ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHH
Confidence            44578888999999999999988764333    6888888865555432        22222333333221       10


Q ss_pred             ------CCCccHHHHHHHH----------------------------------HHHhh--cCcHHHHHHHHHHHHhcCCC
Q 040261           82 ------CFTPDAVTFTSLI----------------------------------KGLCA--ESRIMEAAALFTKLRAFGCK  119 (343)
Q Consensus        82 ------~~~~~~~~~~~l~----------------------------------~~~~~--~~~~~~a~~~~~~~~~~~~~  119 (343)
                            .+-|.......++                                  ..+..  ..+.+++..+.+.+....+.
T Consensus       212 d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f~~~~e~~~~~ce~ia~~~i~  291 (549)
T PF07079_consen  212 DQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLMQILENWENFYVHPNYDLVIEPLKQQFMSDPEQVGHFCEAIASSKIE  291 (549)
T ss_pred             hhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHHHHHHHHHhhccCCchhHHHHHHHHHHhcChHHHHHHHHHHHHHhHH
Confidence                  0111111111111                                  11110  01334444444433332111


Q ss_pred             C----CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH-------HHHHHHHHh-c---CChHHHHH
Q 040261          120 P----DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY-------STITDGLCK-E---GFVDKAKE  184 (343)
Q Consensus       120 ~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~-------~~l~~~~~~-~---~~~~~a~~  184 (343)
                      +    -..+|..++....+.++...|.+.+.-+...+        |+...-       ..+-+..+. .   -+...-+.
T Consensus       292 ~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL~~ld--------p~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~  363 (549)
T PF07079_consen  292 KLKEELIDRFGNLLSFKVKQVQTEEAKQYLALLKILD--------PRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLN  363 (549)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcC--------CcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHH
Confidence            1    23456677777888888888888888777654        332211       112222221 1   11223344


Q ss_pred             HHHHhhhCCCCCChhhHHHHHH---HHhccC-cHHHHHHHHHHHHHcCCCCCHHHHHH----HHHHHHh---CCChhHHH
Q 040261          185 LFLKMKDENINPDVVTYTSLIR---GFCYAN-DWNEAKCLFIEMMDQGVQPNVVTFNV----IMNELCK---NGKMDEAS  253 (343)
Q Consensus       185 ~~~~~~~~~~~~~~~~~~~l~~---~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~----l~~~~~~---~~~~~~a~  253 (343)
                      +++.+...++.. ...-..++.   -+-+.| .-++|+.+++.+.+-. +-|...-|.    +=.+|.+   .....+-.
T Consensus       364 lwe~~qs~DiDr-qQLvh~L~~~Ak~lW~~g~~dekalnLLk~il~ft-~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLl  441 (549)
T PF07079_consen  364 LWEEIQSYDIDR-QQLVHYLVFGAKHLWEIGQCDEKALNLLKLILQFT-NYDIECENIVFLFVKQAYKQALSMHAIPRLL  441 (549)
T ss_pred             HHHHHHhhcccH-HHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            555554443321 112222222   222334 4788899988887642 222222222    2223322   23344444


Q ss_pred             HHHHHHHHcCCCCC----HHHHHHHHH--HHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHH
Q 040261          254 RLLELMIQIGVRPD----ASVYNTLMD--GFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS  327 (343)
Q Consensus       254 ~~~~~~~~~~~~~~----~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  327 (343)
                      .+-+-+.+.|++|-    ...-|.|.+  -+..+|++.++.-.-.-+.+  +.|++.+|..+.-+.....++++|..++.
T Consensus       442 kLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~  519 (549)
T PF07079_consen  442 KLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQ  519 (549)
T ss_pred             HHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            44455556676653    333444444  34577899988877666666  47899999999999999999999999987


Q ss_pred             HH
Q 040261          328 EM  329 (343)
Q Consensus       328 ~~  329 (343)
                      ++
T Consensus       520 ~L  521 (549)
T PF07079_consen  520 KL  521 (549)
T ss_pred             hC
Confidence            75

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.98  E-value=0.16  Score=43.69  Aligned_cols=163  Identities=17%  Similarity=0.127  Sum_probs=110.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCCh-----hhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHH
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDEN-INPDV-----VTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVT  235 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-----~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  235 (343)
                      +..++....=.||-+.+++.+....+.+ +.-..     -.|...+..++.    ..+.+.|.+++..+.+.  -|+...
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~l  268 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSAL  268 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHH
Confidence            3445555666799999999998876542 22111     223333333332    45678999999999987  677666


Q ss_pred             HHHH-HHHHHhCCChhHHHHHHHHHHHcCC---CCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHH
Q 040261          236 FNVI-MNELCKNGKMDEASRLLELMIQIGV---RPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILIN  311 (343)
Q Consensus       236 ~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  311 (343)
                      |... .+.+...|++++|.+.|++......   +.....+--+...+.-.++|++|...|..+.+.. ..+...|.-+..
T Consensus       269 fl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a  347 (468)
T PF10300_consen  269 FLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAA  347 (468)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHH
Confidence            6543 4567789999999999998764211   2234455667777888999999999999999864 334445544443


Q ss_pred             -HHHhcCCh-------HHHHHHHHHHHh
Q 040261          312 -GYCKNKEI-------EGALSLYSEMLS  331 (343)
Q Consensus       312 -~~~~~~~~-------~~a~~~~~~~~~  331 (343)
                       ++...|+.       ++|.+++++...
T Consensus       348 ~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  348 ACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence             35567777       888888887754

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.

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=96.95  E-value=0.094  Score=38.83  Aligned_cols=68  Identities=18%  Similarity=0.093  Sum_probs=37.0

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           13 SPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        13 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      .|.-+.+||.+.-.+...|+++.|.+.|+...+.+..-+-...|.-+ ++.-.|++..|.+-+...-+.
T Consensus        95 ~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi-~~YY~gR~~LAq~d~~~fYQ~  162 (297)
T COG4785          95 RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGI-ALYYGGRYKLAQDDLLAFYQD  162 (297)
T ss_pred             CCCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhccce-eeeecCchHhhHHHHHHHHhc
Confidence            33456667777777777777777777777666644211111222222 233446666666655555544

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.93  E-value=0.11  Score=39.54  Aligned_cols=53  Identities=8%  Similarity=-0.025  Sum_probs=27.3

Q ss_pred             hcCCcchHHHHHHHHHHcCC--CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           64 KMGRVSPGFVVLGRILRSCF--TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        64 ~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      +.|++++|.+.|+.+..+.+  +-...+...++-++.+.++++.|+..+++....
T Consensus        46 ~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~l  100 (254)
T COG4105          46 QKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRL  100 (254)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            44666666666666554321  112333444445555556666666666655554

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.81  E-value=0.093  Score=45.06  Aligned_cols=165  Identities=16%  Similarity=0.157  Sum_probs=107.1

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH----hcCChHHHHHHHHHhhhCCCCCChhhHHH
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC----KEGFVDKAKELFLKMKDENINPDVVTYTS  203 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  203 (343)
                      ++....-.|+-+.+++.+.+..+..+-.++....-.-.|...+..+.    ...+.+.|.++++.+.+.-  |+...|..
T Consensus       194 ll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~y--P~s~lfl~  271 (468)
T PF10300_consen  194 LLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRY--PNSALFLF  271 (468)
T ss_pred             HHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhC--CCcHHHHH
Confidence            44455568999999999998877543111100111122333333333    2556789999999998863  56555544


Q ss_pred             H-HHHHhccCcHHHHHHHHHHHHHcC--C-CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHH-HH
Q 040261          204 L-IRGFCYANDWNEAKCLFIEMMDQG--V-QPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD-GF  278 (343)
Q Consensus       204 l-~~~~~~~~~~~~a~~~~~~~~~~~--~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~-~~  278 (343)
                      . .+.+...|+.++|.+.++......  . +.....+--+...+.-..++++|...|..+.+.. ..+..+|.-+.- ++
T Consensus       272 ~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c~  350 (468)
T PF10300_consen  272 FEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAACL  350 (468)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHH
Confidence            3 456778899999999999766421  1 1223344556777888999999999999999864 445555554444 34


Q ss_pred             hcCCch-------HHHHHHHHHHH
Q 040261          279 CLTGRV-------NRAKELFVSME  295 (343)
Q Consensus       279 ~~~~~~-------~~a~~~~~~~~  295 (343)
                      ...|+.       ++|.++|.+..
T Consensus       351 ~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  351 LMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HhhccchhhhhhHHHHHHHHHHHH
Confidence            456666       88888887664

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.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.77  E-value=0.06  Score=43.70  Aligned_cols=96  Identities=15%  Similarity=0.070  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHH-HHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYG-ILING  312 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~  312 (343)
                      .++..+..++.+.+++..|+..-+...+.+ ++|....-.=..++...|+++.|+..|+++.+.  .|+..... .++..
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~l  334 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIKL  334 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHH
Confidence            445666777777788888888877777776 666766666677777788888888888887775  35444333 33333


Q ss_pred             HHhcCChH-HHHHHHHHHHhC
Q 040261          313 YCKNKEIE-GALSLYSEMLSK  332 (343)
Q Consensus       313 ~~~~~~~~-~a~~~~~~~~~~  332 (343)
                      -.+..+.. ...++|..|...
T Consensus       335 ~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  335 KQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHhhc
Confidence            33333333 336677777643

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.68  E-value=0.11  Score=43.96  Aligned_cols=159  Identities=14%  Similarity=0.092  Sum_probs=96.8

Q ss_pred             HHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHh
Q 040261          130 NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFC  209 (343)
Q Consensus       130 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  209 (343)
                      +...-.++++.+.+..+.-.-..       ..+..-.+.++..+.+.|.++.|+++..+-..            -.....
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~-------~i~~~~~~~i~~fL~~~G~~e~AL~~~~D~~~------------rFeLAl  329 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLP-------NIPKDQGQSIARFLEKKGYPELALQFVTDPDH------------RFELAL  329 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGG-------G--HHHHHHHHHHHHHTT-HHHHHHHSS-HHH------------HHHHHH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcc-------cCChhHHHHHHHHHHHCCCHHHHHhhcCChHH------------HhHHHH
Confidence            34455778888766665211110       11244577888888889999988887644221            233445


Q ss_pred             ccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHH
Q 040261          210 YANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKE  289 (343)
Q Consensus       210 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  289 (343)
                      +.|+++.|.++.+.      ..+...|..|.....+.|+++-|...|.+...         +..|+-.|...|+.+.-.+
T Consensus       330 ~lg~L~~A~~~a~~------~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~k  394 (443)
T PF04053_consen  330 QLGNLDIALEIAKE------LDDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSK  394 (443)
T ss_dssp             HCT-HHHHHHHCCC------CSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHH
T ss_pred             hcCCHHHHHHHHHh------cCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHH
Confidence            67888888776543      34677888888888889999888888877532         4456667778888888888


Q ss_pred             HHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHH
Q 040261          290 LFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSE  328 (343)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  328 (343)
                      +.+.....|      -++....++.-.|+.++..+++.+
T Consensus       395 l~~~a~~~~------~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  395 LAKIAEERG------DINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHHHHHHcc------CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            877777665      244555556666777777766654

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.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.65  E-value=0.062  Score=43.61  Aligned_cols=126  Identities=14%  Similarity=0.134  Sum_probs=94.1

Q ss_pred             HHHHHhcCChHHHHHHHHHhhhC-----CCC---------CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHH
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDE-----NIN---------PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVT  235 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~-----~~~---------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  235 (343)
                      ...+.+.|++..|...|++....     +.+         .-..++..+..++.+.+++.+|+......++.+ ++|...
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KA  293 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKA  293 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhH
Confidence            35678899999999888875432     111         123457778889999999999999999999885 667777


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch-HHHHHHHHHHHhC
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV-NRAKELFVSMESN  297 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~  297 (343)
                      .-.-..++...|+++.|+..|+++.+.. +-|-.+-+.|+.+-.+.... +...++|..|...
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k~~-P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALKLE-PSNKAARAELIKLKQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7778899999999999999999999974 44555555666555555444 3447788887653

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.65  E-value=0.11  Score=43.37  Aligned_cols=66  Identities=11%  Similarity=-0.085  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH---HHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA---VTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .+...++.+..+|.+.|++++|+..|++.++.++. +.   .+|..+..+|...|+.++|++.+++..+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd-~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALELNPN-PDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            35668888999999999999999999998886433 22   35888999999999999999999998875

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.62  E-value=0.098  Score=41.46  Aligned_cols=153  Identities=18%  Similarity=0.175  Sum_probs=104.3

Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhCCChh
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV----VTFNVIMNELCKNGKMD  250 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~  250 (343)
                      -.|+..+|...++++.+. .|.|...+...=.+|...|+...-...++++... ..++.    ..-..+.-++...|-++
T Consensus       115 ~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~  192 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYD  192 (491)
T ss_pred             ccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccch
Confidence            457777777788887775 4557777777778888889888888888887654 12333    33334455567889999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC---CCCccHHHHHHHHHHHHhcCChHHHHHHHH
Q 040261          251 EASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN---GCMRDVFSYGILINGYCKNKEIEGALSLYS  327 (343)
Q Consensus       251 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  327 (343)
                      +|++.-++..+.+ +.|.-...++...+.-.|++.++.++..+-...   +...-..-|-...-.+...+.++.|+++|+
T Consensus       193 dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD  271 (491)
T KOG2610|consen  193 DAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYD  271 (491)
T ss_pred             hHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHH
Confidence            9999999988876 667777777888888888999988877654321   000011122233344566688999998887


Q ss_pred             HHH
Q 040261          328 EML  330 (343)
Q Consensus       328 ~~~  330 (343)
                      .-+
T Consensus       272 ~ei  274 (491)
T KOG2610|consen  272 REI  274 (491)
T ss_pred             HHH
Confidence            543

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.62  E-value=0.15  Score=43.17  Aligned_cols=130  Identities=13%  Similarity=0.061  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC  133 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  133 (343)
                      ..+.++.-+.+.|-.+.|+++...         +   ..-.....+.|+++.|.++.++.      .+...|..|.....
T Consensus       297 ~~~~i~~fL~~~G~~e~AL~~~~D---------~---~~rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~AL  358 (443)
T PF04053_consen  297 QGQSIARFLEKKGYPELALQFVTD---------P---DHRFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEAL  358 (443)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHSS----------H---HHHHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHhhcCC---------h---HHHhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHHH
Confidence            345555555555555555444322         1   11223333445555555443321      24445555555555


Q ss_pred             hcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc
Q 040261          134 RTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND  213 (343)
Q Consensus       134 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  213 (343)
                      +.|+++.|.+.+.+..               -+..|+-.|.-.|+.+...++.+.....|-      ++....++.-.|+
T Consensus       359 ~~g~~~lAe~c~~k~~---------------d~~~L~lLy~~~g~~~~L~kl~~~a~~~~~------~n~af~~~~~lgd  417 (443)
T PF04053_consen  359 RQGNIELAEECYQKAK---------------DFSGLLLLYSSTGDREKLSKLAKIAEERGD------INIAFQAALLLGD  417 (443)
T ss_dssp             HTTBHHHHHHHHHHCT----------------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-
T ss_pred             HcCCHHHHHHHHHhhc---------------CccccHHHHHHhCCHHHHHHHHHHHHHccC------HHHHHHHHHHcCC
Confidence            5555555555555422               244444555555555555555544444331      3333334444455


Q ss_pred             HHHHHHHHH
Q 040261          214 WNEAKCLFI  222 (343)
Q Consensus       214 ~~~a~~~~~  222 (343)
                      .++..+++.
T Consensus       418 ~~~cv~lL~  426 (443)
T PF04053_consen  418 VEECVDLLI  426 (443)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555554443

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.

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.59  E-value=0.22  Score=38.15  Aligned_cols=137  Identities=8%  Similarity=-0.014  Sum_probs=106.3

Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHH-----HH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVY-----NT  273 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-----~~  273 (343)
                      ...+.++.++.-.|.+.-..+.++.+++...+.++.....+++.-.+.||.+.|...|++..+..-+.|...+     ..
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            3456677788888999999999999999876778888899999999999999999999987664334443333     33


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCC
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRP  336 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  336 (343)
                      ....|.-++++..|...+.+..... +.++...|.-.-+..-.|+...|++.++.|...-..|
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~  319 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRH  319 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCcc
Confidence            3445667788999999998888764 4466677777777777899999999999999764433

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.57  E-value=0.28  Score=39.02  Aligned_cols=227  Identities=12%  Similarity=0.091  Sum_probs=120.5

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHH-------HHHHHHhcC-ChHHHHHHHHHHHcc----CCCCCccccCC----
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTT-------LINGLCRTG-HTIVALNLFEEMANG----NGEFGVVCKPD----  162 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------l~~~~~~~~-~~~~a~~~~~~~~~~----~~~~~~~~~~~----  162 (343)
                      +.|+.+.|..++.+........++.....       +.......+ +++.|..++++..+.    +....  ..++    
T Consensus         5 ~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~--~~~~~~el   82 (278)
T PF08631_consen    5 KQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDK--LSPDGSEL   82 (278)
T ss_pred             hhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccc--cCCcHHHH
Confidence            45666666666666554321112211111       122233344 777777777665443    11000  1222    


Q ss_pred             -cchHHHHHHHHHhcCChH---HHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          163 -AITYSTITDGLCKEGFVD---KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV  238 (343)
Q Consensus       163 -~~~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  238 (343)
                       ..+...++.+|...+..+   +|..+++.+.... +-.+..+..-+..+.+.++.+++.+.+.+|...- .-....+..
T Consensus        83 r~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~  160 (278)
T PF08631_consen   83 RLSILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDS  160 (278)
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHH
Confidence             245677778888777755   5555666664443 2235556666777777899999999999999872 323344555


Q ss_pred             HHHHH---HhCCChhHHHHHHHHHHHcCCCCCHH-HHHH-HHH---HHhcCCc------hHHHHHHHHHHHhC-CCCccH
Q 040261          239 IMNEL---CKNGKMDEASRLLELMIQIGVRPDAS-VYNT-LMD---GFCLTGR------VNRAKELFVSMESN-GCMRDV  303 (343)
Q Consensus       239 l~~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~-l~~---~~~~~~~------~~~a~~~~~~~~~~-~~~~~~  303 (343)
                      ++..+   .. .....+...+..+....+.|... .... ++.   ...+.++      .+....+++.+.+. +.+.+.
T Consensus       161 ~l~~i~~l~~-~~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i~~l~~~~~~v~~~~~~~ls~  239 (278)
T PF08631_consen  161 ILHHIKQLAE-KSPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKIESLEELLSIVEHSLGKQLSA  239 (278)
T ss_pred             HHHHHHHHHh-hCcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhcCCCCH
Confidence            55444   33 33456667776666654555543 1111 111   1112211      44455555543322 222333


Q ss_pred             HHHH---HH----HHHHHhcCChHHHHHHHHHHH
Q 040261          304 FSYG---IL----INGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       304 ~~~~---~l----~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      .+-.   ++    +..+.+.++|+.|.++|+-..
T Consensus       240 ~~~~a~~~LLW~~~~~~~~~k~y~~A~~w~~~al  273 (278)
T PF08631_consen  240 EAASAIHTLLWNKGKKHYKAKNYDEAIEWYELAL  273 (278)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence            3322   22    344667899999999998544

It is also involved in sporulation [].

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

Probab=96.56  E-value=0.31  Score=39.42  Aligned_cols=111  Identities=16%  Similarity=0.232  Sum_probs=87.0

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      .+.+..+.-+...|+...|.++-++..    .|+..-|...+.+++..++|++...+...      +-++.-|..++.+|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHH
Confidence            355666777788899988888876653    37899999999999999999988876532      22457789999999


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      .+.|+..+|..+..++     ++     ..-+..|.+.|++.+|.+...+.
T Consensus       248 ~~~~~~~eA~~yI~k~-----~~-----~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKI-----PD-----EERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             HHCCCHHHHHHHHHhC-----Ch-----HHHHHHHHHCCCHHHHHHHHHHc
Confidence            9999999999988772     22     44577889999999998775544

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

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.48  E-value=0.011  Score=31.64  Aligned_cols=40  Identities=15%  Similarity=0.144  Sum_probs=23.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNIL   58 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   58 (343)
                      .++..+...|.+.|++++|.++|++..+.. +-|...+..+
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~-P~~~~a~~~L   41 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALD-PDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCCHHHHHHh
Confidence            356666677777777777777777766643 3344444433

>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=96.45  E-value=0.15  Score=34.50  Aligned_cols=65  Identities=15%  Similarity=0.256  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCC
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGC  299 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  299 (343)
                      ......+......|..++..+++..+.+.+ .+++...-.+..+|.+.|+..++.+++.+..+.|+
T Consensus        87 e~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   87 EYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            344455666666777777777777766533 56666667777777777777777777777776663

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.45  E-value=0.54  Score=41.01  Aligned_cols=201  Identities=18%  Similarity=0.204  Sum_probs=108.4

Q ss_pred             HHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCc-cHHHHHH-----HHHHHhhcCcHHHHHHHHHHH
Q 040261           40 FKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTP-DAVTFTS-----LIKGLCAESRIMEAAALFTKL  113 (343)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~-----l~~~~~~~~~~~~a~~~~~~~  113 (343)
                      ++++++.|-.|+...   +...++-.|++.+|.++|.+-   |.+. -...|.-     ...-+...|..++-..+.++-
T Consensus       623 L~~~k~rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~---G~enRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKR  696 (1081)
T KOG1538|consen  623 LEERKKRGETPNDLL---LADVFAYQGKFHEAAKLFKRS---GHENRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKR  696 (1081)
T ss_pred             HHHHHhcCCCchHHH---HHHHHHhhhhHHHHHHHHHHc---CchhhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHH
Confidence            455666776677643   445567778888888888653   2220 0111111     222333444444433333332


Q ss_pred             HhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHH------HHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHH
Q 040261          114 RAFGCKPDVFTYTTLINGLCRTGHTIVALNLFE------EMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFL  187 (343)
Q Consensus       114 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~------~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  187 (343)
                      .+-  ..+..--.+....+...|+..+|..+.-      -+.+.+...   ...+..+...+...+.+...+..|.++|.
T Consensus       697 A~W--Ar~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkl---d~~ere~l~~~a~ylk~l~~~gLAaeIF~  771 (1081)
T KOG1538|consen  697 ADW--ARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKL---DKAEREPLLLCATYLKKLDSPGLAAEIFL  771 (1081)
T ss_pred             HHH--hhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhc---chhhhhHHHHHHHHHhhccccchHHHHHH
Confidence            111  1111111234455666777777665431      111111000   12233455555555666777788888888


Q ss_pred             HhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHH-----------HHHHHHHHHHhCCChhHHHHHH
Q 040261          188 KMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVV-----------TFNVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       188 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----------~~~~l~~~~~~~~~~~~a~~~~  256 (343)
                      +|-.         ...+++.+...++|.+|..+-+...+.  .|+..           -|...-.+|.+.|+-.+|.+++
T Consensus       772 k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vL  840 (1081)
T KOG1538|consen  772 KMGD---------LKSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVL  840 (1081)
T ss_pred             Hhcc---------HHHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHH
Confidence            7754         335678888999999999988776553  33321           2333445677777777777777


Q ss_pred             HHHHHc
Q 040261          257 ELMIQI  262 (343)
Q Consensus       257 ~~~~~~  262 (343)
                      +.+...
T Consensus       841 eQLtnn  846 (1081)
T KOG1538|consen  841 EQLTNN  846 (1081)
T ss_pred             HHhhhh
Confidence            776543

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.45  E-value=0.31  Score=38.12  Aligned_cols=51  Identities=14%  Similarity=0.228  Sum_probs=22.9

Q ss_pred             HhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHH
Q 040261           28 AKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRIL   79 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   79 (343)
                      ...|++.+|..+|....... +-+...-..+..++...|+.+.|..++..+.
T Consensus       145 ~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP  195 (304)
T COG3118         145 IEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALP  195 (304)
T ss_pred             hhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCc
Confidence            34445555555554444322 1223333444445555555555555554443

>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=96.44  E-value=0.15  Score=34.47  Aligned_cols=139  Identities=14%  Similarity=0.143  Sum_probs=78.3

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      -.|..++..++..+....   .+..-++-++--....-+-+-..++++..-+..         |.          ..+|+
T Consensus        14 ldG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiF---------Di----------s~C~N   71 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIF---------DI----------SKCGN   71 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS----------G----------GG-S-
T ss_pred             HhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhc---------Cc----------hhhcc
Confidence            347777777777777665   244444545544444445555555555544332         11          23344


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHH
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLEL  258 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  258 (343)
                      .......+-.+-.     +.......+......|.-++..++...+.+.+ .+++...-.+..+|.+.|+..++.+++.+
T Consensus        72 lKrVi~C~~~~n~-----~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~  145 (161)
T PF09205_consen   72 LKRVIECYAKRNK-----LSEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKE  145 (161)
T ss_dssp             THHHHHHHHHTT--------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             hHHHHHHHHHhcc-----hHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            4444444433221     34456666777788888888888888887643 67777788888888889998888888888


Q ss_pred             HHHcCCC
Q 040261          259 MIQIGVR  265 (343)
Q Consensus       259 ~~~~~~~  265 (343)
                      +.+.|++
T Consensus       146 ACekG~k  152 (161)
T PF09205_consen  146 ACEKGLK  152 (161)
T ss_dssp             HHHTT-H
T ss_pred             HHHhchH
Confidence            8888754

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=96.39  E-value=0.18  Score=34.86  Aligned_cols=56  Identities=13%  Similarity=0.054  Sum_probs=32.0

Q ss_pred             HHhccCcHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGV--QPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ...+.|++++|.+.|+.+...-.  +-....--.++.++.+.++++.|...+++.++.
T Consensus        19 ~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL   76 (142)
T PF13512_consen   19 EALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL   76 (142)
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            34456666666666666665510  112334445566666666666666666666665

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.37  E-value=0.19  Score=38.77  Aligned_cols=97  Identities=11%  Similarity=0.116  Sum_probs=65.0

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC--CCCCHHHHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGV--QPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG--VRPDASVYNTLM  275 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~  275 (343)
                      .|+..+.. .+.|++..|...|...++...  .-....+-.|..++...|+++.|..+|..+.+.-  .+.-+..+.-|.
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            56666654 456678888888888777621  1112334457778888888888888887777642  122245666677


Q ss_pred             HHHhcCCchHHHHHHHHHHHhC
Q 040261          276 DGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       276 ~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ....+.|+.++|..+|+++.+.
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHH
Confidence            7777888888888888888776

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.36  E-value=0.29  Score=39.37  Aligned_cols=56  Identities=5%  Similarity=-0.107  Sum_probs=25.4

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCC-----CCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGV-----QPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      +..++...+.++++++.|+...+...     -....++-.|...|.+..|+++|..+..++
T Consensus       128 ~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA  188 (518)
T KOG1941|consen  128 MGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKA  188 (518)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhH
Confidence            33444444555555555554443210     111234445555555555555555444443

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.35  E-value=0.36  Score=37.77  Aligned_cols=145  Identities=14%  Similarity=0.096  Sum_probs=79.0

Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHH
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGF  208 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  208 (343)
                      .......|++.+|...|+......       +.+...-..+..+|...|+.+.|..++..+....-.........-+..+
T Consensus       141 ~~~~~~~e~~~~a~~~~~~al~~~-------~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll  213 (304)
T COG3118         141 AKELIEAEDFGEAAPLLKQALQAA-------PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELL  213 (304)
T ss_pred             hhhhhhccchhhHHHHHHHHHHhC-------cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHH
Confidence            344566778888888888777764       3445666777778888888888888887765542222222222223333


Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC-CCCHHHHHHHHHHHhcCC
Q 040261          209 CYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV-RPDASVYNTLMDGFCLTG  282 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  282 (343)
                      .+.....+...+-.+.-..  +-|...--.+...+...|+.+.|...+-.+.+.+. --|...-..++..+.--|
T Consensus       214 ~qaa~~~~~~~l~~~~aad--Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g  286 (304)
T COG3118         214 EQAAATPEIQDLQRRLAAD--PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFG  286 (304)
T ss_pred             HHHhcCCCHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcC
Confidence            3333333333333333321  22444444566666667777777666655554321 223344455555554444

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=96.33  E-value=0.2  Score=34.65  Aligned_cols=88  Identities=13%  Similarity=0.083  Sum_probs=61.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCC--CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGL--FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      .+...+..-.....+.|++++|.+.|+.+...-.  +-...+-..++.++.+.++++.|...+++.++..+......|..
T Consensus         8 ~~~~~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~   87 (142)
T PF13512_consen    8 KSPQELYQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAY   87 (142)
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            3444555566667788999999999988876421  22345667788889999999999999999988765544455666


Q ss_pred             HHHHHhhcCc
Q 040261           93 LIKGLCAESR  102 (343)
Q Consensus        93 l~~~~~~~~~  102 (343)
                      .+.+++....
T Consensus        88 Y~~gL~~~~~   97 (142)
T PF13512_consen   88 YMRGLSYYEQ   97 (142)
T ss_pred             HHHHHHHHHH
Confidence            6666554433

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.26  E-value=0.14  Score=39.37  Aligned_cols=99  Identities=12%  Similarity=0.126  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC--CCChhhH
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENI--NPDVVTY  201 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~  201 (343)
                      .|+.-+.. .+.|++..|...|....+..+..    .-....+-.|..++...|+++.|..+|..+.+.-.  +--+..+
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s----~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdal  218 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNS----TYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDAL  218 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCC----cccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHH
Confidence            34444433 33455666666666666654221    12234455556666666666666666666554311  1112344


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      --+..+..+.|+.++|...|+++.+.
T Consensus       219 lKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         219 LKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            44555555666666666666666554

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.22  E-value=0.36  Score=36.59  Aligned_cols=207  Identities=14%  Similarity=0.102  Sum_probs=114.3

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 040261           53 YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGL  132 (343)
Q Consensus        53 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  132 (343)
                      ..|.....+|....++++|...+.+..+. .+.+...|+ ..      ..+++|.-+.+++...  .--...|......|
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfh-AA------KayEqaamLake~~kl--sEvvdl~eKAs~lY  101 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFH-AA------KAYEQAAMLAKELSKL--SEVVDLYEKASELY  101 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHH-HH------HHHHHHHHHHHHHHHh--HHHHHHHHHHHHHH
Confidence            45777777888888999988877776642 232333332 11      2345555555555543  11233455666778


Q ss_pred             HhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC---CC--CCChhhHHHHHHH
Q 040261          133 CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE---NI--NPDVVTYTSLIRG  207 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~--~~~~~~~~~l~~~  207 (343)
                      ...|.++.|-..+++.-+.                      ...-++++|++++++...-   +-  .--...+..+-+.
T Consensus       102 ~E~GspdtAAmaleKAak~----------------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~  159 (308)
T KOG1585|consen  102 VECGSPDTAAMALEKAAKA----------------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRV  159 (308)
T ss_pred             HHhCCcchHHHHHHHHHHH----------------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhH
Confidence            8888887777766665432                      1223445555555443221   00  0012233444455


Q ss_pred             HhccCcHHHHHHHHHHHHH----cCCCCCH-HHHHHHHHHHHhCCChhHHHHHHHHHHHcCC---CCCHHHHHHHHHHHh
Q 040261          208 FCYANDWNEAKCLFIEMMD----QGVQPNV-VTFNVIMNELCKNGKMDEASRLLELMIQIGV---RPDASVYNTLMDGFC  279 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~----~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~  279 (343)
                      +++...+.+|-..+.+-..    -.-.++. ..|-..+-.+.-..|+..|.+.++.-.+.+-   +.+..+...|+.+| 
T Consensus       160 lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-  238 (308)
T KOG1585|consen  160 LVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-  238 (308)
T ss_pred             hhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-
Confidence            6666666666554433211    1112222 3344555566667788888888887655421   33456777777665 


Q ss_pred             cCCchHHHHHHHH
Q 040261          280 LTGRVNRAKELFV  292 (343)
Q Consensus       280 ~~~~~~~a~~~~~  292 (343)
                      ..|+.+++..++.
T Consensus       239 d~gD~E~~~kvl~  251 (308)
T KOG1585|consen  239 DEGDIEEIKKVLS  251 (308)
T ss_pred             ccCCHHHHHHHHc
Confidence            4677777776653

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.15  E-value=0.4  Score=36.41  Aligned_cols=206  Identities=12%  Similarity=0.025  Sum_probs=115.0

Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      ..|.....+|-...++++|...+.+..+- ...+...|       .....++.|.-+.+++...        +.-...|.
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslf-------hAAKayEqaamLake~~kl--------sEvvdl~e   95 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLF-------HAAKAYEQAAMLAKELSKL--------SEVVDLYE   95 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHH-------HHHHHHHHHHHHHHHHHHh--------HHHHHHHH
Confidence            34555566677778888887776665531 11111111       1223344555555555442        12234555


Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---C--CCCCHHHHHHHHHH
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---G--VQPNVVTFNVIMNE  242 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--~~~~~~~~~~l~~~  242 (343)
                      .-...|..+|.++.|-..+++.-+.                ..+-++++|+.++++....   +  ..--...+..+.+.
T Consensus        96 KAs~lY~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~  159 (308)
T KOG1585|consen   96 KASELYVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRV  159 (308)
T ss_pred             HHHHHHHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhH
Confidence            6667788888888888888775432                1223344455554443321   1  01112234445556


Q ss_pred             HHhCCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHhcCCchHHHHHHHHHHHhCC---CCccHHHHHHHHHHHH
Q 040261          243 LCKNGKMDEASRLLELMIQI----GVRPD-ASVYNTLMDGFCLTGRVNRAKELFVSMESNG---CMRDVFSYGILINGYC  314 (343)
Q Consensus       243 ~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~  314 (343)
                      +.+...+++|-..+.+-...    .--++ ...|...|-.+....++..|.+.++.-.+.+   -+-+..+...|+.+|-
T Consensus       160 lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd  239 (308)
T KOG1585|consen  160 LVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD  239 (308)
T ss_pred             hhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc
Confidence            66777777766555443221    11122 2345666667778889999999998855432   2336678888888874


Q ss_pred             hcCChHHHHHHH
Q 040261          315 KNKEIEGALSLY  326 (343)
Q Consensus       315 ~~~~~~~a~~~~  326 (343)
                       .|+.+++.+++
T Consensus       240 -~gD~E~~~kvl  250 (308)
T KOG1585|consen  240 -EGDIEEIKKVL  250 (308)
T ss_pred             -cCCHHHHHHHH
Confidence             47878776654

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.09  E-value=0.54  Score=37.40  Aligned_cols=18  Identities=11%  Similarity=0.204  Sum_probs=13.5

Q ss_pred             HhcCChhHHHHHHHHhHh
Q 040261           28 AKNKHYDTVLSLFKRLNS   45 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~   45 (343)
                      .+.|+.+.|..++.+...
T Consensus         4 ~~~~~~~~A~~~~~K~~~   21 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKD   21 (278)
T ss_pred             hhhCCHHHHHHHHHHhhh
Confidence            467888888888877754

It is also involved in sporulation [].

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

Probab=95.98  E-value=0.086  Score=40.70  Aligned_cols=105  Identities=20%  Similarity=0.226  Sum_probs=59.6

Q ss_pred             CChhhHHHHHHHHHhc-----CChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           15 PPVCSFNILFGCLAKN-----KHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      .+-.+|-..+..+...     +..+-....++.|.+.|+..|..+|+.|++.+-+-.-                .|. ..
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkf----------------iP~-nv  127 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKF----------------IPQ-NV  127 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCccccc----------------ccH-HH
Confidence            3455566666555432     4455556666677777777777777777766543211                111 01


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCh
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT  138 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  138 (343)
                      +....--|-  .+-+-+++++++|...|+.||..+-..+++++.+.+..
T Consensus       128 fQ~~F~HYP--~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  128 FQKVFLHYP--QQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             HHHHHhhCc--hhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence            111111111  12244677777888788777877777777777776653

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

Probab=95.96  E-value=0.14  Score=40.04  Aligned_cols=77  Identities=18%  Similarity=0.252  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh-----CCCCccHHHHHHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES-----NGCMRDVFSYGIL  309 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~l  309 (343)
                      ++..++..+...|+.+.+...++++.... +-+...|..++.+|.+.|+...|...|+.+.+     .|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            34445555555555555555555555554 44555556666666666666666555555443     3555555554444


Q ss_pred             HHH
Q 040261          310 ING  312 (343)
Q Consensus       310 ~~~  312 (343)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            443

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

Probab=95.96  E-value=0.12  Score=39.94  Aligned_cols=34  Identities=29%  Similarity=0.337  Sum_probs=23.3

Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          250 DEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      +-+++++++|..+|+-||..+-..|+.+|.+.+-
T Consensus       140 ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  140 NCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             hHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            3466777777777777777777777777766654

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.95  E-value=0.044  Score=29.25  Aligned_cols=23  Identities=30%  Similarity=0.426  Sum_probs=9.1

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHH
Q 040261          239 IMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      +..+|...|++++|.++++++++
T Consensus         7 la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    7 LARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            33333344444444444444333

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.94  E-value=1.1  Score=39.67  Aligned_cols=180  Identities=14%  Similarity=0.069  Sum_probs=107.9

Q ss_pred             hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHH-----HHhcCChHHHHHHHHHhhh-------CCCCCChhhHHHHH
Q 040261          138 TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDG-----LCKEGFVDKAKELFLKMKD-------ENINPDVVTYTSLI  205 (343)
Q Consensus       138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-----~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~l~  205 (343)
                      ...+.++++.....+         +...-..+..+     +....|.+.|+.+|+.+.+       .+   .......+.
T Consensus       228 ~~~a~~~~~~~a~~g---------~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg  295 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---------HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLG  295 (552)
T ss_pred             hhHHHHHHHHHHhhc---------chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHH
Confidence            567888888887766         22222222222     4467789999999998866       44   334566677


Q ss_pred             HHHhccC-----cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          206 RGFCYAN-----DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK-NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       206 ~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      .+|.+..     +.+.|..++....+.| .|+....-..+..... ..+...|..+|..+.+.|. +....+..++....
T Consensus       296 ~~Y~~g~~~~~~d~~~A~~~~~~aA~~g-~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~-~~A~~~la~~y~~G  373 (552)
T KOG1550|consen  296 RLYLQGLGVEKIDYEKALKLYTKAAELG-NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGH-ILAIYRLALCYELG  373 (552)
T ss_pred             HHHhcCCCCccccHHHHHHHHHHHHhcC-CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCC-hHHHHHHHHHHHhC
Confidence            7776643     6788999999988887 4554433222222222 2467899999999999883 33322222222111


Q ss_pred             --cCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          280 --LTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       280 --~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                        ...+...|..++.+..+.| .|....-...+..+.. ++++.+.-.+..+...|
T Consensus       374 ~gv~r~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  374 LGVERNLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             CCcCCCHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence              2347889999999999887 3322222222233333 66666665555554443

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.92  E-value=0.51  Score=37.65  Aligned_cols=153  Identities=12%  Similarity=0.071  Sum_probs=95.8

Q ss_pred             HhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhcCCh
Q 040261           63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV----FTYTTLINGLCRTGHT  138 (343)
Q Consensus        63 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~  138 (343)
                      .-.|+..+|-..++++++. .+.|...+...=+++...|+...-...++++... ..++.    ..-..+.-++...|-+
T Consensus       114 ~~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             hccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccc
Confidence            3456777777777777765 3446666666667777778877777777777654 12222    2223344456678888


Q ss_pred             HHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC---CCCCChhhHHHHHHHHhccCcHH
Q 040261          139 IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE---NINPDVVTYTSLIRGFCYANDWN  215 (343)
Q Consensus       139 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~  215 (343)
                      ++|.+.-++..+.+       +.|..+..+....+...|+..++.+...+-...   +.-.-.+-|-...-.+...+.++
T Consensus       192 ~dAEk~A~ralqiN-------~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye  264 (491)
T KOG2610|consen  192 DDAEKQADRALQIN-------RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYE  264 (491)
T ss_pred             hhHHHHHHhhccCC-------CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchh
Confidence            88888888877764       445666667777777788888888776654321   10011122333344556667888


Q ss_pred             HHHHHHHHH
Q 040261          216 EAKCLFIEM  224 (343)
Q Consensus       216 ~a~~~~~~~  224 (343)
                      .|+++|++-
T Consensus       265 ~aleIyD~e  273 (491)
T KOG2610|consen  265 KALEIYDRE  273 (491)
T ss_pred             HHHHHHHHH
Confidence            888888653

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.88  E-value=0.31  Score=32.94  Aligned_cols=93  Identities=17%  Similarity=0.052  Sum_probs=63.5

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHH---HHHHHHHHHhhc
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAV---TFTSLIKGLCAE  100 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~  100 (343)
                      ..++...|+.+.|++.|.+.+..- +.....||.-..++.-.|+.++|++-+++.++..-.....   .|..-...|...
T Consensus        50 ~valaE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~  128 (175)
T KOG4555|consen   50 AIALAEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLL  128 (175)
T ss_pred             HHHHHhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHh
Confidence            455667788888888888776643 4466788888888888888888888888777643222222   233334456667


Q ss_pred             CcHHHHHHHHHHHHhcC
Q 040261          101 SRIMEAAALFTKLRAFG  117 (343)
Q Consensus       101 ~~~~~a~~~~~~~~~~~  117 (343)
                      |+-+.|..-|+..-+.|
T Consensus       129 g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  129 GNDDAARADFEAAAQLG  145 (175)
T ss_pred             CchHHHHHhHHHHHHhC
Confidence            77788877777776665

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=95.85  E-value=0.23  Score=36.24  Aligned_cols=100  Identities=13%  Similarity=0.111  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc--HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH---
Q 040261           53 YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD--AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT---  127 (343)
Q Consensus        53 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---  127 (343)
                      ..+..+...|.+.|+.+.|++.|.++......+.  ...+-.+++.....+++..+...+.+....--.+.......   
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            3677888889999999999999999887543332  45667788888888999888888777654321211111111   


Q ss_pred             HH--HHHHhcCChHHHHHHHHHHHccC
Q 040261          128 LI--NGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       128 l~--~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ..  -.+...+++..|-+.|-......
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~~t~  143 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSLSTF  143 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccCcCC
Confidence            11  12345778888888877765443

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.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.82  E-value=0.55  Score=37.91  Aligned_cols=237  Identities=11%  Similarity=0.036  Sum_probs=140.8

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCC--CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc--CCCc---cHHHHHHHHHH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIG--LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS--CFTP---DAVTFTSLIKG   96 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~---~~~~~~~l~~~   96 (343)
                      ..-+....+..+|+..|.+-...-  ...-..++..+..+.++.|.+++++..--.-++.  ..+.   --..|..+.++
T Consensus        13 g~~Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~   92 (518)
T KOG1941|consen   13 GLQLYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARS   92 (518)
T ss_pred             HHhHhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334556778888888887755421  1112346777788888888887765442221110  0111   12345555666


Q ss_pred             HhhcCcHHHHHHHHHHHHhc-CCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHH
Q 040261           97 LCAESRIMEAAALFTKLRAF-GCKP---DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDG  172 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  172 (343)
                      +-+..++.+++.+-..-... |..|   .-.....+..+....+.++++++.|+...+.....+- ......++..+...
T Consensus        93 ~e~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D-~~LElqvcv~Lgsl  171 (518)
T KOG1941|consen   93 NEKLCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDD-AMLELQVCVSLGSL  171 (518)
T ss_pred             HHHHHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCC-ceeeeehhhhHHHH
Confidence            66666666666665554432 2222   1123445667777788899999999887654321110 12234678899999


Q ss_pred             HHhcCChHHHHHHHHHhhh----CCCCCChhhH-----HHHHHHHhccCcHHHHHHHHHHHHH----cCCCCC-HHHHHH
Q 040261          173 LCKEGFVDKAKELFLKMKD----ENINPDVVTY-----TSLIRGFCYANDWNEAKCLFIEMMD----QGVQPN-VVTFNV  238 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~-----~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~-~~~~~~  238 (343)
                      |.+..|+++|.-+..+..+    .++..-..-|     ..+.-++...|....|.+.-++..+    .|-.+. ......
T Consensus       172 f~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~  251 (518)
T KOG1941|consen  172 FAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLC  251 (518)
T ss_pred             HHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHH
Confidence            9999999999877666533    2222111122     2334456677887777777766554    343322 344556


Q ss_pred             HHHHHHhCCChhHHHHHHHHHHH
Q 040261          239 IMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      +...|...|+.+.|..-|+.+..
T Consensus       252 ~aDIyR~~gd~e~af~rYe~Am~  274 (518)
T KOG1941|consen  252 FADIYRSRGDLERAFRRYEQAMG  274 (518)
T ss_pred             HHHHHHhcccHhHHHHHHHHHHH
Confidence            77888899999998888876543

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.76  E-value=0.36  Score=32.68  Aligned_cols=92  Identities=17%  Similarity=0.131  Sum_probs=72.2

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCH---HHHHHHHHHHhcCC
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDA---SVYNTLMDGFCLTG  282 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~  282 (343)
                      -+....|+.+.|++.|.+.+.. .+-....||.-.+++.-.|+.++|+.-+++..+..-....   ..|..-...|...|
T Consensus        51 valaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g  129 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhC
Confidence            4667889999999999998876 3556888999999999999999999999998886322222   23444445677889


Q ss_pred             chHHHHHHHHHHHhCC
Q 040261          283 RVNRAKELFVSMESNG  298 (343)
Q Consensus       283 ~~~~a~~~~~~~~~~~  298 (343)
                      +-+.|..-|+...+.|
T Consensus       130 ~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLG  145 (175)
T ss_pred             chHHHHHhHHHHHHhC
Confidence            9999999999998877

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=95.74  E-value=0.66  Score=35.60  Aligned_cols=187  Identities=16%  Similarity=0.125  Sum_probs=101.1

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGC--KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI  164 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  164 (343)
                      ...|+.-+. -.+.|++++|.+.|+.+....+  +-...+...++.++.+.++++.|...+++.....+.     .| ..
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 SELYNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPT-----HP-NA  107 (254)
T ss_pred             HHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCC-----CC-Ch
Confidence            344444443 3477899999999999887632  123445666777888899999999999998887631     22 23


Q ss_pred             hHHHHHHHHHh-------cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH
Q 040261          165 TYSTITDGLCK-------EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN  237 (343)
Q Consensus       165 ~~~~l~~~~~~-------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  237 (343)
                      .|...+.+.+.       ..|...+...+..+.            .++.-|-...-...|..-+..+...   . ...=.
T Consensus       108 dY~~YlkgLs~~~~i~~~~rDq~~~~~A~~~f~------------~~i~ryPnS~Ya~dA~~~i~~~~d~---L-A~~Em  171 (254)
T COG4105         108 DYAYYLKGLSYFFQIDDVTRDQSAARAAFAAFK------------ELVQRYPNSRYAPDAKARIVKLNDA---L-AGHEM  171 (254)
T ss_pred             hHHHHHHHHHHhccCCccccCHHHHHHHHHHHH------------HHHHHCCCCcchhhHHHHHHHHHHH---H-HHHHH
Confidence            44444444431       122222222222221            1222222222222222222222111   0 00112


Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHHcCCCC---CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          238 VIMNELCKNGKMDEASRLLELMIQIGVRP---DASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       238 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+.+.|.+.|.+..|..-++++++. .+-   ....+-.+..+|...|-.++|.+.-.-+...
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            3556677778887777777777775 121   2234555666777777777777766655544

>PRK11906 transcriptional regulator; Provisional

Probab=95.73  E-value=1.1  Score=37.83  Aligned_cols=81  Identities=9%  Similarity=-0.078  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261           70 PGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMA  149 (343)
Q Consensus        70 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  149 (343)
                      +|.+..++..+.+ +.|+.....+..+....++++.|...|++....++. ...+|....-.+.-.|+.++|.+.+++..
T Consensus       322 ~a~~~A~rAveld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn-~A~~~~~~~~~~~~~G~~~~a~~~i~~al  399 (458)
T PRK11906        322 KALELLDYVSDIT-TVDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTD-IASLYYYRALVHFHNEKIEEARICIDKSL  399 (458)
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            4455555555544 225555555555555556666677777766665322 33344444444555666777777666655


Q ss_pred             ccC
Q 040261          150 NGN  152 (343)
Q Consensus       150 ~~~  152 (343)
                      +..
T Consensus       400 rLs  402 (458)
T PRK11906        400 QLE  402 (458)
T ss_pred             ccC
Confidence            543

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.71  E-value=1  Score=37.61  Aligned_cols=133  Identities=14%  Similarity=0.143  Sum_probs=82.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhH
Q 040261          122 VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTY  201 (343)
Q Consensus       122 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  201 (343)
                      ..+|...++...+..-.+.|..+|-++.+.+-     ..+++..+++++..++ .|+..-|..+|+--... .+.+..--
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~-----~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~-f~d~~~y~  469 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGI-----VGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK-FPDSTLYK  469 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCC-----CCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh-CCCchHHH
Confidence            34556666666677777777777777776652     3456667777776554 46677777777664433 12222223


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMDQGVQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      +-.+..+...++-+.|..+|+...++ +..+  ...|..++..-..-|+...+..+=+++.+.
T Consensus       470 ~kyl~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         470 EKYLLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHHHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH
Confidence            34455566677777777777755543 2222  456777777777777777777666666553

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.63  E-value=1.2  Score=37.79  Aligned_cols=165  Identities=11%  Similarity=0.120  Sum_probs=86.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCCCCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLY-TYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE  100 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  100 (343)
                      .+|....+..+.+.-+++-.+..+  +.|+-. .|..|..  -......++.+++++..+.|-.    .+.   .    .
T Consensus       173 ~IMq~AWRERnp~aRIkaA~eALe--i~pdCAdAYILLAE--EeA~Ti~Eae~l~rqAvkAgE~----~lg---~----s  237 (539)
T PF04184_consen  173 EIMQKAWRERNPQARIKAAKEALE--INPDCADAYILLAE--EEASTIVEAEELLRQAVKAGEA----SLG---K----S  237 (539)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHH--hhhhhhHHHhhccc--ccccCHHHHHHHHHHHHHHHHH----hhc---h----h
Confidence            344444555566655555555555  234432 3332222  2234466777777777654310    110   0    0


Q ss_pred             CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH
Q 040261          101 SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD  180 (343)
Q Consensus       101 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  180 (343)
                      ...+..-..++........+-..+-..+..++-+.|+.++|.+.++++.+..+     ......+...|+.++...+.+.
T Consensus       238 ~~~~~~g~~~e~~~~Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLlke~p-----~~~~l~IrenLie~LLelq~Ya  312 (539)
T PF04184_consen  238 QFLQHHGHFWEAWHRRDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLLKEFP-----NLDNLNIRENLIEALLELQAYA  312 (539)
T ss_pred             hhhhcccchhhhhhccccchhhhhHHHHHHHHHHhCChHHHHHHHHHHHhhCC-----ccchhhHHHHHHHHHHhcCCHH
Confidence            00000001112222222222233334566677788888888888888876541     1123446677888888888888


Q ss_pred             HHHHHHHHhhhCCCCC-ChhhHHHHHH
Q 040261          181 KAKELFLKMKDENINP-DVVTYTSLIR  206 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~-~~~~~~~l~~  206 (343)
                      ++..++.+..+...+. -...|+..+-
T Consensus       313 d~q~lL~kYdDi~lpkSAti~YTaALL  339 (539)
T PF04184_consen  313 DVQALLAKYDDISLPKSATICYTAALL  339 (539)
T ss_pred             HHHHHHHHhccccCCchHHHHHHHHHH
Confidence            8888888875443222 2345665543

The molecular function of this protein is uncertain.

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.59  E-value=1.6  Score=39.54  Aligned_cols=178  Identities=16%  Similarity=0.131  Sum_probs=109.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH--HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL--YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      ...-+..+.+..-++-|+.+-+.   .+..++.  ........-+.+.|++++|...|-+.+.. ++|.     .++.-|
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk~---~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kf  407 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAKS---QHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKF  407 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHh---cCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHh
Confidence            44556677777777777777543   2222222  23333445566789999998887666543 2332     255556


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      ....+..+--.+++.+.+.|.. +...-..|+.+|.+.++.++-.++.+... .+.     .   ..-....+..+.+.+
T Consensus       408 Ldaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~-----~---~fd~e~al~Ilr~sn  477 (933)
T KOG2114|consen  408 LDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGE-----W---FFDVETALEILRKSN  477 (933)
T ss_pred             cCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccc-----e---eeeHHHHHHHHHHhC
Confidence            6677788888889999998877 66667789999999999988777766644 210     0   123455566666666


Q ss_pred             ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHH
Q 040261          178 FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEM  224 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  224 (343)
                      -.++|..+-.+...     .......++   -..+++++|++.+..+
T Consensus       478 yl~~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  478 YLDEAELLATKFKK-----HEWVLDILL---EDLHNYEEALRYISSL  516 (933)
T ss_pred             hHHHHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcC
Confidence            66666655544332     222233333   2446677776666543

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

Probab=95.56  E-value=0.25  Score=38.68  Aligned_cols=80  Identities=16%  Similarity=0.202  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHh-----cCCCCCHHHHH
Q 040261           52 LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRA-----FGCKPDVFTYT  126 (343)
Q Consensus        52 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~  126 (343)
                      ..++..++..+...|+++.+.+.++++.... +-+...|..++.+|.+.|+...|+..|+.+.+     .|+.|...+..
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            5678888888999999999999999998875 44788899999999999999999999888765     58888888877


Q ss_pred             HHHHHH
Q 040261          127 TLINGL  132 (343)
Q Consensus       127 ~l~~~~  132 (343)
                      ......
T Consensus       232 ~y~~~~  237 (280)
T COG3629         232 LYEEIL  237 (280)
T ss_pred             HHHHHh
Confidence            766663

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.52  E-value=1.7  Score=38.77  Aligned_cols=88  Identities=15%  Similarity=0.089  Sum_probs=54.1

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHH---cCCCccHHHHHHHHHHHh
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILR---SCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~   98 (343)
                      .+++-+...+.+..|+++-..+...-... ..+|.....-+.+..+... .++++.+.+   ... .+...|..+.+-..
T Consensus       442 ~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~Wa~~kI~~~d~~d-~~vld~I~~kls~~~-~~~iSy~~iA~~Ay  518 (829)
T KOG2280|consen  442 VVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMD-EEVLDKIDEKLSAKL-TPGISYAAIARRAY  518 (829)
T ss_pred             hhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccc-hHHHHHHHHHhcccC-CCceeHHHHHHHHH
Confidence            35777788889999999887765322122 5677777777776643221 233333332   212 23455667777777


Q ss_pred             hcCcHHHHHHHHHH
Q 040261           99 AESRIMEAAALFTK  112 (343)
Q Consensus        99 ~~~~~~~a~~~~~~  112 (343)
                      ..|+.+-|..+++.
T Consensus       519 ~~GR~~LA~kLle~  532 (829)
T KOG2280|consen  519 QEGRFELARKLLEL  532 (829)
T ss_pred             hcCcHHHHHHHHhc
Confidence            88988888877754

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.50  E-value=0.53  Score=32.87  Aligned_cols=84  Identities=12%  Similarity=0.028  Sum_probs=35.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG  247 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  247 (343)
                      .++..+...+.......+++.+...+ ..+....+.++..|++.+ .......+..      ..+......++..|.+.+
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~   83 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAK   83 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcC
Confidence            34444444444555555555444443 134444444554444332 1222222221      112222333455555555


Q ss_pred             ChhHHHHHHHHH
Q 040261          248 KMDEASRLLELM  259 (343)
Q Consensus       248 ~~~~a~~~~~~~  259 (343)
                      -++++..++.++
T Consensus        84 l~~~~~~l~~k~   95 (140)
T smart00299       84 LYEEAVELYKKD   95 (140)
T ss_pred             cHHHHHHHHHhh
Confidence            555555555443

>PRK11906 transcriptional regulator; Provisional

Probab=95.42  E-value=1.4  Score=37.17  Aligned_cols=159  Identities=13%  Similarity=0.045  Sum_probs=104.6

Q ss_pred             chH--HHHHHHHHhc-----CChHHHHHHHHHhhh-CCCCCC-hhhHHHHHHHHhc---------cCcHHHHHHHHHHHH
Q 040261          164 ITY--STITDGLCKE-----GFVDKAKELFLKMKD-ENINPD-VVTYTSLIRGFCY---------ANDWNEAKCLFIEMM  225 (343)
Q Consensus       164 ~~~--~~l~~~~~~~-----~~~~~a~~~~~~~~~-~~~~~~-~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~  225 (343)
                      ..|  ..++.+....     ...+.|..+|.+... +...|+ ...|..+..++..         .....+|.++.+...
T Consensus       252 ~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAv  331 (458)
T PRK11906        252 NHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVS  331 (458)
T ss_pred             cchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHH
Confidence            456  5555554442     235678888988872 223344 4445444443322         234567778888888


Q ss_pred             HcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHH-
Q 040261          226 DQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVF-  304 (343)
Q Consensus       226 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-  304 (343)
                      +.+ +-|......+..+..-.++++.|..+|++....+ +-...+|........-.|+.++|.+.+++..+.  .|... 
T Consensus       332 eld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~-Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrL--sP~~~~  407 (458)
T PRK11906        332 DIT-TVDGKILAIMGLITGLSGQAKVSHILFEQAKIHS-TDIASLYYYRALVHFHNEKIEEARICIDKSLQL--EPRRRK  407 (458)
T ss_pred             hcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHhcc--CchhhH
Confidence            875 5677888888887788889999999999999875 444566666666777899999999999997775  34332 


Q ss_pred             --HHHHHHHHHHhcCChHHHHHHHH
Q 040261          305 --SYGILINGYCKNKEIEGALSLYS  327 (343)
Q Consensus       305 --~~~~l~~~~~~~~~~~~a~~~~~  327 (343)
                        .....++.|..+ ..++|+++|-
T Consensus       408 ~~~~~~~~~~~~~~-~~~~~~~~~~  431 (458)
T PRK11906        408 AVVIKECVDMYVPN-PLKNNIKLYY  431 (458)
T ss_pred             HHHHHHHHHHHcCC-chhhhHHHHh
Confidence              222233355554 4566766654

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=95.33  E-value=1.6  Score=37.23  Aligned_cols=183  Identities=14%  Similarity=0.112  Sum_probs=117.5

Q ss_pred             cCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           10 MHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        10 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      -...|.+....-+++..+.++...+-...+..+|...|  .+-..|..++.+|... ..++-..+++++.+..+. |++.
T Consensus        59 ~s~~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~  134 (711)
T COG1747          59 LSKQLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVI  134 (711)
T ss_pred             hhhccccchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHH
Confidence            33445667777788888888888888888888888865  5667788888888887 557778888888876543 4444


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKP-----DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI  164 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  164 (343)
                      -..+...| ..++.+.+..+|.++...=++.     -...|..+....  ..+.+..+.+...+....+     ...-..
T Consensus       135 ~ReLa~~y-Ekik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg-----~~~~~V  206 (711)
T COG1747         135 GRELADKY-EKIKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLG-----EGRGSV  206 (711)
T ss_pred             HHHHHHHH-HHhchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhc-----cchHHH
Confidence            44444444 4477788888887776542210     112344443321  3466666776666665443     223345


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHH
Q 040261          165 TYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLI  205 (343)
Q Consensus       165 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  205 (343)
                      .+.-+-.-|....++++|++++..+.+.+-+ |...-..++
T Consensus       207 l~qdv~~~Ys~~eN~~eai~Ilk~il~~d~k-~~~ar~~~i  246 (711)
T COG1747         207 LMQDVYKKYSENENWTEAIRILKHILEHDEK-DVWARKEII  246 (711)
T ss_pred             HHHHHHHHhccccCHHHHHHHHHHHhhhcch-hhhHHHHHH
Confidence            5566667788888999999999877765422 444433443

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=95.28  E-value=0.68  Score=32.79  Aligned_cols=112  Identities=15%  Similarity=0.074  Sum_probs=67.2

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN-VIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV  284 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  284 (343)
                      ..-.+.++.+++..++..+.-.  .|...... .-...+...|++.+|..+|+++.+..  |....-..|+..|....+-
T Consensus        18 ~~al~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kALlA~CL~~~~D   93 (160)
T PF09613_consen   18 SVALRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA--PGFPYAKALLALCLYALGD   93 (160)
T ss_pred             HHHHccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC--CCChHHHHHHHHHHHHcCC
Confidence            4446778899999999888775  55543333 23455678899999999999987653  4444445555555544443


Q ss_pred             HHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHH
Q 040261          285 NRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       285 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                      ..-...-+++.+.+.  |+.+ ..+++.+....+...|..
T Consensus        94 ~~Wr~~A~evle~~~--d~~a-~~Lv~~Ll~~~~~~~a~~  130 (160)
T PF09613_consen   94 PSWRRYADEVLESGA--DPDA-RALVRALLARADLEPAHE  130 (160)
T ss_pred             hHHHHHHHHHHhcCC--ChHH-HHHHHHHHHhccccchhh
Confidence            344444555666542  3333 345555555555555444

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

Probab=95.27  E-value=0.056  Score=27.32  Aligned_cols=26  Identities=23%  Similarity=0.304  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      +|..|...|.+.|++++|+++|++.+
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            46678888888888888888888855

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=95.19  E-value=0.78  Score=32.94  Aligned_cols=137  Identities=12%  Similarity=0.140  Sum_probs=88.8

Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      .+.++.+.+.+++|+...+..++..+.+.|++....    .+...++-+|.......+-.+.  +....+.++--.|...
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~----qllq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLH----QLLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHH----HHHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHH
Confidence            455666777889999999999999999999866544    4455566677665554443332  2334444444444332


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      =    ...+..+++.+...|++-+|.++.+.....    +......++.+-...+|..--..+++-...++
T Consensus        88 L----~~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~n  150 (167)
T PF07035_consen   88 L----GTAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEERN  150 (167)
T ss_pred             h----hhhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence            0    114556777889999999999998876332    22223456777778888777666666665543

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.19  E-value=0.77  Score=32.90  Aligned_cols=133  Identities=20%  Similarity=0.204  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcc-h
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVF-TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI-T  165 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~  165 (343)
                      ..|...+.. .+.+..++|+.-|..+.+.|...-+. ............|+...|...|+++-....      .|... -
T Consensus        60 d~flaAL~l-A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~------~P~~~rd  132 (221)
T COG4649          60 DAFLAALKL-AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTS------IPQIGRD  132 (221)
T ss_pred             HHHHHHHHH-HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCC------CcchhhH
Confidence            334433332 34455566666666665554332111 112223344555666666666666555431      11111 1


Q ss_pred             HHH--HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          166 YST--ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       166 ~~~--l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      ..-  -...+...|.++......+.+...+-+.....-..|.-+-.+.|++..|...|..+...
T Consensus       133 ~ARlraa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~D  196 (221)
T COG4649         133 LARLRAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAND  196 (221)
T ss_pred             HHHHHHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHcc
Confidence            111  11223455556666555555554443333344445555555666666666666655543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.18  E-value=1.3  Score=35.48  Aligned_cols=136  Identities=13%  Similarity=0.180  Sum_probs=83.7

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh--cC----ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCR--TG----HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE  176 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  176 (343)
                      +++.+.+++.|.+.|...+..++.+..-....  ..    ....+..+++.|.+..+..   ..++...+..++..  ..
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fL---Ts~~D~~~a~lLA~--~~  152 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFL---TSPEDYPFAALLAM--TS  152 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccc---cCccchhHHHHHhc--cc
Confidence            45677888999999988777666554333333  22    3457888999998876432   23444555555444  34


Q ss_pred             CCh----HHHHHHHHHhhhCCCCCC--hhhHHHHHHHHhccCc--HHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          177 GFV----DKAKELFLKMKDENINPD--VVTYTSLIRGFCYAND--WNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       177 ~~~----~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      ++.    +.+..+|+.+.+.|+..+  ....+.++..+.....  ...+..+++.+.+.|+++....|..+.-..
T Consensus       153 ~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLa  227 (297)
T PF13170_consen  153 EDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLA  227 (297)
T ss_pred             ccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHH
Confidence            443    455667777777665543  2334444443333222  347788888888888888877776554443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.16  E-value=1.6  Score=36.49  Aligned_cols=145  Identities=14%  Similarity=0.259  Sum_probs=105.0

Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHH-HHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTF-NVIM  240 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~  240 (343)
                      ..+|...+....+..-.+.|..+|-+..+.+ +.+++..+++++..++ .|+...|..+|+--...  -||...| +..+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            4567777888888888999999999998887 5677888888888765 57888899999876665  3444333 4566


Q ss_pred             HHHHhCCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          241 NELCKNGKMDEASRLLELMIQIGVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       241 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      ..+...++-+.|..+|+..+.. +..+  ..+|..++.-=..-|+...+..+-+++.+.  .|...+......-|
T Consensus       474 ~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry  545 (660)
T COG5107         474 LFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRY  545 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHH
Confidence            7778889999999999966553 1222  457888888778889988888888877764  34444444344333

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.13  E-value=1.8  Score=36.79  Aligned_cols=78  Identities=10%  Similarity=0.127  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHcC-CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc-HHHHHHHH
Q 040261          233 VVTFNVIMNELCKNGKMDEASRLLELMIQIG-VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD-VFSYGILI  310 (343)
Q Consensus       233 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~  310 (343)
                      ..+=..+..++-+.|+.++|.+.++++.+.. ..-+..+...|+.++...+.+.++..++.+..+...+.+ ..+|+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            3333456677778899999999998887643 112345677788889999999999998888765432222 23455444

The molecular function of this protein is uncertain.

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=95.12  E-value=0.44  Score=34.83  Aligned_cols=98  Identities=14%  Similarity=0.009  Sum_probs=69.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC--HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD--LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      ...+..+...|.+.|+.+.|++.|.++......+.  ...+-.+++.....+++..+.....+....--.........-+
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrl  115 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRL  115 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHH
Confidence            45788999999999999999999999987654443  3467788899999999999998888876532111111111111


Q ss_pred             -----HHHhhcCcHHHHHHHHHHHH
Q 040261           95 -----KGLCAESRIMEAAALFTKLR  114 (343)
Q Consensus        95 -----~~~~~~~~~~~a~~~~~~~~  114 (343)
                           -.+...+++..|-+.|-...
T Consensus       116 k~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  116 KVYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHHhchHHHHHHHHHccC
Confidence                 12334678888888776654

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.

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

Probab=95.01  E-value=0.062  Score=27.15  Aligned_cols=24  Identities=13%  Similarity=0.292  Sum_probs=14.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRL   43 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~   43 (343)
                      |+.|...|.+.|++++|+++|++.
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            556666666666666666666663

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.01  E-value=2.4  Score=37.62  Aligned_cols=178  Identities=15%  Similarity=0.056  Sum_probs=102.5

Q ss_pred             cchHHHHHHHHHHcCCCccHHHHHHHHHH-----HhhcCcHHHHHHHHHHHHh-------cCCCCCHHHHHHHHHHHHhc
Q 040261           68 VSPGFVVLGRILRSCFTPDAVTFTSLIKG-----LCAESRIMEAAALFTKLRA-------FGCKPDVFTYTTLINGLCRT  135 (343)
Q Consensus        68 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-----~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~  135 (343)
                      ...|.++++...+.|   +...-..+..+     +....+.+.|+.+++...+       .|   .+.....+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            356778888777765   22222222222     3355678888888888766       44   233455666666664


Q ss_pred             C-----ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh-cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHh
Q 040261          136 G-----HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK-EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFC  209 (343)
Q Consensus       136 ~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  209 (343)
                      .     +.+.|..++.+....+       .|+.......+..... ..+...|.++|......|..   ..+-.+..+|.
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~g-------~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~---~A~~~la~~y~  371 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAELG-------NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHI---LAIYRLALCYE  371 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhcC-------CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCCh---HHHHHHHHHHH
Confidence            3     5667888888887766       3333333333322222 24677888888888887742   22333333322


Q ss_pred             ----ccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          210 ----YANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       210 ----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                          ...+...|..++.+..+.| .|....-...+..+.. ++++.+...+..+.+.|
T Consensus       372 ~G~gv~r~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  372 LGLGVERNLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             hCCCcCCCHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence                2346788888888888887 3332222222333333 66777666666666654

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=94.98  E-value=0.91  Score=32.60  Aligned_cols=135  Identities=16%  Similarity=0.192  Sum_probs=72.8

Q ss_pred             HHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           37 LSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .+.++.+.+.+++|+...+..++..+.+.|++..    +..+++.++-+|.......+-.+.  +....+.++--.|..+
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHH
Confidence            3455556667777888888888888888777554    334444444445444433332222  2223333333333322


Q ss_pred             CCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhh
Q 040261          117 GCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       117 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  191 (343)
                          =...+..++..+...|++-+|+++.+......          ......++.+..+.+|...-..+++-...
T Consensus        88 ----L~~~~~~iievLL~~g~vl~ALr~ar~~~~~~----------~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   88 ----LGTAYEEIIEVLLSKGQVLEALRYARQYHKVD----------SVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             ----hhhhHHHHHHHHHhCCCHHHHHHHHHHcCCcc----------cCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                11134456667777788888877776653321          22334556666666665555555554443

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.90  E-value=0.047  Score=27.19  Aligned_cols=31  Identities=13%  Similarity=0.308  Sum_probs=19.1

Q ss_pred             HHHHhcCCCCCChhhHHHHHHHHHhcCChhHHH
Q 040261            5 DYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVL   37 (343)
Q Consensus         5 ~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   37 (343)
                      +...+..|  .++.+|+.+...|...|++++|+
T Consensus         3 ~kAie~~P--~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELNP--NNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHCC--CCHHHHHHHHHHHHHCcCHHhhc
Confidence            33344444  36677777777777777776664

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.86  E-value=3  Score=37.90  Aligned_cols=217  Identities=13%  Similarity=0.086  Sum_probs=137.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHh----HhCC----------C--CCCHHHHHHHHHHHHhcCCcchHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRL----NSIG----------L--FPDLYTYNILINCFCKMGRVSPGFVVLGRIL   79 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~----------~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   79 (343)
                      +..+.+.++.++...+++--=.-+++..    ...+          +  .........-+..+.+..-+..|+.+-+.  
T Consensus       282 s~ss~~~i~~~~d~~n~~v~ys~vl~~l~d~l~~w~~~~~vltsdg~~~~L~ek~le~kL~iL~kK~ly~~Ai~LAk~--  359 (933)
T KOG2114|consen  282 SNSSSNRIFKAYDLRNRYVLYSSVLEDLSDNLIEWSFDCLVLTSDGVVHELIEKDLETKLDILFKKNLYKVAINLAKS--  359 (933)
T ss_pred             CccchhheeehhhhcCcccchHHhHHHHHHHHHhcCCcEEEEecCCceeeeeeccHHHHHHHHHHhhhHHHHHHHHHh--
Confidence            4456777778887777754333333322    2222          0  01122344556666677777777666543  


Q ss_pred             HcCCCcc--HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCc
Q 040261           80 RSCFTPD--AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGV  157 (343)
Q Consensus        80 ~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  157 (343)
                       .+..++  ........+-+.+.|++++|...|-+.+.. +.|     ..++.-|........-..+++.+.+.+     
T Consensus       360 -~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLdaq~IknLt~YLe~L~~~g-----  427 (933)
T KOG2114|consen  360 -QHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDAQRIKNLTSYLEALHKKG-----  427 (933)
T ss_pred             -cCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCHHHHHHHHHHHHHHHHcc-----
Confidence             222222  223444555667889999999988776643 232     235566677777788888899998887     


Q ss_pred             cccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH
Q 040261          158 VCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN  237 (343)
Q Consensus       158 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  237 (343)
                        -.+...-..|+.+|.+.++.++..+..+... .|..  ..-....+..+.+.+-.++|..+-.....     +.....
T Consensus       428 --la~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~~a~~LA~k~~~-----he~vl~  497 (933)
T KOG2114|consen  428 --LANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYLDEAELLATKFKK-----HEWVLD  497 (933)
T ss_pred             --cccchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHHHHHHHHHHhcc-----CHHHHH
Confidence              3566777889999999999999888887665 3321  22355667777777888888776655432     233333


Q ss_pred             HHHHHHHhCCChhHHHHHHHHH
Q 040261          238 VIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       238 ~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      .   .+...+++++|.+++..+
T Consensus       498 i---lle~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  498 I---LLEDLHNYEEALRYISSL  516 (933)
T ss_pred             H---HHHHhcCHHHHHHHHhcC
Confidence            3   344678899999988765

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.80  E-value=1  Score=32.32  Aligned_cols=136  Identities=15%  Similarity=0.077  Sum_probs=92.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH-
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLY-TYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL-   93 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-   93 (343)
                      +-..|..-+. +.+.+..++|+..|..+.+.|...-.. ..........+.|+...|...|+++-.....|-..-=..- 
T Consensus        58 sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARl  136 (221)
T COG4649          58 SGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARL  136 (221)
T ss_pred             chHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHH
Confidence            4445554444 457788999999999998876432221 2233344567889999999999999876444433211111 


Q ss_pred             --HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           94 --IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        94 --~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                        .-.+...|.+++.....+-+...+-+.-...-..|.-+-.+.|++..|.++|.++....
T Consensus       137 raa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da  197 (221)
T COG4649         137 RAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDA  197 (221)
T ss_pred             HHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccc
Confidence              22356778899988888877665544344455667777889999999999999988754

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.63  E-value=1  Score=31.46  Aligned_cols=14  Identities=7%  Similarity=0.003  Sum_probs=5.4

Q ss_pred             CcHHHHHHHHHHHH
Q 040261          101 SRIMEAAALFTKLR  114 (343)
Q Consensus       101 ~~~~~a~~~~~~~~  114 (343)
                      +.......+++.+.
T Consensus        21 ~~~~~l~~yLe~~~   34 (140)
T smart00299       21 NLLEELIPYLESAL   34 (140)
T ss_pred             CcHHHHHHHHHHHH
Confidence            33333333333333

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.59  E-value=1.9  Score=34.56  Aligned_cols=132  Identities=14%  Similarity=0.186  Sum_probs=83.2

Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc--cC----cHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHhCCC-
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCY--AN----DWNEAKCLFIEMMDQGV---QPNVVTFNVIMNELCKNGK-  248 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~-  248 (343)
                      +++.+.+++.+.+.|+.-+..+|-+.......  ..    ....+..+++.|.+...   .++...+..++..  ..++ 
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            34556677888888888777666554333322  22    35678899999998732   2445556655443  3333 


Q ss_pred             ---hhHHHHHHHHHHHcCCCCCH--HHHHHHHHHHhcCCc--hHHHHHHHHHHHhCCCCccHHHHHHHHHH
Q 040261          249 ---MDEASRLLELMIQIGVRPDA--SVYNTLMDGFCLTGR--VNRAKELFVSMESNGCMRDVFSYGILING  312 (343)
Q Consensus       249 ---~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  312 (343)
                         .+.++.+|+.+.+.|+..+.  .....++..+.....  ..++.++++.+.+.|+++....|..+.-.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlL  226 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLL  226 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHH
Confidence               35577888888887776543  333444433332222  45788899999999998888777665543

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=94.46  E-value=0.1  Score=25.78  Aligned_cols=28  Identities=14%  Similarity=0.195  Sum_probs=18.8

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHh
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNS   45 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~   45 (343)
                      .+|..+..++...|++++|+..|++.++
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            4566677777777777777777777665

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=94.42  E-value=1.7  Score=33.06  Aligned_cols=223  Identities=18%  Similarity=0.068  Sum_probs=127.3

Q ss_pred             CCcchHHHHHHHHHHcCCCc-cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhcCChHHHHH
Q 040261           66 GRVSPGFVVLGRILRSCFTP-DAVTFTSLIKGLCAESRIMEAAALFTKLRAF-GCKPDVFTYTTLINGLCRTGHTIVALN  143 (343)
Q Consensus        66 ~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~  143 (343)
                      +....+...+.......... ....+......+...+.+..+...+...... ........+......+...+++..+..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            45555555555555443221 2455666666677777777777777776642 223345556666666777777777777


Q ss_pred             HHHHHHccCCCCCccccCCcchHHHHHH-HHHhcCChHHHHHHHHHhhhCCC--CCChhhHHHHHHHHhccCcHHHHHHH
Q 040261          144 LFEEMANGNGEFGVVCKPDAITYSTITD-GLCKEGFVDKAKELFLKMKDENI--NPDVVTYTSLIRGFCYANDWNEAKCL  220 (343)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~  220 (343)
                      .+........       .+......... .+...|+++.+...+.+......  ......+......+...++.+.+...
T Consensus       117 ~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  189 (291)
T COG0457         117 LLEKALALDP-------DPDLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALEL  189 (291)
T ss_pred             HHHHHHcCCC-------CcchHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHH
Confidence            7777776541       11222333333 67777777777777777644211  01223333333334556677777777


Q ss_pred             HHHHHHcCCCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          221 FIEMMDQGVQP-NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       221 ~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      +....... .. ....+..+...+...++.+.+...+....... +.....+..+...+...+..+.+...+......
T Consensus       190 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         190 LEKALKLN-PDDDAEALLNLGLLYLKLGKYEEALEYYEKALELD-PDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHhhC-cccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhC-cccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            77776652 22 34556666666667777777777777766653 112333333333444555677777666666654

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=94.40  E-value=1.7  Score=33.04  Aligned_cols=225  Identities=20%  Similarity=0.142  Sum_probs=114.0

Q ss_pred             CChhHHHHHHHHhHhCCCC-CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc-CCCccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           31 KHYDTVLSLFKRLNSIGLF-PDLYTYNILINCFCKMGRVSPGFVVLGRILRS-CFTPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      +....+...+......... .....+......+...+++..+...+...... ........+......+...+++..+.+
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            4444555555554443211 02345555556666666666666666665541 122344445555555555666666666


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHH-HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHH
Q 040261          109 LFTKLRAFGCKPDVFTYTTLIN-GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFL  187 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  187 (343)
                      .+.........+ ......... .+...|+++.+...+.+.....+.    .......+......+...++.+.+...+.
T Consensus       117 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  191 (291)
T COG0457         117 LLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPE----LNELAEALLALGALLEALGRYEEALELLE  191 (291)
T ss_pred             HHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC----ccchHHHHHHhhhHHHHhcCHHHHHHHHH
Confidence            666666543332 111222222 566666777777766666442100    00122223333333455666666666666


Q ss_pred             HhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          188 KMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       188 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      .............+..+...+...++++.+...+.......  |+ ...+..+...+...+..+.+...+......
T Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         192 KALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELD--PDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhC--cccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66554211124555556666666666666666666666542  22 233333333333555566666666666554

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.36  E-value=0.064  Score=26.69  Aligned_cols=20  Identities=30%  Similarity=0.424  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHhcCCchHHH
Q 040261          268 ASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       268 ~~~~~~l~~~~~~~~~~~~a  287 (343)
                      ...|..+...|...|++++|
T Consensus        13 ~~a~~nla~~~~~~g~~~~A   32 (34)
T PF13431_consen   13 AEAYNNLANLYLNQGDYEEA   32 (34)
T ss_pred             HHHHHHHHHHHHHCcCHHhh
Confidence            33344444444444444333

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.19  E-value=1.8  Score=34.34  Aligned_cols=103  Identities=17%  Similarity=0.161  Sum_probs=62.7

Q ss_pred             CCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHH
Q 040261          193 NINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG---VQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDAS  269 (343)
Q Consensus       193 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  269 (343)
                      |.+....+...++..-....+++.+...+-.+....   ..|+...+ ..++.+. .-++++++.++..=++.|+-||..
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~-~~irlll-ky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIH-TWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHH-HHHHHHH-ccChHHHHHHHhCcchhccccchh
Confidence            444455555666655555666777777766665431   11222222 1223222 336667777777777777778888


Q ss_pred             HHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          270 VYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       270 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      +++.+++.+.+.+++.+|.++...|..+
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            8888888888888877777777666543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.05  E-value=4.3  Score=36.42  Aligned_cols=142  Identities=13%  Similarity=0.051  Sum_probs=72.2

Q ss_pred             CCCCCCHHHHHH-----HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH--HHHHHHHHHHHhcCC
Q 040261           46 IGLFPDLYTYNI-----LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI--MEAAALFTKLRAFGC  118 (343)
Q Consensus        46 ~~~~~~~~~~~~-----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~a~~~~~~~~~~~~  118 (343)
                      .|++.+..-|..     ++.-+...+.+..|.++...+-..-.. ....|.....-+.+..+.  +++++..++-.+...
T Consensus       426 ~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~-~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~  504 (829)
T KOG2280|consen  426 IGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQ-GDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKL  504 (829)
T ss_pred             cCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCcccc-ccHHHHHHHHHHHhccCccchHHHHHHHHHhcccC
Confidence            455544444433     344455566677777766655322111 145555555555554321  233333333222212


Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhh
Q 040261          119 KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       119 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  191 (343)
                       .....|..+..-....|+.+-|..+++.=...+..  ...-.+..-+...+.-+.+.|+.+....++-.+..
T Consensus       505 -~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~q--V~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~  574 (829)
T KOG2280|consen  505 -TPGISYAAIARRAYQEGRFELARKLLELEPRSGEQ--VPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKN  574 (829)
T ss_pred             -CCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccch--hHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHH
Confidence             24456777777777788888888777642222110  00111233445555666677777777666655543

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.97  E-value=0.15  Score=25.10  Aligned_cols=28  Identities=11%  Similarity=0.177  Sum_probs=18.6

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHh
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNS   45 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~   45 (343)
                      ..|..+..++.+.|++++|++.|++..+
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            3566667777777777777777777665

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=93.91  E-value=0.58  Score=30.05  Aligned_cols=60  Identities=12%  Similarity=0.148  Sum_probs=34.0

Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      +..+-+..+....+.|++....+.+++|.+.+++..|.++++.+..+- .+....|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHH
Confidence            445555666666667777777777777777777777777777666551 222225554443

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=93.90  E-value=0.69  Score=29.39  Aligned_cols=46  Identities=13%  Similarity=0.167  Sum_probs=26.6

Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHH
Q 040261          181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMD  226 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  226 (343)
                      ++.+-+..+....+.|++....+.+++|.+.+++..|.++++-+..
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~   70 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKD   70 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4444455555555556666666666666666666666666665543

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.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.86  E-value=3.5  Score=34.70  Aligned_cols=252  Identities=12%  Similarity=0.097  Sum_probs=133.4

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC----CHHHHHHHHHHHHhcCCcchHHHHHHHH
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP----DLYTYNILINCFCKMGRVSPGFVVLGRI   78 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~   78 (343)
                      +++...+....|...-+...+...+.+  +.+++..+-+.+....+.+    =..++..++....+.++...|.+.+.-+
T Consensus       247 ~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL  324 (549)
T PF07079_consen  247 ILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLALL  324 (549)
T ss_pred             HHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            444445555554444445555555554  5566666555544322211    2346788888888999999998888877


Q ss_pred             HHcCCCccHHHHHHH-------HHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHHH---HHHHHHhcCC-hHHHHH
Q 040261           79 LRSCFTPDAVTFTSL-------IKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYTT---LINGLCRTGH-TIVALN  143 (343)
Q Consensus        79 ~~~~~~~~~~~~~~l-------~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~---l~~~~~~~~~-~~~a~~  143 (343)
                      ...  .|+...-..+       -+..+.    ..+...-+.+|+.....++..- ....-   -..-+.+.|. -++|++
T Consensus       325 ~~l--dp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrq-QLvh~L~~~Ak~lW~~g~~dekaln  401 (549)
T PF07079_consen  325 KIL--DPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQ-QLVHYLVFGAKHLWEIGQCDEKALN  401 (549)
T ss_pred             Hhc--CCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHH-HHHHHHHHHHHHHHhcCCccHHHHH
Confidence            654  3333322211       122221    1123344556666665533211 11112   2334555666 788999


Q ss_pred             HHHHHHccCCCCCccccCCcchHHHHH----HHHHh---cCChHHHHHHHHHhhhCCCCCChhh----HHHHH--HHHhc
Q 040261          144 LFEEMANGNGEFGVVCKPDAITYSTIT----DGLCK---EGFVDKAKELFLKMKDENINPDVVT----YTSLI--RGFCY  210 (343)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~----~~~l~--~~~~~  210 (343)
                      +++.+.+-.       +-|..+-+.+.    ..|..   ......-+.+-+.+.+.|++|-...    -|.+.  ..+..
T Consensus       402 LLk~il~ft-------~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLys  474 (549)
T PF07079_consen  402 LLKLILQFT-------NYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYS  474 (549)
T ss_pred             HHHHHHHhc-------cccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHh
Confidence            998887742       23333333222    12221   2223333444444555666553222    22222  23345


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNT  273 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  273 (343)
                      .|++.++.-.-..+.+  +.|++.+|..+.-+.....++++|..++..+     ||+..+++.
T Consensus       475 qgey~kc~~ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L-----P~n~~~~ds  530 (549)
T PF07079_consen  475 QGEYHKCYLYSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQKL-----PPNERMRDS  530 (549)
T ss_pred             cccHHHHHHHHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC-----CCchhhHHH
Confidence            6777777655555544  4677777777777777777777777777664     666665554

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=93.85  E-value=1.5  Score=30.57  Aligned_cols=52  Identities=21%  Similarity=0.251  Sum_probs=29.0

Q ss_pred             hccCcHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          209 CYANDWNEAKCLFIEMMDQGVQPNVVTFN-VIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ...++.+++..++..|.-.  .|+..-.. .-...+...|++.+|.++|+++.+.
T Consensus        21 L~~~d~~D~e~lLdALrvL--rP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVL--RPNLKELDMFDGWLLIARGNYDEAARILRELLSS   73 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHh--CCCccccchhHHHHHHHcCCHHHHHHHHHhhhcc
Confidence            3456666666666666553  33322221 1233455667777777777776654

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.81  E-value=6.3  Score=37.51  Aligned_cols=110  Identities=17%  Similarity=0.282  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHH
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVV--TFNVIMNEL  243 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~  243 (343)
                      |.+....+.....+++|.-.|+..-+         ..-.+.+|...|+|.+|..+..++...   -+..  +-..|..-+
T Consensus       942 ~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L 1009 (1265)
T KOG1920|consen  942 YEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKECGDWREALSLAAQLSEG---KDELVILAEELVSRL 1009 (1265)
T ss_pred             HHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHHhccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHH
Confidence            33444445556667777666655432         223456777788888888877766422   1221  124566777


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      ...+++-+|-++..+....   |.     ..+..+++...+++|.++.....
T Consensus      1010 ~e~~kh~eAa~il~e~~sd---~~-----~av~ll~ka~~~~eAlrva~~~~ 1053 (1265)
T KOG1920|consen 1010 VEQRKHYEAAKILLEYLSD---PE-----EAVALLCKAKEWEEALRVASKAK 1053 (1265)
T ss_pred             HHcccchhHHHHHHHHhcC---HH-----HHHHHHhhHhHHHHHHHHHHhcc
Confidence            7888888888887776542   21     22344566667777777665443

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.44  E-value=7.4  Score=37.10  Aligned_cols=84  Identities=13%  Similarity=0.106  Sum_probs=50.2

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHH--HHHHHHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDAS--VYNTLMDGF  278 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~  278 (343)
                      |.+....+.....+++|.-.|+..-+         ....+.+|..+|++.+|+.+..++...   .+..  +-..|+.-+
T Consensus       942 ~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L 1009 (1265)
T KOG1920|consen  942 YEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKECGDWREALSLAAQLSEG---KDELVILAEELVSRL 1009 (1265)
T ss_pred             HHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHHhccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHH
Confidence            33334444555666666666654322         123466777778888888777766321   1211  225567777


Q ss_pred             hcCCchHHHHHHHHHHHh
Q 040261          279 CLTGRVNRAKELFVSMES  296 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~  296 (343)
                      ..+++.-+|-++..+...
T Consensus      1010 ~e~~kh~eAa~il~e~~s 1027 (1265)
T KOG1920|consen 1010 VEQRKHYEAAKILLEYLS 1027 (1265)
T ss_pred             HHcccchhHHHHHHHHhc
Confidence            788888888887776655

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=93.40  E-value=1.3  Score=28.47  Aligned_cols=66  Identities=9%  Similarity=0.056  Sum_probs=39.1

Q ss_pred             ChhhHHHHHHHHHhcCCh--hHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           16 PVCSFNILFGCLAKNKHY--DTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.+.|..--..+....+.  -+..+-++.+....+.|++.+..+.+++|.+.+++..|.++++-+...
T Consensus         7 t~eeF~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen    7 TDEEFDARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             -HHHHHHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            334455544455444433  356666677777777777777777788888888888888777776643

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=93.23  E-value=2.2  Score=30.36  Aligned_cols=114  Identities=12%  Similarity=0.044  Sum_probs=65.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHH-HHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTY-NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      ++..-.+.++.+++..++..+.-.  .|..... ..-...+...|++.+|..+|+.+....  |.......|+..|....
T Consensus        16 ~~~~al~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kALlA~CL~~~   91 (160)
T PF09613_consen   16 VLSVALRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA--PGFPYAKALLALCLYAL   91 (160)
T ss_pred             HHHHHHccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC--CCChHHHHHHHHHHHHc
Confidence            344445788999999999988763  3443322 223345678899999999999987653  34444445555554443


Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALN  143 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  143 (343)
                      +-..=...-+++.+.+..|+.   ..+++.+....+...|..
T Consensus        92 ~D~~Wr~~A~evle~~~d~~a---~~Lv~~Ll~~~~~~~a~~  130 (160)
T PF09613_consen   92 GDPSWRRYADEVLESGADPDA---RALVRALLARADLEPAHE  130 (160)
T ss_pred             CChHHHHHHHHHHhcCCChHH---HHHHHHHHHhccccchhh
Confidence            323333334455655444333   234445544444444433

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.23  E-value=0.33  Score=23.85  Aligned_cols=28  Identities=32%  Similarity=0.376  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +|..+...|...|++++|+..|++.++.
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            4556666666666666666666666643

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.20  E-value=2.5  Score=31.07  Aligned_cols=91  Identities=10%  Similarity=0.043  Sum_probs=47.4

Q ss_pred             HHHHhCCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          241 NELCKNGKMDEASRLLELMIQIGVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       241 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                      ..+...+++++|..-++.........+  ..+--.|.+.....|.+|+|...++.....+  ........-.+.+...|+
T Consensus        97 k~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~--w~~~~~elrGDill~kg~  174 (207)
T COG2976          97 KAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEES--WAAIVAELRGDILLAKGD  174 (207)
T ss_pred             HHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccccc--HHHHHHHHhhhHHHHcCc
Confidence            345556666666666665543211100  1112234445556666666666666655432  223333444555666666


Q ss_pred             hHHHHHHHHHHHhCC
Q 040261          319 IEGALSLYSEMLSKG  333 (343)
Q Consensus       319 ~~~a~~~~~~~~~~~  333 (343)
                      -++|..-|++.+..+
T Consensus       175 k~~Ar~ay~kAl~~~  189 (207)
T COG2976         175 KQEARAAYEKALESD  189 (207)
T ss_pred             hHHHHHHHHHHHHcc
Confidence            666666666666554

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.87  E-value=0.4  Score=23.46  Aligned_cols=28  Identities=18%  Similarity=0.266  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .|..+...+...|++++|++.|++.+..
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l   30 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4455666666666666666666666643

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=92.82  E-value=5.5  Score=33.89  Aligned_cols=119  Identities=13%  Similarity=0.025  Sum_probs=73.1

Q ss_pred             cCcHHHHH-HHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261          100 ESRIMEAA-ALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus       100 ~~~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      .|+.-.|- +++..++...-.|+....  ........|+++.+...+......       +.....+...+++...+.|+
T Consensus       302 ~gd~~aas~~~~~~lr~~~~~p~~i~l--~~~i~~~lg~ye~~~~~~s~~~~~-------~~s~~~~~~~~~r~~~~l~r  372 (831)
T PRK15180        302 DGDIIAASQQLFAALRNQQQDPVLIQL--RSVIFSHLGYYEQAYQDISDVEKI-------IGTTDSTLRCRLRSLHGLAR  372 (831)
T ss_pred             ccCHHHHHHHHHHHHHhCCCCchhhHH--HHHHHHHhhhHHHHHHHhhchhhh-------hcCCchHHHHHHHhhhchhh
Confidence            35554443 344444444333443333  334466788888888877766554       23456677778888888888


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG  228 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  228 (343)
                      ++.|...-.-|....+. ++.............|-++++...|+++...+
T Consensus       373 ~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        373 WREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             HHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            88888888777766543 34344333333445567788888888877654

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=92.65  E-value=1.9  Score=31.97  Aligned_cols=41  Identities=10%  Similarity=0.118  Sum_probs=17.6

Q ss_pred             CChhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHhcCCchHHH
Q 040261          247 GKMDEASRLLELMIQI---GVRPDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      .|.+++..++.+..+.   +-.+|+..+..|+..+.+.|+++.|
T Consensus       154 rD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  154 RDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             cCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            3444444444444332   1133444444444444444444443

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=92.61  E-value=5.8  Score=33.73  Aligned_cols=126  Identities=12%  Similarity=0.035  Sum_probs=83.9

Q ss_pred             HHHHHHhcCChhHHHH-HHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           23 LFGCLAKNKHYDTVLS-LFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      -|..-...|+...|.+ ++..+....-.|+.....  .......|+++.+.+.+...... +.....+...+++...+.|
T Consensus       295 si~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~--~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~  371 (831)
T PRK15180        295 SITKQLADGDIIAASQQLFAALRNQQQDPVLIQLR--SVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLA  371 (831)
T ss_pred             HHHHHhhccCHHHHHHHHHHHHHhCCCCchhhHHH--HHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchh
Confidence            3444455677766654 444444433334444333  33456779999988887766543 2335567778888888999


Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ++++|...-+.|....+. ++..........-..|-++++.-.|+++....
T Consensus       372 r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        372 RWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             hHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            999999999998887665 55555444444556777889999999887765

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.57  E-value=3.5  Score=32.85  Aligned_cols=102  Identities=18%  Similarity=0.144  Sum_probs=53.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhh
Q 040261          121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVT  200 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  200 (343)
                      ...+...++..-....+++.+...+-++.......   ..++. +-..+++.+. .-++++++.++..-...|+-||..+
T Consensus        63 s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~---~~~~~-~~~~~irlll-ky~pq~~i~~l~npIqYGiF~dqf~  137 (418)
T KOG4570|consen   63 SSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAW---YLRNW-TIHTWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQFT  137 (418)
T ss_pred             ceeehhhhhhccccccchhHHHHHHHHHhcCcchh---hhccc-cHHHHHHHHH-ccChHHHHHHHhCcchhccccchhh
Confidence            33444444444444555666666665555432110   11111 1122222222 2355566666666666677777777


Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      ++.++..+.+.+++.+|..+.-.|...
T Consensus       138 ~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  138 FCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            777777777777777766666555544

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=92.38  E-value=1.3  Score=35.65  Aligned_cols=93  Identities=8%  Similarity=-0.083  Sum_probs=65.1

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      --..-|.++|.+++|+..|....... +-|..++..-..+|.+..++..|..-....+..+ ..-...|..-+.+-...|
T Consensus       102 E~GN~yFKQgKy~EAIDCYs~~ia~~-P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg  179 (536)
T KOG4648|consen  102 ERGNTYFKQGKYEEAIDCYSTAIAVY-PHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLG  179 (536)
T ss_pred             HhhhhhhhccchhHHHHHhhhhhccC-CCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHh
Confidence            34567888999999999998877643 2388888888899999999988887777766542 112334444444444456


Q ss_pred             cHHHHHHHHHHHHhc
Q 040261          102 RIMEAAALFTKLRAF  116 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~  116 (343)
                      ...+|.+-++...+.
T Consensus       180 ~~~EAKkD~E~vL~L  194 (536)
T KOG4648|consen  180 NNMEAKKDCETVLAL  194 (536)
T ss_pred             hHHHHHHhHHHHHhh
Confidence            677777777776665

>PRK11619 lytic murein transglycosylase; Provisional

Probab=92.36  E-value=8.4  Score=34.96  Aligned_cols=252  Identities=9%  Similarity=-0.029  Sum_probs=123.0

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 040261           56 NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRT  135 (343)
Q Consensus        56 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  135 (343)
                      ...+..+.+.+++......+.    . .+.+...-.....+....|+.++|.+....+-..|.. .+..+..++..+.+.
T Consensus       103 ~~~l~~La~~~~w~~~~~~~~----~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g~~-~p~~cd~l~~~~~~~  176 (644)
T PRK11619        103 SRFVNELARREDWRGLLAFSP----E-KPKPVEARCNYYYAKWATGQQQEAWQGAKELWLTGKS-LPNACDKLFSVWQQS  176 (644)
T ss_pred             HHHHHHHHHccCHHHHHHhcC----C-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCC-CChHHHHHHHHHHHc
Confidence            344455556666665554221    1 1334444455666777778877777766666555533 445666677666655


Q ss_pred             CChHHHH--HHHHHHHccCCCCCccccCCcchHHHHHHHHHh------------cCChHHHHHHHHHhhhCCCCCChhhH
Q 040261          136 GHTIVAL--NLFEEMANGNGEFGVVCKPDAITYSTITDGLCK------------EGFVDKAKELFLKMKDENINPDVVTY  201 (343)
Q Consensus       136 ~~~~~a~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~  201 (343)
                      |......  +-+..+...+         +...-..+......            ..+...+...+..     ++|+...-
T Consensus       177 g~lt~~d~w~R~~~al~~~---------~~~lA~~l~~~l~~~~~~~a~a~~al~~~p~~~~~~~~~-----~~~~~~~~  242 (644)
T PRK11619        177 GKQDPLAYLERIRLAMKAG---------NTGLVTYLAKQLPADYQTIASALIKLQNDPNTVETFART-----TGPTDFTR  242 (644)
T ss_pred             CCCCHHHHHHHHHHHHHCC---------CHHHHHHHHHhcChhHHHHHHHHHHHHHCHHHHHHHhhc-----cCCChhhH
Confidence            5544322  1122222221         11122222221100            0111111111111     11222111


Q ss_pred             HHHHHH--HhccCcHHHHHHHHHHHHHcC-CCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          202 TSLIRG--FCYANDWNEAKCLFIEMMDQG-VQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD  276 (343)
Q Consensus       202 ~~l~~~--~~~~~~~~~a~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  276 (343)
                      ..++.+  -....+.+.|..++....... ..+.  ......+.......+...++...+......  ..+......-+.
T Consensus       243 ~~~~~~l~Rlar~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~--~~~~~~~e~r~r  320 (644)
T PRK11619        243 QMAAVAFASVARQDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMR--SQSTSLLERRVR  320 (644)
T ss_pred             HHHHHHHHHHHHhCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccc--cCCcHHHHHHHH
Confidence            111111  123445677888887764442 2222  122333333333332255566666554332  224444555555


Q ss_pred             HHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          277 GFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       277 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      .....++++.+...+..|.... .-...-...+.+++...|+.++|...|+++.
T Consensus       321 ~Al~~~dw~~~~~~i~~L~~~~-~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a  373 (644)
T PRK11619        321 MALGTGDRRGLNTWLARLPMEA-KEKDEWRYWQADLLLEQGRKAEAEEILRQLM  373 (644)
T ss_pred             HHHHccCHHHHHHHHHhcCHhh-ccCHhhHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            6667888888888887775432 2344455567777777888888888888764

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=92.36  E-value=0.37  Score=23.36  Aligned_cols=25  Identities=16%  Similarity=0.387  Sum_probs=15.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          308 ILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       308 ~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .+..++.+.|++++|.+.|+++++.
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHH
Confidence            3455566666777777777666654

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=92.14  E-value=2.6  Score=31.26  Aligned_cols=79  Identities=13%  Similarity=0.071  Sum_probs=58.3

Q ss_pred             HHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHhCCCh
Q 040261          173 LCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---GVQPNVVTFNVIMNELCKNGKM  249 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~  249 (343)
                      +.+.|+ +.|.+.|-.+...+.--++.....+...|. ..+.+++..++.+..+.   +-.+|+..+..|+..+.+.|++
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~  194 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNY  194 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcch
Confidence            445555 566777777777665555666666655554 67889999999888765   3367899999999999999999


Q ss_pred             hHHH
Q 040261          250 DEAS  253 (343)
Q Consensus       250 ~~a~  253 (343)
                      +.|-
T Consensus       195 e~AY  198 (203)
T PF11207_consen  195 EQAY  198 (203)
T ss_pred             hhhh
Confidence            8874

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

Probab=91.93  E-value=0.42  Score=24.73  Aligned_cols=27  Identities=19%  Similarity=0.299  Sum_probs=16.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLN   44 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~   44 (343)
                      .+++.+...|...|++++|..++++..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            356666666666666666666666654

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

Probab=91.82  E-value=0.57  Score=24.20  Aligned_cols=28  Identities=32%  Similarity=0.342  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          304 FSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       304 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      .+++.+...|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4566777777777777777777777653

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.80  E-value=1.9  Score=37.52  Aligned_cols=132  Identities=20%  Similarity=0.188  Sum_probs=78.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHH
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTS  203 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  203 (343)
                      .-+.+...+.+.|-.++|+++-               +|+.-   -.....+.|+.+.|.++..+..      +..-|..
T Consensus       616 ~rt~va~Fle~~g~~e~AL~~s---------------~D~d~---rFelal~lgrl~iA~~la~e~~------s~~Kw~~  671 (794)
T KOG0276|consen  616 IRTKVAHFLESQGMKEQALELS---------------TDPDQ---RFELALKLGRLDIAFDLAVEAN------SEVKWRQ  671 (794)
T ss_pred             hhhhHHhHhhhccchHhhhhcC---------------CChhh---hhhhhhhcCcHHHHHHHHHhhc------chHHHHH
Confidence            3445666666777766666531               11111   1123445677777776665432      4556778


Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      |..+..+.+++..|.+.|.+...         |..|+-.+...|+.+....+-....+.| +.|.     ..-+|...|+
T Consensus       672 Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g-~~N~-----AF~~~~l~g~  736 (794)
T KOG0276|consen  672 LGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASLAKKQG-KNNL-----AFLAYFLSGD  736 (794)
T ss_pred             HHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHHHHhhc-ccch-----HHHHHHHcCC
Confidence            88888888888888877766543         3455666666777666666666655555 3332     2334556677


Q ss_pred             hHHHHHHHHHH
Q 040261          284 VNRAKELFVSM  294 (343)
Q Consensus       284 ~~~a~~~~~~~  294 (343)
                      ++++.+++..-
T Consensus       737 ~~~C~~lLi~t  747 (794)
T KOG0276|consen  737 YEECLELLIST  747 (794)
T ss_pred             HHHHHHHHHhc
Confidence            77777776543

>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=91.78  E-value=0.079  Score=37.22  Aligned_cols=85  Identities=12%  Similarity=0.089  Sum_probs=51.7

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.++.++...+++..       +..-...++..|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~-------~~yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS-------NNYDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS-------SSS-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc-------cccCHHHHHHHHHhcch
Confidence            45666666777777777777776554555666777777777776666666666511       11222345566667777


Q ss_pred             hHHHHHHHHHHH
Q 040261          284 VNRAKELFVSME  295 (343)
Q Consensus       284 ~~~a~~~~~~~~  295 (343)
                      ++++.-++.++.
T Consensus        86 ~~~a~~Ly~~~~   97 (143)
T PF00637_consen   86 YEEAVYLYSKLG   97 (143)
T ss_dssp             HHHHHHHHHCCT
T ss_pred             HHHHHHHHHHcc
Confidence            777777666543

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.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.67  E-value=3.4  Score=30.61  Aligned_cols=92  Identities=12%  Similarity=0.009  Sum_probs=46.4

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPD----LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      ..-+.+.|++++|..-|...+..-.+..    ...|..-..++.+.+.++.|+.-..+.++.++. ..........+|.+
T Consensus       102 GN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pt-y~kAl~RRAeayek  180 (271)
T KOG4234|consen  102 GNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPT-YEKALERRAEAYEK  180 (271)
T ss_pred             HHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCch-hHHHHHHHHHHHHh
Confidence            4445556666666666666554321111    112333444555666666666666655554322 22223333445555


Q ss_pred             cCcHHHHHHHHHHHHhc
Q 040261          100 ESRIMEAAALFTKLRAF  116 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~  116 (343)
                      ...+++|+.-|..+.+.
T Consensus       181 ~ek~eealeDyKki~E~  197 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILES  197 (271)
T ss_pred             hhhHHHHHHHHHHHHHh
Confidence            56666666666666654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=91.31  E-value=2.6  Score=26.92  Aligned_cols=62  Identities=10%  Similarity=0.137  Sum_probs=41.9

Q ss_pred             ChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           32 HYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      +.-++.+-++.+....+.|++.+..+.+++|.+.+++..|.++++-++... ..+...|..++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~-~~~~~~y~~~l   83 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC-GAHKEIYPYIL   83 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cCchhhHHHHH
Confidence            445667777777777777888888888888888888888888887766331 11333454444

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.

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=91.31  E-value=7.4  Score=32.16  Aligned_cols=65  Identities=14%  Similarity=0.021  Sum_probs=43.4

Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCC---ChhhHHHHHHHHhccCcHHHHHHHHHHHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINP---DVVTYTSLIRGFCYANDWNEAKCLFIEMMD  226 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  226 (343)
                      ...++..++..+.+.|.++.|...+..+...+...   .+...-.-+...-..|+..+|...++....
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34567777788888888888888888776643111   233344445555667777888888777776

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=91.26  E-value=9.6  Score=33.37  Aligned_cols=296  Identities=10%  Similarity=0.007  Sum_probs=157.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHH-HhcCCcchHHHHHHHHHHc-CCC-ccHHHHHHHHHH
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCF-CKMGRVSPGFVVLGRILRS-CFT-PDAVTFTSLIKG   96 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~~~~~-~~~-~~~~~~~~l~~~   96 (343)
                      |......=.+.|..+.+..+|++.+. +++.+...|......+ ...|+.+.....|+..... |.. .+...|...+..
T Consensus        82 W~kfA~~E~klg~~~~s~~Vfergv~-aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~  160 (577)
T KOG1258|consen   82 WKKFADYEYKLGNAENSVKVFERGVQ-AIPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEF  160 (577)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHH-hhhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHH
Confidence            34444444567888888888888775 4566666676665443 3456666777777777653 211 245567777877


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh---------cCChHHHHHHHHHHHcc--CCCCC---------
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR---------TGHTIVALNLFEEMANG--NGEFG---------  156 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~--~~~~~---------  156 (343)
                      -...+++.....+++++++.    ....++....-|.+         ....+++.++-......  .....         
T Consensus       161 en~qks~k~v~~iyeRilei----P~~~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~  236 (577)
T KOG1258|consen  161 ENGQKSWKRVANIYERILEI----PLHQLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDVAERSKITHSQEPLEELEIG  236 (577)
T ss_pred             HhccccHHHHHHHHHHHHhh----hhhHhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhHHhhhhcccccChhHHHHHH
Confidence            77788888888888888865    22222222222211         11223332222222210  00000         


Q ss_pred             --ccccCC---cchHHHHHH-------HHHhcCChHHHHHHHHHhhhC---CC----CCChhhHHHHHHHHhccCcHHHH
Q 040261          157 --VVCKPD---AITYSTITD-------GLCKEGFVDKAKELFLKMKDE---NI----NPDVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       157 --~~~~~~---~~~~~~l~~-------~~~~~~~~~~a~~~~~~~~~~---~~----~~~~~~~~~l~~~~~~~~~~~~a  217 (343)
                        ....|.   ....+.+..       ++............|+.-..+   .+    +++..+|...+..-...|+++.+
T Consensus       237 v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~  316 (577)
T KOG1258|consen  237 VKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRV  316 (577)
T ss_pred             HhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHH
Confidence              000000   011111111       111122222222333332222   11    22456677777777888888888


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          218 KCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .-++++..-- +.-=...|-..+.-....|+.+-|..++....+..++..+.+.-.-....-..|+++.|..+++.+.+.
T Consensus       317 ~~l~ercli~-cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e  395 (577)
T KOG1258|consen  317 FILFERCLIP-CALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEARFEESNGNFDDAKVILQRIESE  395 (577)
T ss_pred             HHHHHHHHhH-HhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhh
Confidence            8888877642 111233444445555555888888888887777654433333222222345568999999999998876


Q ss_pred             CCCccHH-HHHHHHHHHHhcCChHHHH
Q 040261          298 GCMRDVF-SYGILINGYCKNKEIEGAL  323 (343)
Q Consensus       298 ~~~~~~~-~~~~l~~~~~~~~~~~~a~  323 (343)
                      -  |+.. .-..-+....+.|..+.+.
T Consensus       396 ~--pg~v~~~l~~~~~e~r~~~~~~~~  420 (577)
T KOG1258|consen  396 Y--PGLVEVVLRKINWERRKGNLEDAN  420 (577)
T ss_pred             C--CchhhhHHHHHhHHHHhcchhhhh
Confidence            3  4432 2223344455667777766

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=91.23  E-value=3.8  Score=32.08  Aligned_cols=88  Identities=11%  Similarity=-0.049  Sum_probs=36.6

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH----
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC----  133 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~----  133 (343)
                      -|++++..+++.+++.+.-+..+.--+..+.+...-|-.|.+.+.+..+.++-.......-..+...|..++..|.    
T Consensus        89 GIQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VL  168 (309)
T PF07163_consen   89 GIQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVL  168 (309)
T ss_pred             hHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHH
Confidence            3455555555555544433333221111223333344445555555555555444443321112223444333332    


Q ss_pred             -hcCChHHHHHHH
Q 040261          134 -RTGHTIVALNLF  145 (343)
Q Consensus       134 -~~~~~~~a~~~~  145 (343)
                       =.|.+++|.++.
T Consensus       169 lPLG~~~eAeelv  181 (309)
T PF07163_consen  169 LPLGHFSEAEELV  181 (309)
T ss_pred             hccccHHHHHHHH
Confidence             245555555544

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=90.99  E-value=0.54  Score=25.02  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=17.8

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          309 LINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       309 l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      +..+|...|+.+.|.+++++++..|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5667777777777777777777543

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=90.90  E-value=8.2  Score=31.91  Aligned_cols=67  Identities=13%  Similarity=0.082  Sum_probs=48.7

Q ss_pred             CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          196 PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP---NVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ....+|..++..+.+.|.++.|...+..+...+...   .+...-.-+...-..|+..+|...++.....
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~  213 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC  213 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            345678888888999999999999998887753211   2333444556666788889999988888773

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>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=90.75  E-value=0.14  Score=36.01  Aligned_cols=83  Identities=10%  Similarity=0.102  Sum_probs=46.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.++.+...++++..       +..-...+++.|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~-------~~yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS-------NNYDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS-------SSS-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc-------cccCHHHHHHHHHhcch
Confidence            45566666777777777777765554455666777777777776666666655511       11122335555555555


Q ss_pred             HHHHHHHHHH
Q 040261          103 IMEAAALFTK  112 (343)
Q Consensus       103 ~~~a~~~~~~  112 (343)
                      ++++.-++.+
T Consensus        86 ~~~a~~Ly~~   95 (143)
T PF00637_consen   86 YEEAVYLYSK   95 (143)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            5555555544

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.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.60  E-value=14  Score=34.16  Aligned_cols=199  Identities=12%  Similarity=0.047  Sum_probs=109.7

Q ss_pred             HHhcCChHHHHHHHHHHHccCCCCCccccCCcc-------hHHHHH-HHHHhcCChHHHHHHHHHhhhC----CCCCChh
Q 040261          132 LCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI-------TYSTIT-DGLCKEGFVDKAKELFLKMKDE----NINPDVV  199 (343)
Q Consensus       132 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-------~~~~l~-~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~  199 (343)
                      .....++.+|..++.++...-+      .|+..       .++.+- ......|+++.|.++-+.....    -..+...
T Consensus       425 ~~s~~r~~ea~~li~~l~~~l~------~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~  498 (894)
T COG2909         425 LASQHRLAEAETLIARLEHFLK------APMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIV  498 (894)
T ss_pred             HHHccChHHHHHHHHHHHHHhC------cCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhh
Confidence            4557789999999988876542      22211       233332 2334578889998887776543    2233456


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHH---HHHHH--HHHHHhCCChhHH--HHHHHHHHHc---CCC---C
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVV---TFNVI--MNELCKNGKMDEA--SRLLELMIQI---GVR---P  266 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l--~~~~~~~~~~~~a--~~~~~~~~~~---~~~---~  266 (343)
                      .+..+..+..-.|++++|..+.....+..-.-+..   .|..+  ...+...|....+  +..+......   ..+   +
T Consensus       499 ~~sv~~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f  578 (894)
T COG2909         499 ALSVLGEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEF  578 (894)
T ss_pred             hhhhhhHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchh
Confidence            67777788888999999999988776542122222   23322  2345566743332  2333332221   111   1


Q ss_pred             CHHHHHHHHHHHhcC-CchHHHHHHHHHHHhCCCCccHHHH--HHHHHHHHhcCChHHHHHHHHHHHhCCCCC
Q 040261          267 DASVYNTLMDGFCLT-GRVNRAKELFVSMESNGCMRDVFSY--GILINGYCKNKEIEGALSLYSEMLSKGIRP  336 (343)
Q Consensus       267 ~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  336 (343)
                      -..+...++.++.+. +...++..-++-.......|-....  ..|+......|+.++|...++++......+
T Consensus       579 ~~~~r~~ll~~~~r~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~  651 (894)
T COG2909         579 LVRIRAQLLRAWLRLDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNG  651 (894)
T ss_pred             HHHHHHHHHHHHHHHhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCC
Confidence            223445555555542 1222333333322222222222222  256778889999999999998887654333

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=90.52  E-value=7.4  Score=30.80  Aligned_cols=134  Identities=13%  Similarity=0.076  Sum_probs=83.3

Q ss_pred             ChHHHHHHHHHhhh-CCCCCChhhHHHHHHHHhcc-C-cHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhCCChhHHH
Q 040261          178 FVDKAKELFLKMKD-ENINPDVVTYTSLIRGFCYA-N-DWNEAKCLFIEMMDQ-GVQPNVVTFNVIMNELCKNGKMDEAS  253 (343)
Q Consensus       178 ~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~-~-~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~  253 (343)
                      ...+|+++|+.... ..+--|......+++..... + ....-.++.+.+... +-.++..+...++..+++.+++.+..
T Consensus       143 ~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~  222 (292)
T PF13929_consen  143 IVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLF  222 (292)
T ss_pred             HHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHH
Confidence            34566666663322 23444666677777666552 1 233333444444432 34677777788888888888888888


Q ss_pred             HHHHHHHHc-CCCCCHHHHHHHHHHHhcCCchHHHHHHHHH-----HHhCCCCccHHHHHHHHH
Q 040261          254 RLLELMIQI-GVRPDASVYNTLMDGFCLTGRVNRAKELFVS-----MESNGCMRDVFSYGILIN  311 (343)
Q Consensus       254 ~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-----~~~~~~~~~~~~~~~l~~  311 (343)
                      ++++..... +...|...|..+++.....|+..-...+.++     +++.++..+...-..+-+
T Consensus       223 ~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L~~  286 (292)
T PF13929_consen  223 QFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQLSE  286 (292)
T ss_pred             HHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHHHH
Confidence            888877665 4456777888888888888888777776653     234455555544444333

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=90.32  E-value=11  Score=32.50  Aligned_cols=63  Identities=13%  Similarity=0.177  Sum_probs=29.3

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      |.....+++..+.....+.-+..+..+|...|  -+-..+..++++|... ..+.-..+|+++.+.
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~  127 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEY  127 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHh
Confidence            33444444555544444555555555554442  2334444555555444 334444455544443

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=90.30  E-value=1.1  Score=21.82  Aligned_cols=28  Identities=25%  Similarity=0.233  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +|..+...|...|++++|.+.|++.++.
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~   30 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5667777888888888888888877653

...

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.20  E-value=12  Score=32.90  Aligned_cols=29  Identities=17%  Similarity=0.218  Sum_probs=14.8

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHH
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLR  114 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  114 (343)
                      +..-|..|.++....+++..|.+.|.+..
T Consensus       665 s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~  693 (794)
T KOG0276|consen  665 SEVKWRQLGDAALSAGELPLASECFLRAR  693 (794)
T ss_pred             chHHHHHHHHHHhhcccchhHHHHHHhhc
Confidence            33445555555555555555555554433

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=90.03  E-value=0.96  Score=22.08  Aligned_cols=27  Identities=15%  Similarity=0.224  Sum_probs=18.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNS   45 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~   45 (343)
                      +|..+...+.+.|++++|...|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            566667777777777777777776654

...

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=90.00  E-value=0.58  Score=21.45  Aligned_cols=23  Identities=17%  Similarity=0.075  Sum_probs=14.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFK   41 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~   41 (343)
                      +...+...+...|++++|..+++
T Consensus         3 a~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    3 ARLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHh
Confidence            34456666777777777776654

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=89.82  E-value=1.1  Score=23.89  Aligned_cols=23  Identities=22%  Similarity=0.352  Sum_probs=11.6

Q ss_pred             HHHHHhcCCchHHHHHHHHHHHh
Q 040261          274 LMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      +..+|...|+.+.|..+++++..
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            34445555555555555555444

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=89.56  E-value=5.6  Score=27.93  Aligned_cols=54  Identities=13%  Similarity=0.083  Sum_probs=35.4

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHHH-HHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLYT-YNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      -...++++++..+++.|.-.  .|+... -..-...+...|++.+|.++|+.+.+.+
T Consensus        20 aL~~~d~~D~e~lLdALrvL--rP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        20 ALRSADPYDAQAMLDALRVL--RPNLKELDMFDGWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HHhcCCHHHHHHHHHHHHHh--CCCccccchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence            34578888888888887653  233322 1222334567888899998888887754

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=89.45  E-value=7.6  Score=29.33  Aligned_cols=159  Identities=16%  Similarity=0.090  Sum_probs=83.3

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCChhh
Q 040261          122 VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPDVVT  200 (343)
Q Consensus       122 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~  200 (343)
                      +..||-+.--+...|+++.|.+.|+...+.++       ....+...-.-++.-.|++.-|.+-+-+.-+.+ -.|-...
T Consensus        99 ~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp-------~y~Ya~lNRgi~~YY~gR~~LAq~d~~~fYQ~D~~DPfR~L  171 (297)
T COG4785          99 PEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP-------TYNYAHLNRGIALYYGGRYKLAQDDLLAFYQDDPNDPFRSL  171 (297)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHhhhHhccCC-------cchHHHhccceeeeecCchHhhHHHHHHHHhcCCCChHHHH
Confidence            45677777777788888888888888887652       112222222222334577777777665554442 1222222


Q ss_pred             HHHHHHHHhccCcHHHHHHHH-HHHHHcCCCCCHHHHHH-HHHHHHhCCChhHHHHHHHHHHHcCCCC-------CHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLF-IEMMDQGVQPNVVTFNV-IMNELCKNGKMDEASRLLELMIQIGVRP-------DASVY  271 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~-~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------~~~~~  271 (343)
                      |-.+.   -+.-++.+|..-+ ++....    |..-|.. ++..|.  |... ...+++++.... ..       =..+|
T Consensus       172 WLYl~---E~k~dP~~A~tnL~qR~~~~----d~e~WG~~iV~~yL--gkiS-~e~l~~~~~a~a-~~n~~~Ae~LTEty  240 (297)
T COG4785         172 WLYLN---EQKLDPKQAKTNLKQRAEKS----DKEQWGWNIVEFYL--GKIS-EETLMERLKADA-TDNTSLAEHLTETY  240 (297)
T ss_pred             HHHHH---HhhCCHHHHHHHHHHHHHhc----cHhhhhHHHHHHHH--hhcc-HHHHHHHHHhhc-cchHHHHHHHHHHH
Confidence            22222   2333555555433 333322    3333332 233332  2211 122333333221 11       13567


Q ss_pred             HHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          272 NTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       272 ~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      --+.+.+...|+.++|..+|+-....+
T Consensus       241 FYL~K~~l~~G~~~~A~~LfKLaiann  267 (297)
T COG4785         241 FYLGKYYLSLGDLDEATALFKLAVANN  267 (297)
T ss_pred             HHHHHHHhccccHHHHHHHHHHHHHHh
Confidence            778888888899999999988777643

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=89.42  E-value=7.2  Score=29.02  Aligned_cols=95  Identities=12%  Similarity=0.110  Sum_probs=68.6

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCH-----HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNV-----VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL  280 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  280 (343)
                      .-+...|++++|..-|...++. +++..     ..|..-..++.+.+.++.|+.-..+.++.+ +........-..+|.+
T Consensus       103 N~~F~ngdyeeA~skY~~Ale~-cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek  180 (271)
T KOG4234|consen  103 NELFKNGDYEEANSKYQEALES-CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEK  180 (271)
T ss_pred             HHhhhcccHHHHHHHHHHHHHh-CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHh
Confidence            4567889999999999998886 23332     334444566778888999988888888876 3344444455567888


Q ss_pred             CCchHHHHHHHHHHHhCCCCccHH
Q 040261          281 TGRVNRAKELFVSMESNGCMRDVF  304 (343)
Q Consensus       281 ~~~~~~a~~~~~~~~~~~~~~~~~  304 (343)
                      ...+++|+.=+..+.+.  .|...
T Consensus       181 ~ek~eealeDyKki~E~--dPs~~  202 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILES--DPSRR  202 (271)
T ss_pred             hhhHHHHHHHHHHHHHh--CcchH
Confidence            88999999999998886  35443

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=89.19  E-value=7.6  Score=30.53  Aligned_cols=87  Identities=14%  Similarity=0.082  Sum_probs=37.9

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh-----
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC-----   98 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----   98 (343)
                      |++++..+++.+++...-+--+.--+....+...-|-.|.+.+++..+.++-....+..-.-+..-|..++..|.     
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLl  169 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLL  169 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHh
Confidence            455555555555544433222111111223334444445555555555555555544322222333444443332     


Q ss_pred             hcCcHHHHHHHH
Q 040261           99 AESRIMEAAALF  110 (343)
Q Consensus        99 ~~~~~~~a~~~~  110 (343)
                      -.|.+++|+++.
T Consensus       170 PLG~~~eAeelv  181 (309)
T PF07163_consen  170 PLGHFSEAEELV  181 (309)
T ss_pred             ccccHHHHHHHH
Confidence            235555555544

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=89.15  E-value=17  Score=32.95  Aligned_cols=32  Identities=16%  Similarity=0.308  Sum_probs=17.2

Q ss_pred             HHHHHHHHHH-----HHhcCChHHHHHHHHHHHhCCCCCC
Q 040261          303 VFSYGILING-----YCKNKEIEGALSLYSEMLSKGIRPT  337 (343)
Q Consensus       303 ~~~~~~l~~~-----~~~~~~~~~a~~~~~~~~~~~~~p~  337 (343)
                      ..++..|++.     +...|++++|++.++++   ++-|.
T Consensus       500 ~~t~~~Ll~L~~ff~~~~~g~~~~AL~~i~~L---~liP~  536 (613)
T PF04097_consen  500 RETFQLLLDLAEFFDLYHAGQYEQALDIIEKL---DLIPL  536 (613)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHT---T-S-S
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhC---CCCCC
Confidence            3445544432     45678888887776665   55563

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=88.95  E-value=1.9  Score=34.70  Aligned_cols=90  Identities=16%  Similarity=0.059  Sum_probs=57.0

Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQP-NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      ..-|.+.|.+++|++.+......  .| +.+++..-..+|.+...+..|+.-...++..+ ..-...|..-+.+-...|.
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~--~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd-~~Y~KAYSRR~~AR~~Lg~  180 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAV--YPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD-KLYVKAYSRRMQARESLGN  180 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhcc--CCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh-HHHHHHHHHHHHHHHHHhh
Confidence            45678888899999888877665  44 77777777888888888887777666665543 1122233333333333455


Q ss_pred             hHHHHHHHHHHHhC
Q 040261          284 VNRAKELFVSMESN  297 (343)
Q Consensus       284 ~~~a~~~~~~~~~~  297 (343)
                      ..+|.+-++...+.
T Consensus       181 ~~EAKkD~E~vL~L  194 (536)
T KOG4648|consen  181 NMEAKKDCETVLAL  194 (536)
T ss_pred             HHHHHHhHHHHHhh
Confidence            55555555555553

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=88.85  E-value=0.78  Score=22.12  Aligned_cols=26  Identities=31%  Similarity=0.484  Sum_probs=15.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNS   45 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~   45 (343)
                      +-.+..++.+.|++++|.+.|+++.+
T Consensus         3 ~~~~a~~~~~~g~~~~A~~~~~~~~~   28 (33)
T PF13174_consen    3 LYRLARCYYKLGDYDEAIEYFQRLIK   28 (33)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            33455555566666666666666554

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=88.48  E-value=6  Score=29.85  Aligned_cols=54  Identities=20%  Similarity=0.126  Sum_probs=29.1

Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHh
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKM  189 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  189 (343)
                      +..+.+.+...+++...+.-.+..       +.+...-..+...++-.|+|++|..-++-.
T Consensus         8 ~seLL~~~sL~dai~~a~~qVkak-------Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~   61 (273)
T COG4455           8 ISELLDDNSLQDAIGLARDQVKAK-------PTDAGGRHFLFQLLCVAGDWEKALAQLNLA   61 (273)
T ss_pred             HHHHHHhccHHHHHHHHHHHHhcC-------CccccchhHHHHHHhhcchHHHHHHHHHHH
Confidence            344455555566655555544442       344445555556666666666665555444

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=88.38  E-value=5.6  Score=30.00  Aligned_cols=76  Identities=20%  Similarity=0.243  Sum_probs=54.6

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC--CCCCHHHHHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG--VRPDASVYNTLMD  276 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~  276 (343)
                      |.+.-++.+.+.+...+++...+.-++.. +.+...-..+++.++-.|++++|..-++-..+..  ..+-..+|..++.
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir   80 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIR   80 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHH
Confidence            45556777888899999999988877763 3345555667889999999999998888776642  1233456666654

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=88.06  E-value=12  Score=29.75  Aligned_cols=66  Identities=6%  Similarity=0.034  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040261          118 CKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK  188 (343)
Q Consensus       118 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  188 (343)
                      ..++..+...++..++..+++.+-.++++.......     ...|...|..++......|+..-...+..+
T Consensus       198 ~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~-----~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  198 KSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSV-----PGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             cCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCC-----CCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            455666667777777777777777777777665521     245666777777777777777666666554

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=87.44  E-value=15  Score=30.16  Aligned_cols=145  Identities=12%  Similarity=0.009  Sum_probs=96.5

Q ss_pred             HHHHHhcCCCCCChhhHHHHHHHHHhcCC------------hhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchH
Q 040261            4 FDYMLRMHPSPPPVCSFNILFGCLAKNKH------------YDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPG   71 (343)
Q Consensus         4 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~------------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   71 (343)
                      |+.-.+.+|  .++.+|-.++..--..-.            .+.-+.++++.++.+ +.+......++..+.+..+.+..
T Consensus         8 l~~~v~~~P--~di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~n-p~~~~L~l~~l~~~~~~~~~~~l   84 (321)
T PF08424_consen    8 LNRRVRENP--HDIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHN-PDSERLLLGYLEEGEKVWDSEKL   84 (321)
T ss_pred             HHHHHHhCc--ccHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCCHHHH
Confidence            344444444  588999888865544322            355677889888775 46677888889999998888888


Q ss_pred             HHHHHHHHHcCCCccHHHHHHHHHHHhhc---CcHHHHHHHHHHHHhc------CC----CCCH-------HHHHHHHHH
Q 040261           72 FVVLGRILRSCFTPDAVTFTSLIKGLCAE---SRIMEAAALFTKLRAF------GC----KPDV-------FTYTTLING  131 (343)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~------~~----~~~~-------~~~~~l~~~  131 (343)
                      .+-++++...... +...|...++.....   -.+.....+|.+..+.      +.    .+..       ..+..+...
T Consensus        85 ~~~we~~l~~~~~-~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l~~L~~~~~~~~~~~~~~~~~e~~~l~v~~r~~~f  163 (321)
T PF08424_consen   85 AKKWEELLFKNPG-SPELWREYLDFRQSNFASFTVSDVRDVYEKCLRALSRRRSGRMTSHPDLPELEEFMLYVFLRLCRF  163 (321)
T ss_pred             HHHHHHHHHHCCC-ChHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHH
Confidence            8999999887433 677888888765442   2355555555554321      11    1111       123334455


Q ss_pred             HHhcCChHHHHHHHHHHHccC
Q 040261          132 LCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       132 ~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      +...|..+.|..+++.+.+..
T Consensus       164 l~~aG~~E~Ava~~Qa~lE~n  184 (321)
T PF08424_consen  164 LRQAGYTERAVALWQALLEFN  184 (321)
T ss_pred             HHHCCchHHHHHHHHHHHHHH
Confidence            667999999999999998866

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=87.41  E-value=9.3  Score=27.88  Aligned_cols=29  Identities=17%  Similarity=0.163  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLC  133 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  133 (343)
                      +++|...|++..+.  +|+...|+.-+....
T Consensus        96 F~kA~~~FqkAv~~--~P~ne~Y~ksLe~~~  124 (186)
T PF06552_consen   96 FEKATEYFQKAVDE--DPNNELYRKSLEMAA  124 (186)
T ss_dssp             HHHHHHHHHHHHHH---TT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc--CCCcHHHHHHHHHHH
Confidence            45566666666655  678888887777663

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.37  E-value=26  Score=32.96  Aligned_cols=115  Identities=14%  Similarity=0.043  Sum_probs=72.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCC---CCCCHHHHHHHHHHHHhcCCc--chHHHHHHHHHHcCCCccHHHHHH--
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIG---LFPDLYTYNILINCFCKMGRV--SPGFVVLGRILRSCFTPDAVTFTS--   92 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~--   92 (343)
                      |..|+..|...|+.++|+++|.+.....   -.--...+..+++-+.+.+..  +..+++-+...+.........+..  
T Consensus       507 y~~Li~LY~~kg~h~~AL~ll~~l~d~~~~~d~~~~~~~e~ii~YL~~l~~~~~~Li~~y~~wvl~~~p~~gi~Ift~~~  586 (877)
T KOG2063|consen  507 YRELIELYATKGMHEKALQLLRDLVDEDSDTDSFQLDGLEKIIEYLKKLGAENLDLILEYADWVLNKNPEAGIQIFTSED  586 (877)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHhccccccccchhhhHHHHHHHHHHhcccchhHHHHHhhhhhccCchhheeeeeccC
Confidence            8999999999999999999999987622   111122344466655566655  566666666655432211111111  


Q ss_pred             ----------HHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040261           93 ----------LIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR  134 (343)
Q Consensus        93 ----------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  134 (343)
                                .+-.+......+-+..+++.+....-.++....+.++..|..
T Consensus       587 ~~~~~sis~~~Vl~~l~~~~~~l~I~YLE~li~~~~~~~~~lht~ll~ly~e  638 (877)
T KOG2063|consen  587 KQEAESISRDDVLNYLKSKEPKLLIPYLEHLISDNRLTSTLLHTVLLKLYLE  638 (877)
T ss_pred             hhhhccCCHHHHHHHhhhhCcchhHHHHHHHhHhccccchHHHHHHHHHHHH
Confidence                      122344556667788888888876656677777777777765

>PRK09687 putative lyase; Provisional

Probab=87.09  E-value=14  Score=29.56  Aligned_cols=235  Identities=10%  Similarity=-0.022  Sum_probs=141.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH----HHHHHHHHHHHhcCCCCCHHH
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI----MEAAALFTKLRAFGCKPDVFT  124 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~  124 (343)
                      .+|..+....+.++...|. ..+...+..+...   +|...-...+.++.+.|+.    .++...+..+...  .++...
T Consensus        34 d~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~V  107 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACV  107 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHH
Confidence            3567777777777777775 3444444455443   3555555666677777653    4677777766443  356666


Q ss_pred             HHHHHHHHHhcCCh-----HHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChh
Q 040261          125 YTTLINGLCRTGHT-----IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVV  199 (343)
Q Consensus       125 ~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  199 (343)
                      -...+.++...+..     ..+...+.....         .++..+-...+.++.+.++. .+...+-.+.+.   ++..
T Consensus       108 R~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---------D~~~~VR~~a~~aLg~~~~~-~ai~~L~~~L~d---~~~~  174 (280)
T PRK09687        108 RASAINATGHRCKKNPLYSPKIVEQSQITAF---------DKSTNVRFAVAFALSVINDE-AAIPLLINLLKD---PNGD  174 (280)
T ss_pred             HHHHHHHHhcccccccccchHHHHHHHHHhh---------CCCHHHHHHHHHHHhccCCH-HHHHHHHHHhcC---CCHH
Confidence            65666666655422     223333333332         23556666777777777764 566666666553   3555


Q ss_pred             hHHHHHHHHhccC-cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          200 TYTSLIRGFCYAN-DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGF  278 (343)
Q Consensus       200 ~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  278 (343)
                      .-...+.++.+.+ +...+...+..+..   .++..+-...+.++.+.++. .+...+-...+.+   +  .....+.++
T Consensus       175 VR~~A~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~AL  245 (280)
T PRK09687        175 VRNWAAFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAA  245 (280)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHH
Confidence            5555566666543 23456666666653   34666677778888888874 4555555555543   2  234677788


Q ss_pred             hcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHH
Q 040261          279 CLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  314 (343)
                      ...|+. +|...+..+...  .||...-...+.++.
T Consensus       246 g~ig~~-~a~p~L~~l~~~--~~d~~v~~~a~~a~~  278 (280)
T PRK09687        246 GELGDK-TLLPVLDTLLYK--FDDNEIITKAIDKLK  278 (280)
T ss_pred             HhcCCH-hHHHHHHHHHhh--CCChhHHHHHHHHHh
Confidence            888885 688888888764  357766666666554

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=86.42  E-value=3.2  Score=24.12  Aligned_cols=29  Identities=21%  Similarity=0.158  Sum_probs=14.4

Q ss_pred             cHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          302 DVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       302 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      |..-...++.+|...|++++|.++++++.
T Consensus        22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~   50 (62)
T PF14689_consen   22 DFLNHLQVIYGLLQLGKYEEAKEYIKELS   50 (62)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            33344445555555555555555555543

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=86.27  E-value=7.2  Score=26.40  Aligned_cols=45  Identities=16%  Similarity=0.225  Sum_probs=27.3

Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      .+.+..+...++.|++......+++|.+.+++..|.++|+-+..+
T Consensus        69 rkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K  113 (149)
T KOG4077|consen   69 RKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK  113 (149)
T ss_pred             HHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            334444455556666666666666666666666666666665544

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=86.25  E-value=15  Score=29.18  Aligned_cols=71  Identities=20%  Similarity=0.151  Sum_probs=48.0

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH-----cCCCCCHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ-----IGVRPDASVY  271 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  271 (343)
                      ++......|..+|.+.+|..+.+..+..+ +.+...+-.++..+...||--.+.+-++++.+     .|+..+...+
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsie  356 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSIE  356 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhHH
Confidence            35555677777788888888777777664 55666777777777778877777776666643     3555554443

>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human

Probab=85.89  E-value=26  Score=31.50  Aligned_cols=62  Identities=6%  Similarity=0.011  Sum_probs=21.9

Q ss_pred             ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          197 DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       197 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      +...-.-++..|.+.|-.+.+..+.+.+-.+-.  ...-|...+..+.+.|+...+..+.+.+.
T Consensus       404 t~~~~~k~l~iC~~~~L~~~a~~I~~~~~~~~~--~~~~~g~AL~~~~ra~d~~~v~~i~~~ll  465 (566)
T PF07575_consen  404 TNDDAEKLLEICAELGLEDVAREICKILGQRLL--KEGRYGEALSWFIRAGDYSLVTRIADRLL  465 (566)
T ss_dssp             SHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHH--HHHHHHHHHHHHH----------------
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334445555566666666666665554443311  12334444555555555555444444443

Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=85.51  E-value=8.6  Score=26.05  Aligned_cols=43  Identities=9%  Similarity=0.176  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          254 RLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      +-++.+...++.|++.+...-+++|.+.+|+..|.++|+.++.
T Consensus        70 kglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~  112 (149)
T KOG4077|consen   70 KGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKD  112 (149)
T ss_pred             HHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3334444444455555555555555555555555555555443

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=84.58  E-value=18  Score=28.45  Aligned_cols=186  Identities=12%  Similarity=0.112  Sum_probs=103.0

Q ss_pred             cCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC---CC--CCChhhHHHHHHHHh
Q 040261          135 TGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE---NI--NPDVVTYTSLIRGFC  209 (343)
Q Consensus       135 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~--~~~~~~~~~l~~~~~  209 (343)
                      ..++++|+.-|++..+..++-+   .-.-.+...++....+.+++++....+.++...   .+  .-+..+.+.++..-.
T Consensus        40 e~~p~~Al~sF~kVlelEgEKg---eWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiS  116 (440)
T KOG1464|consen   40 EDEPKEALSSFQKVLELEGEKG---EWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKSINSILDYIS  116 (440)
T ss_pred             ccCHHHHHHHHHHHHhcccccc---hhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHh
Confidence            3466777777777766542110   011223445677778888888888877776431   11  124556677776666


Q ss_pred             ccCcHHHHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC----C-------CCHHHHHH
Q 040261          210 YANDWNEAKCLFIEMMDQ-----GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV----R-------PDASVYNT  273 (343)
Q Consensus       210 ~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~-------~~~~~~~~  273 (343)
                      ...+.+-...+++.-.+.     +-..--.|-..|...|...+.+.+..++++++.+.--    .       .=..+|..
T Consensus       117 tS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAl  196 (440)
T KOG1464|consen  117 TSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYAL  196 (440)
T ss_pred             hhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhh
Confidence            666555554444433221     1011112334566777777888888888877765311    1       11345666


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhC-CCCccHHHHHHHHHH-----HHhcCChHHHHH
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESN-GCMRDVFSYGILING-----YCKNKEIEGALS  324 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~-----~~~~~~~~~a~~  324 (343)
                      -++.|..+.+-.+...++++.... ..-|.+.... +++-     ..+.|++++|..
T Consensus       197 EIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlImG-vIRECGGKMHlreg~fe~AhT  252 (440)
T KOG1464|consen  197 EIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIMG-VIRECGGKMHLREGEFEKAHT  252 (440)
T ss_pred             HhhhhhhhcccHHHHHHHHHHHHhhccCCchHHHh-HHHHcCCccccccchHHHHHh
Confidence            677777777777777777765421 1234444333 3332     345677777653

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=84.32  E-value=23  Score=29.63  Aligned_cols=166  Identities=11%  Similarity=0.052  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHcC--CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc---------CCCCCH
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF---------GCKPDV  122 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~  122 (343)
                      .+.-+...|...|+++.|++.|.+....-  .......|..+|..-.-.|+|.....+..+..+.         .+.+..
T Consensus       152 a~~Dl~dhy~~cG~l~~Alr~YsR~RdYCTs~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl  231 (466)
T KOG0686|consen  152 ALEDLGDHYLDCGQLDNALRCYSRARDYCTSAKHVINMCLNLILVSIYMGNWGHVLSYISKAESTPDANENLAQEVPAKL  231 (466)
T ss_pred             HHHHHHHHHHHhccHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCchhhhhHHHhcCcch
Confidence            56677788888899999999888855421  1223455666666667778888777777666554         122233


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHH-----HHHhhhCCCCCC
Q 040261          123 FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKEL-----FLKMKDENINPD  197 (343)
Q Consensus       123 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-----~~~~~~~~~~~~  197 (343)
                      ..+..+...+.+  ++..|.+.|-.......++...+.|...+.-..+.+...-++-+--..+     |+...+    ..
T Consensus       232 ~C~agLa~L~lk--kyk~aa~~fL~~~~~~~d~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~Fk~fle----l~  305 (466)
T KOG0686|consen  232 KCAAGLANLLLK--KYKSAAKYFLLAEFDHCDYPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESFKLFLE----LE  305 (466)
T ss_pred             HHHHHHHHHHHH--HHHHHHHHHHhCCCCccCccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhhhhHHh----cC
Confidence            344444444433  6666666554443333222222333333333333444433333322222     222222    23


Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      +.....+...|  .+++..++++++++...
T Consensus       306 Pqlr~il~~fy--~sky~~cl~~L~~~k~~  333 (466)
T KOG0686|consen  306 PQLREILFKFY--SSKYASCLELLREIKPR  333 (466)
T ss_pred             hHHHHHHHHHh--hhhHHHHHHHHHHhccc
Confidence            34444444433  35677888887776543

>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane

Probab=84.32  E-value=6  Score=24.24  Aligned_cols=46  Identities=13%  Similarity=0.078  Sum_probs=29.1

Q ss_pred             cCCchHHHHHHHHHHHhCCCCcc--HHHHHHHHHHHHhcCChHHHHHH
Q 040261          280 LTGRVNRAKELFVSMESNGCMRD--VFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      ...+.++|+..|....+.-..+.  -.++..++.+|+..|++.++++.
T Consensus        18 ~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~~L~f   65 (80)
T PF10579_consen   18 HQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYREMLAF   65 (80)
T ss_pred             ccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56667777777777665432221  23556667777777777776654

Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane

>smart00028 TPR Tetratricopeptide repeats

Probab=84.28  E-value=2.8  Score=19.30  Aligned_cols=27  Identities=30%  Similarity=0.331  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          305 SYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      .|..+...+...|+++.|...+++.++
T Consensus         3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~   29 (34)
T smart00028        3 ALYNLGNAYLKLGDYDEALEYYEKALE   29 (34)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            445566666667777777777766653

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=83.21  E-value=10  Score=24.57  Aligned_cols=81  Identities=12%  Similarity=0.096  Sum_probs=49.4

Q ss_pred             cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHH
Q 040261           30 NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAAL  109 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  109 (343)
                      ....++|..+-+.+...+- ....+-.+-+.++...|+++.|..+.+..    ..||...|..+...  +.|..+.+..-
T Consensus        18 ~HcHqEA~tIAdwL~~~~~-~~E~v~lIRlsSLmNrG~Yq~Al~l~~~~----~~pdlepw~ALce~--rlGl~s~l~~r   90 (115)
T TIGR02508        18 HHCHQEANTIADWLHLKGE-SEEAVQLIRLSSLMNRGDYQSALQLGNKL----CYPDLEPWLALCEW--RLGLGSALESR   90 (115)
T ss_pred             chHHHHHHHHHHHHhcCCc-hHHHHHHHHHHHHHccchHHHHHHhcCCC----CCchHHHHHHHHHH--hhccHHHHHHH
Confidence            3456777777777765431 12222233344566778888887776655    36777777666543  55666666666


Q ss_pred             HHHHHhcC
Q 040261          110 FTKLRAFG  117 (343)
Q Consensus       110 ~~~~~~~~  117 (343)
                      +.+|...|
T Consensus        91 l~rla~sg   98 (115)
T TIGR02508        91 LNRLAASG   98 (115)
T ss_pred             HHHHHhCC
Confidence            66666665

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]

Probab=82.71  E-value=4.2  Score=35.45  Aligned_cols=90  Identities=18%  Similarity=0.131  Sum_probs=65.4

Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHH
Q 040261          242 ELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEG  321 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  321 (343)
                      .+...|+...|.+.+..+..............|.....+.|....|..++.+..... ...+.++..+.+++....+.+.
T Consensus       616 ywr~~gn~~~a~~cl~~a~~~~p~~~~v~~v~la~~~~~~~~~~da~~~l~q~l~~~-~sepl~~~~~g~~~l~l~~i~~  694 (886)
T KOG4507|consen  616 YWRAVGNSTFAIACLQRALNLAPLQQDVPLVNLANLLIHYGLHLDATKLLLQALAIN-SSEPLTFLSLGNAYLALKNISG  694 (886)
T ss_pred             eeeecCCcHHHHHHHHHHhccChhhhcccHHHHHHHHHHhhhhccHHHHHHHHHhhc-ccCchHHHhcchhHHHHhhhHH
Confidence            334568888888888777654211122334556666677778888888887776654 4567788889999999999999


Q ss_pred             HHHHHHHHHhC
Q 040261          322 ALSLYSEMLSK  332 (343)
Q Consensus       322 a~~~~~~~~~~  332 (343)
                      |++.|++..+.
T Consensus       695 a~~~~~~a~~~  705 (886)
T KOG4507|consen  695 ALEAFRQALKL  705 (886)
T ss_pred             HHHHHHHHHhc
Confidence            99999998865

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=82.68  E-value=22  Score=28.19  Aligned_cols=132  Identities=12%  Similarity=0.093  Sum_probs=61.4

Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHhCCChhHHHHHHHHHHH----cCCCCCHHHHHHHHH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPNV-------VTFNVIMNELCKNGKMDEASRLLELMIQ----IGVRPDASVYNTLMD  276 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~~~l~~  276 (343)
                      ..+.+++++|+..+.++...|+..+.       .+...+...|...|++....+......+    ..-+....+...|+.
T Consensus        13 ~v~~~~~~~ai~~yk~iL~kg~s~dek~~nEqE~tvlel~~lyv~~g~~~~l~~~i~~sre~m~~ftk~k~~KiirtLie   92 (421)
T COG5159          13 AVKSNDIEKAIGEYKRILGKGVSKDEKTLNEQEATVLELFKLYVSKGDYCSLGDTITSSREAMEDFTKPKITKIIRTLIE   92 (421)
T ss_pred             hhhhhhHHHHHHHHHHHhcCCCChhhhhhhHHHHHHHHHHHHHHhcCCcchHHHHHHhhHHHHHHhcchhHHHHHHHHHH
Confidence            34445555555555555555443332       2233345555555555544433322211    111223344455555


Q ss_pred             HHhcC-CchHHHHHHHHHHHhCCCCccH-----HHHHHHHHHHHhcCChHHHHHHHHHH----HhCCCCCCcc
Q 040261          277 GFCLT-GRVNRAKELFVSMESNGCMRDV-----FSYGILINGYCKNKEIEGALSLYSEM----LSKGIRPTVV  339 (343)
Q Consensus       277 ~~~~~-~~~~~a~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~~p~~~  339 (343)
                      .+... ..++....++....+....-..     ..-.-++..+.+.|.+.+|+.+...+    .+.+-+|+.+
T Consensus        93 kf~~~~dsl~dqi~v~~~~iewA~rEkr~fLr~~Le~Kli~l~y~~~~YsdalalIn~ll~ElKk~DDK~~Li  165 (421)
T COG5159          93 KFPYSSDSLEDQIKVLTALIEWADREKRKFLRLELECKLIYLLYKTGKYSDALALINPLLHELKKYDDKINLI  165 (421)
T ss_pred             hcCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHhhcCcccee
Confidence            54433 2355555555544432111111     11234566778888888888665544    3334444443

>PRK09687 putative lyase; Provisional

Probab=82.29  E-value=24  Score=28.25  Aligned_cols=219  Identities=15%  Similarity=0.099  Sum_probs=113.1

Q ss_pred             ccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCh----HHHHHHHHHHHccCCCCCcccc
Q 040261           85 PDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT----IVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        85 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      +|.......+.++...|. .++...+..+...   ++...-...+.++...|+.    .++...+..+...+        
T Consensus        35 ~d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~D--------  102 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALED--------  102 (280)
T ss_pred             CCHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhcC--------
Confidence            355555555566655554 3333334344332   3555555556666666653    35666666653332        


Q ss_pred             CCcchHHHHHHHHHhcCCh-----HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHH
Q 040261          161 PDAITYSTITDGLCKEGFV-----DKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVT  235 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  235 (343)
                      ++..+-...+.++...+..     ..+...+......   ++..+-...+.++.+.++ .++...+-.+.+.   ++..+
T Consensus       103 ~d~~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~D---~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~V  175 (280)
T PRK09687        103 KSACVRASAINATGHRCKKNPLYSPKIVEQSQITAFD---KSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDV  175 (280)
T ss_pred             CCHHHHHHHHHHHhcccccccccchHHHHHHHHHhhC---CCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHH
Confidence            4445555555555444321     2233333333322   345555566666666665 3455555555542   33334


Q ss_pred             HHHHHHHHHhCC-ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHH
Q 040261          236 FNVIMNELCKNG-KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       236 ~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  314 (343)
                      -...+.++.+.+ +...+...+..+..   .++..+-...+.++.+.|+. .|...+-...+.+   +  .....+.++.
T Consensus       176 R~~A~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg  246 (280)
T PRK09687        176 RNWAAFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAG  246 (280)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHH
Confidence            344444444432 23345555555543   44666666677777777764 4555555544432   2  2335667777


Q ss_pred             hcCChHHHHHHHHHHHhC
Q 040261          315 KNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       315 ~~~~~~~a~~~~~~~~~~  332 (343)
                      ..|+. +|+..+.++.+.
T Consensus       247 ~ig~~-~a~p~L~~l~~~  263 (280)
T PRK09687        247 ELGDK-TLLPVLDTLLYK  263 (280)
T ss_pred             hcCCH-hHHHHHHHHHhh
Confidence            77774 577777777653

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.79  E-value=19  Score=26.76  Aligned_cols=93  Identities=10%  Similarity=0.022  Sum_probs=43.7

Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHH
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGF  208 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  208 (343)
                      ...+...+++++|..-++.......+    -.....+-..|.+.....|.+++|+..++.....+..  ......-...+
T Consensus        96 Ak~~ve~~~~d~A~aqL~~~l~~t~D----e~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w~--~~~~elrGDil  169 (207)
T COG2976          96 AKAEVEANNLDKAEAQLKQALAQTKD----ENLKALAALRLARVQLQQKKADAALKTLDTIKEESWA--AIVAELRGDIL  169 (207)
T ss_pred             HHHHHhhccHHHHHHHHHHHHccchh----HHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccHH--HHHHHHhhhHH
Confidence            34455666666666666655532210    0000111222334455556666666666555443211  11222333455


Q ss_pred             hccCcHHHHHHHHHHHHHc
Q 040261          209 CYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~  227 (343)
                      ...|+-++|..-|+..++.
T Consensus       170 l~kg~k~~Ar~ay~kAl~~  188 (207)
T COG2976         170 LAKGDKQEARAAYEKALES  188 (207)
T ss_pred             HHcCchHHHHHHHHHHHHc
Confidence            5556666666666655554

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]

Probab=81.12  E-value=28  Score=28.26  Aligned_cols=132  Identities=14%  Similarity=0.120  Sum_probs=73.8

Q ss_pred             CCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH----cCCCCCHH
Q 040261          195 NPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ-GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ----IGVRPDAS  269 (343)
Q Consensus       195 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~  269 (343)
                      ..|...++.+..+  +....++..+..+...+. |-.--...+......|++.||.+.|.+.+.+..+    .|.+.|..
T Consensus        67 ~~D~~~l~~m~~~--neeki~eld~~iedaeenlGE~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~g~kiDVv  144 (393)
T KOG0687|consen   67 KLDQDLLNSMKKA--NEEKIKELDEKIEDAEENLGESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSLGHKIDVV  144 (393)
T ss_pred             eccHHHHHHHHHh--hHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhcccchhhH
Confidence            3455555555442  233344444555555443 2112234566677889999999999888876544    46666655


Q ss_pred             HHHHHHH-HHhcCCchHHHHHHHHHHHhCCCCccH----HHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          270 VYNTLMD-GFCLTGRVNRAKELFVSMESNGCMRDV----FSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       270 ~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      .+..-+- .|....-+.+-.+..+.+.+.|...+.    .+|..+-  |....++.+|-.+|-+..
T Consensus       145 f~~iRlglfy~D~~lV~~~iekak~liE~GgDWeRrNRlKvY~Gly--~msvR~Fk~Aa~Lfld~v  208 (393)
T KOG0687|consen  145 FYKIRLGLFYLDHDLVTESIEKAKSLIEEGGDWERRNRLKVYQGLY--CMSVRNFKEAADLFLDSV  208 (393)
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHHHHHhCCChhhhhhHHHHHHHH--HHHHHhHHHHHHHHHHHc
Confidence            4443222 333333345555556666666655543    3444333  344567888888876654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	343
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	7e-19
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-18
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	6e-17
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-14
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 87.2 bits (214), Expect = 7e-19
 Identities = 17/173 (9%), Positives = 47/173 (27%), Gaps = 4/173 (2%)

Query: 175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFI---EMMDQGVQP 231
            +  +D  +    +     ++       +  +     +    A  L +       +    
Sbjct: 104 GKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL 163

Query: 232 NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA-KEL 290
            +  +N +M    + G   E   +L ++   G+ PD   Y   +       +     +  
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223

Query: 291 FVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTVVTYNT 343
              M   G         +L++   +   ++    +          P  V  + 
Sbjct: 224 LEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSK 276

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 86.0 bits (211), Expect = 2e-18
 Identities = 22/220 (10%), Positives = 69/220 (31%), Gaps = 4/220 (1%)

Query: 84  TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALN 143
           +P       L++    +  +    A   +                      T    +A +
Sbjct: 89  SPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHH 148

Query: 144 LFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTS 203
           L         +  +        Y+ +  G  ++G   +   +   +KD  + PD+++Y +
Sbjct: 149 LLVVHHGQRQKRKL---LTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA 205

Query: 204 LIRGFCYANDWNEA-KCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI 262
            ++     +      +    +M  +G++   +   V+++E  +   +    ++       
Sbjct: 206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

Query: 263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD 302
              P     + L+             +L + +++  C+ +
Sbjct: 266 PQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFE 305

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 81.4 bits (199), Expect = 6e-17
 Identities = 17/132 (12%), Positives = 37/132 (28%), Gaps = 3/132 (2%)

Query: 215 NEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTL 274
             A CL          P       ++ E      +D          Q  +          
Sbjct: 74  QMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAF 133

Query: 275 MDGFCLTGRVNRAKELFV---SMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS 331
                LT ++  A  L V          +  +  Y  ++ G+ +    +  + +   +  
Sbjct: 134 FKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKD 193

Query: 332 KGIRPTVVTYNT 343
            G+ P +++Y  
Sbjct: 194 AGLTPDLLSYAA 205

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 72.9 bits (177), Expect = 3e-14
 Identities = 18/179 (10%), Positives = 48/179 (26%), Gaps = 10/179 (5%)

Query: 42  RLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVL---GRILRSCFTPDAVTFTSLIKGLC 98
           + +   L            C     ++     +L       +         + +++ G  
Sbjct: 117 QHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWA 176

Query: 99  AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI-VALNLFEEMANGNGEFGV 157
            +    E   +   ++  G  PD+ +Y   +  + R            E+M+        
Sbjct: 177 RQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEG----- 231

Query: 158 VCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNE 216
             K  A+  + +     +   +    ++          P  V  + L+R     +    
Sbjct: 232 -LKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVS 289

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 57.9 bits (138), Expect = 3e-09
 Identities = 15/151 (9%), Positives = 43/151 (28%), Gaps = 3/151 (1%)

Query: 3   IFDYMLRM--HPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILIN 60
           +               +  +N +    A+   +  ++ +   +   GL PDL +Y   + 
Sbjct: 149 LLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208

Query: 61  CFCKMGRVSPGFV-VLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK 119
           C  +  + +      L ++ +      A+    L+      + +     +          
Sbjct: 209 CMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQL 268

Query: 120 PDVFTYTTLINGLCRTGHTIVALNLFEEMAN 150
           P     + L+  +      +    L   +  
Sbjct: 269 PPPVNTSKLLRDVYAKDGRVSYPKLHLPLKT 299

>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 = 45.6 bits (107), Expect = 2e-05
 Identities = 67/497 (13%), Positives = 140/497 (28%), Gaps = 190/497 (38%)

Query: 4   FDYMLRMHPSPPPVCSFNILFGCL--------------AKNKHYDTVLSLFK-------- 41
            D+++    S   V     LF  L                  +Y  ++S  K        
Sbjct: 51  IDHIIM---SKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSM 107

Query: 42  ----------RL-NSIGLFPDLYTYNI--------LINCFCKMGRVSPGFVVLG------ 76
                     RL N   +F     YN+        L     ++ R +   ++ G      
Sbjct: 108 MTRMYIEQRDRLYNDNQVFAK---YNVSRLQPYLKLRQALLEL-RPAKNVLIDGVLGSGK 163

Query: 77  -----RILRS----CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT 127
                 +  S    C     + + +L      E+ +     L  ++      P+   +T+
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI-----DPN---WTS 215

Query: 128 LINGLCRTGHTIVAL-----NLFEEMANGNG--------------EFGVVCKPDAIT-YS 167
             +        I ++      L +     N                F + CK    T + 
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK 275

Query: 168 TITDGL------------CKEGFV-DKAKELFLK---MKDE-------NINPDVVTYTSL 204
            +TD L                   D+ K L LK    + +         NP  +   S+
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL---SI 332

Query: 205 I-----RGFCYANDWNEAKC--------LFIEMMDQGV-----------QPNV-VTFNV- 238
           I      G    ++W    C          + +++               P+  +   + 
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392

Query: 239 --------------IMNELCKNG--KMDEASRLLELM-IQIGVRP----DASVYNTLMDG 277
                         ++N+L K    +       + +  I + ++     + +++ +++D 
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD- 451

Query: 278 FCLTGRVNRAKELFVSMESNGCMRD-----VFSYGILINGY-CKNKEIEGALSLYSEM-- 329
                  N  K      +S+  +        +S+ I   G+  KN E    ++L+  +  
Sbjct: 452 -----HYNIPKTF----DSDDLIPPYLDQYFYSH-I---GHHLKNIEHPERMTLFRMVFL 498

Query: 330 ----LSKGIRPTVVTYN 342
               L + IR     +N
Sbjct: 499 DFRFLEQKIRHDSTAWN 515

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	343
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.98
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.97
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.96
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.93
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.93
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.93
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.92
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.92
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.91
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.91
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.9
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.9
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.89
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.89
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.88
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.88
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.86
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.85
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.83
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.83
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.81
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.81
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.81
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.81
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.8
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.8
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.8
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.8
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.79
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.79
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.79
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.78
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.77
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.77
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.77
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.76
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.76
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.76
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.76
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.75
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.75
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.74
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.74
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.74
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.73
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.71
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.71
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.71
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.71
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.7
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.69
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.67
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.67
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.67
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.67
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.66
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.64
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.64
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.64
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.63
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.62
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.62
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.62
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.6
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.59
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.59
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.59
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.58
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.56
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.55
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.55
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.54
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.53
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.5
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.46
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.46
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.45
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.44
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.39
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.38
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.36
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.35
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.34
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.33
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.33
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.32
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.32
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.32
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.31
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.31
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.31
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.3
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.3
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.29
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.29
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.28
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.28
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.26
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.25
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.25
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.23
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.21
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.2
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.2
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.18
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	99.14
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.11
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.11
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	99.11
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.11
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.07
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.05
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.04
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.03
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	99.03
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.02
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	99.01
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.01
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	99.01
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	99.0
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.99
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.98
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.98
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.97
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.97
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.97
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.96
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.94
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.93
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.93
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.93
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.93
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.92
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.92
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.92
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.91
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.9
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.9
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.9
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.89
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.89
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.87
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.86
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.85
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.82
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.82
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.82
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.81
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.79
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.79
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.78
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.76
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.76
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.76
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.76
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.75
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.73
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.73
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.72
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.71
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.7
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.69
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.69
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.67
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.67
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.66
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.63
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.62
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.57
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.54
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.53
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.53
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.52
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.49
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.49
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.49
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.49
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.48
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.47
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.45
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.43
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.43
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.41
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.4
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.38
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.38
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.37
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.31
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.29
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.27
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.21
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.17
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.13
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.11
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.11
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.1
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	98.1
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.05
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.98
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.92
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.8
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.73
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.63
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.47
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.44
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.42
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.37
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.36
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.34
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.33
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.29
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.29
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.26
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.19
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.99
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.98
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.95
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.93
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.89
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.85
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	96.82
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.81
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.81
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.59
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.32
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.98
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.93
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	95.53
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	95.5
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.33
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.27
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.21
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	95.2
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	95.13
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.1
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	95.03
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.98
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	94.77
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.28
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	94.22
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	94.21
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.17
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	93.93
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	93.81
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.72
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	93.68
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	92.88
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	92.56
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	92.47
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	89.73
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	89.17
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	88.5
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	88.14
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	87.32
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	87.19
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	86.9
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	86.77
2wvi_A	164	Mitotic checkpoint serine/threonine-protein kinase	85.3
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	85.2
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.27
2p58_C	116	Putative type III secretion protein YSCG; type III	83.78
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	82.57
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	82.47
3eiq_C	358	Programmed cell death protein 4; PDCD4, anti-oncog	80.89
4aez_C	223	MAD3, mitotic spindle checkpoint component MAD3; c	80.75

>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=9.3e-34  Score=238.79  Aligned_cols=203  Identities=17%  Similarity=0.246  Sum_probs=175.3

Q ss_pred             hHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC---------cchHHH
Q 040261            3 IFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR---------VSPGFV   73 (343)
Q Consensus         3 i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~~~a~~   73 (343)
                      ++..+.+.+..+.+...++.+|+.|++.|++++|+++|++|.+.|+.||..+|+.+|.+|++.+.         ++.|.+
T Consensus        12 L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~   91 (501)
T 4g26_A           12 LSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFD   91 (501)
T ss_dssp             ------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHH
T ss_pred             HHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHH
Confidence            34556666665233446888999999999999999999999999999999999999999987665         567899


Q ss_pred             HHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCC
Q 040261           74 VLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNG  153 (343)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  153 (343)
                      +|++|...|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.+ 
T Consensus        92 lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G-  170 (501)
T 4g26_A           92 IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESE-  170 (501)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcC-
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999988 


Q ss_pred             CCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          154 EFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       154 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                           +.|+..+|+.|+.+|++.|+.++|.++|++|.+.+..|+..||+.++..+...
T Consensus       171 -----~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          171 -----VVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             -----CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             -----CCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence                 89999999999999999999999999999999999999999999999888764

>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=2e-33  Score=236.82  Aligned_cols=205  Identities=14%  Similarity=0.219  Sum_probs=177.3

Q ss_pred             HHHHHHHHHHcCCCcc-HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC---------hHH
Q 040261           71 GFVVLGRILRSCFTPD-AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH---------TIV  140 (343)
Q Consensus        71 a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~~~  140 (343)
                      +..+.+++.+.+..+. ...++.+|++|++.|++++|+++|++|.+.|+.||..+|+.++.+|++.+.         .+.
T Consensus         9 ~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~   88 (501)
T 4g26_A            9 SENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSR   88 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHH
T ss_pred             HHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHH
Confidence            3444555555554433 345777888888888999999999998888888888899988888887654         678


Q ss_pred             HHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHH
Q 040261          141 ALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCL  220 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  220 (343)
                      |.++|++|...+      +.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++
T Consensus        89 A~~lf~~M~~~G------~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l  162 (501)
T 4g26_A           89 GFDIFKQMIVDK------VVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV  162 (501)
T ss_dssp             HHHHHHHHHHTT------CCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhC------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHH
Confidence            999999999998      89999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC
Q 040261          221 FIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT  281 (343)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  281 (343)
                      |++|.+.|+.||..+|+.|+.+|++.|+.++|.+++++|.+.+..|+..||+.++..|...
T Consensus       163 ~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          163 DAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999999999998764

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.2e-31  Score=232.85  Aligned_cols=298  Identities=10%  Similarity=-0.012  Sum_probs=268.9

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      +..|.+.|++++|.++|+++.+.  +++..+++.++..+.+.|++++|.++|+++.+.+. .+..++..++.++.+.|++
T Consensus       279 ~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~  355 (597)
T 2xpi_A          279 LNKTSHEDELRRAEDYLSSINGL--EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEK  355 (597)
T ss_dssp             SCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCH
T ss_pred             HHHHcCcchHHHHHHHHHHhhcC--CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCH
Confidence            55666889999999999999875  58899999999999999999999999999998763 3788899999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                      ++|.++++++.+.. +.+..++..++.+|.+.|++++|.++|+++.+..       +.+..+|+.++.+|.+.|++++|+
T Consensus       356 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~~~~l~~~~~~~g~~~~A~  427 (597)
T 2xpi_A          356 NKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-------PQFGPAWIGFAHSFAIEGEHDQAI  427 (597)
T ss_dssp             HHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999998764 3478899999999999999999999999998864       456789999999999999999999


Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc-
Q 040261          184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI-  262 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-  262 (343)
                      ++|+++.+.+ +.+..+|..++.+|.+.|++++|..+|+.+.+.. +.+..+|..++..+.+.|++++|..+|+++.+. 
T Consensus       428 ~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  505 (597)
T 2xpi_A          428 SAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLV  505 (597)
T ss_dssp             HHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhh
Confidence            9999998864 4578999999999999999999999999999874 557889999999999999999999999999886 


Q ss_pred             ---CCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCC
Q 040261          263 ---GVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPT  337 (343)
Q Consensus       263 ---~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  337 (343)
                         +..|+  ..+|..++.+|.+.|++++|.+.++++.+.+ +.+..+|..+..+|.+.|++++|.+.|+++.+.  .|+
T Consensus       506 ~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~p~  582 (597)
T 2xpi_A          506 KKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAI--SPN  582 (597)
T ss_dssp             HHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             hccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCC
Confidence               55677  7899999999999999999999999998865 458899999999999999999999999999976  454

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1e-30  Score=228.64  Aligned_cols=308  Identities=13%  Similarity=0.084  Sum_probs=212.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHh-C--------------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNS-I--------------GLFPDLYTYNILINCFCKMGRVSPGFVVLGRIL   79 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~--------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   79 (343)
                      +++.+++.++.+|.+.|++++|.++|+++.. .              +.+++..+|+.++.+|.+.|++++|.++|+++.
T Consensus       148 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  227 (597)
T 2xpi_A          148 RSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEAL  227 (597)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4556666666666666666666666653211 1              112345566666666666666666666666665


Q ss_pred             HcCC----------------------------------------------------------------------CccHHH
Q 040261           80 RSCF----------------------------------------------------------------------TPDAVT   89 (343)
Q Consensus        80 ~~~~----------------------------------------------------------------------~~~~~~   89 (343)
                      +.++                                                                      +++..+
T Consensus       228 ~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  307 (597)
T 2xpi_A          228 MVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDL  307 (597)
T ss_dssp             HHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHH
T ss_pred             HhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHH
Confidence            4331                                                                      134455


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTI  169 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  169 (343)
                      ++.++.++.+.|++++|.++|+++.+.+.. +..++..++.++.+.|++++|..+++++....       +.+..++..+
T Consensus       308 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~~~~l  379 (597)
T 2xpi_A          308 LLCKADTLFVRSRFIDVLAITTKILEIDPY-NLDVYPLHLASLHESGEKNKLYLISNDLVDRH-------PEKAVTWLAV  379 (597)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------TTSHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-------cccHHHHHHH
Confidence            555555566666666666666665554322 44455555666666666666666666655432       4456777788


Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCh
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM  249 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  249 (343)
                      +.+|.+.|++++|.++|+++.+.. +.+..+|+.++.++.+.|++++|..+|+++.+.+ +.+..++..++.+|.+.|++
T Consensus       380 ~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~  457 (597)
T 2xpi_A          380 GIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNI  457 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCH
Confidence            888888888888888888877643 3356788888888888888888888888887764 45677888888888888888


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCcc--HHHHHHHHHHHHhcCChHHHH
Q 040261          250 DEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMRD--VFSYGILINGYCKNKEIEGAL  323 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~~~~~~a~  323 (343)
                      ++|..+|+++.+.. +.+..+|+.++..|.+.|++++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.
T Consensus       458 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  536 (597)
T 2xpi_A          458 LLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAI  536 (597)
T ss_dssp             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHH
Confidence            88888888888765 556788888888888888888888888888765    44566  678888888888888888888


Q ss_pred             HHHHHHHhCC
Q 040261          324 SLYSEMLSKG  333 (343)
Q Consensus       324 ~~~~~~~~~~  333 (343)
                      +.++++.+.+
T Consensus       537 ~~~~~~~~~~  546 (597)
T 2xpi_A          537 DALNQGLLLS  546 (597)
T ss_dssp             HHHHHHHHHS
T ss_pred             HHHHHHHHhC
Confidence            8888887664

>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=99.98  E-value=9e-28  Score=198.91  Aligned_cols=317  Identities=14%  Similarity=0.082  Sum_probs=264.0

Q ss_pred             HHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261            4 FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus         4 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      ++...+..|  .+..+|..+...+.+.|++++|...|+++.+.. +.+...|..+..++.+.|++++|.+.++++.+..+
T Consensus        56 ~~~a~~~~p--~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p  132 (388)
T 1w3b_A           56 STLAIKQNP--LLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNP  132 (388)
T ss_dssp             HHHHHHHCT--TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT
T ss_pred             HHHHHhcCC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            344444443  578888888999999999999999998887754 34556788888888899999999999988887642


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA  163 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  163 (343)
                       .+...+..+...+...|++++|.+.|+++.+..+. +..++..+...+...|++++|...|+++....       +.+.
T Consensus       133 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------p~~~  203 (388)
T 1w3b_A          133 -DLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPN-FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-------PNFL  203 (388)
T ss_dssp             -TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-------TTCH
T ss_pred             -CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-------CCcH
Confidence             24566777888888889999999999998877433 57788888899999999999999999988865       4456


Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      ..+..+...+...|++++|...+++..... +.+..++..+..++...|++++|...++++.+.+ +.+..++..+..++
T Consensus       204 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  281 (388)
T 1w3b_A          204 DAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANAL  281 (388)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            788888899999999999999998887754 3357888899999999999999999999999874 44577899999999


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHH
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGAL  323 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  323 (343)
                      .+.|++++|...++++.+.. +.+..++..+...+...|++++|...++++.+.. +.+..++..+...|.+.|++++|.
T Consensus       282 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~  359 (388)
T 1w3b_A          282 KEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEAL  359 (388)
T ss_dssp             HHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999999875 6788899999999999999999999999998863 446788999999999999999999


Q ss_pred             HHHHHHHhCCCCCCc
Q 040261          324 SLYSEMLSKGIRPTV  338 (343)
Q Consensus       324 ~~~~~~~~~~~~p~~  338 (343)
                      +.|+++++.  .|+.
T Consensus       360 ~~~~~a~~~--~p~~  372 (388)
T 1w3b_A          360 MHYKEAIRI--SPTF  372 (388)
T ss_dssp             HHHHHHHTT--CTTC
T ss_pred             HHHHHHHhh--CCCC
Confidence            999999854  5653

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.97  E-value=4.5e-27  Score=194.69  Aligned_cols=318  Identities=15%  Similarity=0.078  Sum_probs=277.7

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.++.+.+..|  .+...+..+...+.+.|++++|...++...+.. +.+..+|..+..++.+.|++++|...|+++.+.
T Consensus        20 ~~~~~~~~~~p--~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   96 (388)
T 1w3b_A           20 RHCMQLWRQEP--DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRL   96 (388)
T ss_dssp             HHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            35666666665  478889999999999999999999999988755 567889999999999999999999999999986


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      . +.+..+|..+..++.+.|++++|.+.|+++.+..+. +...+..+...+...|++++|.+.|+++....       +.
T Consensus        97 ~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------p~  167 (388)
T 1w3b_A           97 K-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPD-LYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-------PN  167 (388)
T ss_dssp             C-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTT-CTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-------TT
T ss_pred             C-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CC
Confidence            4 335678999999999999999999999999987543 45577788899999999999999999999865       45


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      +..++..+...+.+.|++++|...|+++.+.+ +.+...+..+...+...|++++|...+++..+.. +.+..++..+..
T Consensus       168 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~  245 (388)
T 1w3b_A          168 FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLAC  245 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHH
Confidence            67889999999999999999999999998865 3457888999999999999999999999998874 445788899999


Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHH
Q 040261          242 ELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEG  321 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  321 (343)
                      ++...|++++|...++++.+.+ +.+..++..+...+.+.|++++|...++++.+.. +.+..++..+...+...|++++
T Consensus       246 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~  323 (388)
T 1w3b_A          246 VYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEE  323 (388)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHH
Confidence            9999999999999999999875 5567889999999999999999999999998864 5678899999999999999999


Q ss_pred             HHHHHHHHHhCCCCCC
Q 040261          322 ALSLYSEMLSKGIRPT  337 (343)
Q Consensus       322 a~~~~~~~~~~~~~p~  337 (343)
                      |.+.++++.+.  .|+
T Consensus       324 A~~~~~~al~~--~p~  337 (388)
T 1w3b_A          324 AVRLYRKALEV--FPE  337 (388)
T ss_dssp             HHHHHHHHTTS--CTT
T ss_pred             HHHHHHHHHhc--CCC
Confidence            99999999864  454

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.96  E-value=4.8e-26  Score=192.25  Aligned_cols=308  Identities=14%  Similarity=0.069  Sum_probs=263.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++..+..++..+.+.|++++|+.+|+++.+.. +.+..++..+..++...|++++|...++++.+.+. .+..++..+.
T Consensus        24 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~  101 (450)
T 2y4t_A           24 ADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKM-DFTAARLQRG  101 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CcHHHHHHHH
Confidence            578899999999999999999999999998764 55788999999999999999999999999998753 3688899999


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCH---HHHHHH------------HHHHHhcCChHHHHHHHHHHHccCCCCCccc
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDV---FTYTTL------------INGLCRTGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      .++.+.|++++|.+.|+++.+.... +.   ..+..+            ...+...|++++|...++++....       
T Consensus       102 ~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-------  173 (450)
T 2y4t_A          102 HLLLKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-------  173 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------
Confidence            9999999999999999999987432 33   455544            445899999999999999999865       


Q ss_pred             cCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          160 KPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVI  239 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  239 (343)
                      +.+..++..+..+|.+.|++++|...|+++.+.. +.+..++..+..++...|++++|...++.+.+.. +.+...+..+
T Consensus       174 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~  251 (450)
T 2y4t_A          174 VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHY  251 (450)
T ss_dssp             TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHH
Confidence            4567889999999999999999999999988753 3468899999999999999999999999999763 3344445444


Q ss_pred             ------------HHHHHhCCChhHHHHHHHHHHHcCCCCC----HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH
Q 040261          240 ------------MNELCKNGKMDEASRLLELMIQIGVRPD----ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV  303 (343)
Q Consensus       240 ------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  303 (343)
                                  ...+...|++++|...++++.+.. +.+    ...+..+...+.+.|++++|...++++.+.. +.+.
T Consensus       252 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~  329 (450)
T 2y4t_A          252 KQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNV  329 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccH
Confidence                        788999999999999999999864 223    4578889999999999999999999988753 4478


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          304 FSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       304 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      ..|..+..+|...|++++|...++++++.  .|+.
T Consensus       330 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~  362 (450)
T 2y4t_A          330 NALKDRAEAYLIEEMYDEAIQDYETAQEH--NEND  362 (450)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTT--SSSC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh--Ccch
Confidence            89999999999999999999999999964  5553

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=5.3e-24  Score=179.74  Aligned_cols=311  Identities=10%  Similarity=0.075  Sum_probs=257.4

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ++|+.+....|  .+..+|..+..++.+.|++++|...|+++.+.+ +.+..++..+..++.+.|++++|.+.|+++.+.
T Consensus        47 ~~~~~~l~~~p--~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  123 (450)
T 2y4t_A           47 SQFHAAVDGDP--DNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS  123 (450)
T ss_dssp             HHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHhCC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            46777877765  489999999999999999999999999998866 456789999999999999999999999999986


Q ss_pred             CCCccH---HHHHHH------------HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040261           82 CFTPDA---VTFTSL------------IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFE  146 (343)
Q Consensus        82 ~~~~~~---~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  146 (343)
                      ... +.   ..+..+            ...+...|++++|++.++++.+.... +...+..+..+|...|++++|...++
T Consensus       124 ~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~  201 (450)
T 2y4t_A          124 NPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVW-DAELRELRAECFIKEGEPRKAISDLK  201 (450)
T ss_dssp             CCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCGGGGHHHHH
T ss_pred             CCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            422 34   555555            44488999999999999999987543 78889999999999999999999999


Q ss_pred             HHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHH------------HHHHhccCcH
Q 040261          147 EMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSL------------IRGFCYANDW  214 (343)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l------------~~~~~~~~~~  214 (343)
                      ++.+..       +.+..++..+..++...|++++|...|+++.... +.+...+..+            ...+...|++
T Consensus       202 ~~~~~~-------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  273 (450)
T 2y4t_A          202 AASKLK-------NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRY  273 (450)
T ss_dssp             HHHHHH-------CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence            998864       4567899999999999999999999999998753 2244445444            7889999999


Q ss_pred             HHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHH
Q 040261          215 NEAKCLFIEMMDQGVQPN-----VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKE  289 (343)
Q Consensus       215 ~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  289 (343)
                      ++|...++.+.+.  .|+     ...+..+..++.+.|++++|...++++.+.. +.+..++..+..+|...|++++|..
T Consensus       274 ~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~  350 (450)
T 2y4t_A          274 TDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQ  350 (450)
T ss_dssp             HHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHH
Confidence            9999999999986  344     3478888999999999999999999998875 5578999999999999999999999


Q ss_pred             HHHHHHhCCCCccHHHHHHHHHH------------HHhcC-----ChHHHHHHHHHH
Q 040261          290 LFVSMESNGCMRDVFSYGILING------------YCKNK-----EIEGALSLYSEM  329 (343)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~l~~~------------~~~~~-----~~~~a~~~~~~~  329 (343)
                      .++++.+.. +.+...+..+..+            |...|     +.+++.+.|+++
T Consensus       351 ~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~y~~~  406 (450)
T 2y4t_A          351 DYETAQEHN-ENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKAYRKL  406 (450)
T ss_dssp             HHHHHHTTS-SSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHHHHHH
T ss_pred             HHHHHHHhC-cchHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHHHHHH
Confidence            999999863 2345566666533            33344     566778888863

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.95  E-value=3.9e-23  Score=169.02  Aligned_cols=308  Identities=13%  Similarity=0.057  Sum_probs=258.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ++..+..+...+.+.|++++|+..|+++.+.. +.+...+..+..++...|++++|...++++.+... .+...+..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKM-DFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CcchHHHHHHH
Confidence            46678899999999999999999999998865 45678999999999999999999999999998753 36788999999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCC--CCHHHHHHH------------HHHHHhcCChHHHHHHHHHHHccCCCCCccccC
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCK--PDVFTYTTL------------INGLCRTGHTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      .+...|++++|.+.+++..+....  .+...+..+            ...+...|++++|...++++....       +.
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-------~~  152 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-------VW  152 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TT
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CC
Confidence            999999999999999999987430  134444444            578899999999999999999875       45


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH----
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN----  237 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----  237 (343)
                      +...+..+..++...|++++|...++++.+.. +.+...+..+...+...|++++|...++...+.. +.+...+.    
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~  230 (359)
T 3ieg_A          153 DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQ  230 (359)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHH
Confidence            67889999999999999999999999998864 4578889999999999999999999999999873 33333333    


Q ss_pred             --------HHHHHHHhCCChhHHHHHHHHHHHcCCCCCH----HHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHH
Q 040261          238 --------VIMNELCKNGKMDEASRLLELMIQIGVRPDA----SVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFS  305 (343)
Q Consensus       238 --------~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  305 (343)
                              .+...+.+.|++++|...++++.+.. +.+.    ..+..+...+...|++++|...+++..+.. +.+...
T Consensus       231 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  308 (359)
T 3ieg_A          231 VKKLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQME-PDNVNA  308 (359)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccHHH
Confidence                    23667889999999999999999875 3233    235567889999999999999999998863 447889


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          306 YGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       306 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      +..+...+...|++++|.+.|+++.+.  .|+.
T Consensus       309 ~~~~~~~~~~~g~~~~A~~~~~~a~~~--~p~~  339 (359)
T 3ieg_A          309 LKDRAEAYLIEEMYDEAIQDYEAAQEH--NEND  339 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCC
Confidence            999999999999999999999999965  4553

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.93  E-value=6e-23  Score=176.21  Aligned_cols=232  Identities=14%  Similarity=0.067  Sum_probs=163.5

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      ++..+...+...|++++|...++++.+....  ...+..+..++...|++++|...++++....       +.+..++..
T Consensus       239 ~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~  309 (514)
T 2gw1_A          239 SLEHTGIFKFLKNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-------SNNSSVYYH  309 (514)
T ss_dssp             HHHHHHHHHHHSSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-------TTCTHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-------cCCHHHHHH
Confidence            3444445555555666666666655554322  5555556666666666666666666665543       345567777


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  248 (343)
                      +..++...|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+.. +.+...+..+...+...|+
T Consensus       310 l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~  387 (514)
T 2gw1_A          310 RGQMNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKND  387 (514)
T ss_dssp             HHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCC
Confidence            7778888888888888888877654 2356677778888888888888888888887763 3456677788888888888


Q ss_pred             hhHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhc---CCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChH
Q 040261          249 MDEASRLLELMIQIGVR-PD----ASVYNTLMDGFCL---TGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIE  320 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  320 (343)
                      +++|...++++.+.... ++    ...+..+...+..   .|++++|...++++.+.. +.+..++..+...|...|+++
T Consensus       388 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~  466 (514)
T 2gw1_A          388 FDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDID  466 (514)
T ss_dssp             HHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHH
Confidence            88888888888765211 11    3377788888888   888888888888887753 345677788888888888888


Q ss_pred             HHHHHHHHHHhC
Q 040261          321 GALSLYSEMLSK  332 (343)
Q Consensus       321 ~a~~~~~~~~~~  332 (343)
                      +|...|+++...
T Consensus       467 ~A~~~~~~a~~~  478 (514)
T 2gw1_A          467 EAITLFEESADL  478 (514)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            888888888765

>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=99.93  E-value=1.6e-22  Score=163.44  Aligned_cols=293  Identities=12%  Similarity=0.027  Sum_probs=248.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++..+..+...+...|++++|.++|+++.+.. +.+...+..++.++...|++++|...++++.+.. +.+...+..+.
T Consensus        20 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   97 (330)
T 3hym_B           20 ENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVG   97 (330)
T ss_dssp             CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHH
Confidence            567788899999999999999999999998765 4456677778888999999999999999999875 33678888899


Q ss_pred             HHHhhcC-cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHH
Q 040261           95 KGLCAES-RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGL  173 (343)
Q Consensus        95 ~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  173 (343)
                      ..+...| ++++|.+.+++..+.... +...+..+...+...|++++|...++++....       +.+...+..+...+
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-------~~~~~~~~~l~~~~  169 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKATTLEKT-YGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-------KGCHLPMLYIGLEY  169 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHHTTCTT-CTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-------TTCSHHHHHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-------cccHHHHHHHHHHH
Confidence            9999999 999999999999987543 56788899999999999999999999999875       44567788899999


Q ss_pred             HhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC--------CCCCHHHHHHHHHHHHh
Q 040261          174 CKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG--------VQPNVVTFNVIMNELCK  245 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~~~  245 (343)
                      ...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+..        .+.....+..+..++..
T Consensus       170 ~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~  248 (330)
T 3hym_B          170 GLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRK  248 (330)
T ss_dssp             HHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHH
Confidence            99999999999999998864 3467889999999999999999999999988752        13345788899999999


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH-HhcCChH
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY-CKNKEIE  320 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~  320 (343)
                      .|++++|...++++.+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+..++ ...|+.+
T Consensus       249 ~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          249 LKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGLR-RDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTC-SCCHHHHHHHHHHHHTTTTC--
T ss_pred             hcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHccC-CCchHHHHHHHHHHHHHhCchh
Confidence            999999999999999875 5567889999999999999999999999998764 34677788888877 4556543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.93  E-value=1.9e-22  Score=173.13  Aligned_cols=309  Identities=13%  Similarity=0.006  Sum_probs=256.9

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ....+......+.+.|++++|+..|+++...+  |+...|..+..++.+.|++++|...++++.+.+ +.+..++..+..
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~   81 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRAS   81 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHH
Confidence            35678888999999999999999999998865  789999999999999999999999999999875 336788999999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCC-------------------------------------------------------
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKP-------------------------------------------------------  120 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~-------------------------------------------------------  120 (343)
                      ++...|++++|...|+++...+...                                                       
T Consensus        82 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (514)
T 2gw1_A           82 ANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSV  161 (514)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCH
T ss_pred             HHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchh
Confidence            9999999999999999987764311                                                       


Q ss_pred             -----------------------CHHHHHHHHHHHHh---cCChHHHHHHHHHHHc-----c--CCCCCccccCCcchHH
Q 040261          121 -----------------------DVFTYTTLINGLCR---TGHTIVALNLFEEMAN-----G--NGEFGVVCKPDAITYS  167 (343)
Q Consensus       121 -----------------------~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~--~~~~~~~~~~~~~~~~  167 (343)
                                             +...+......+..   .|++++|...++++..     .  .+......+.+..++.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (514)
T 2gw1_A          162 TSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLE  241 (514)
T ss_dssp             HHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHH
Confidence                                   02233333333443   8999999999999987     3  1100000023456788


Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG  247 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  247 (343)
                      .+...+...|++++|...++++.+..  |+...+..+..++...|++++|...++.+.+.. +.+...+..+...+...|
T Consensus       242 ~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  318 (514)
T 2gw1_A          242 HTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQ  318 (514)
T ss_dssp             HHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhC
Confidence            88999999999999999999998865  338888999999999999999999999998874 456778889999999999


Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHH
Q 040261          248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYS  327 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  327 (343)
                      ++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++
T Consensus       319 ~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~  396 (514)
T 2gw1_A          319 NYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYD  396 (514)
T ss_dssp             CTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            9999999999999875 4567789999999999999999999999998763 3467788999999999999999999999


Q ss_pred             HHHhC
Q 040261          328 EMLSK  332 (343)
Q Consensus       328 ~~~~~  332 (343)
                      ++...
T Consensus       397 ~a~~~  401 (514)
T 2gw1_A          397 LAIEL  401 (514)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99865

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.92  E-value=4.3e-21  Score=156.89  Aligned_cols=299  Identities=9%  Similarity=0.036  Sum_probs=245.5

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.|+.+....|.  ++.++..+..++...|++++|...++++.+.. +.+...+..+..++...|++++|...++++.+.
T Consensus        24 ~~~~~~l~~~p~--~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  100 (359)
T 3ieg_A           24 SQFHAAVDGDPD--NYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS  100 (359)
T ss_dssp             HHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhhCcc--cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc
Confidence            467777777664  88999999999999999999999999998765 446788999999999999999999999999886


Q ss_pred             CCC--ccHHHHHHH------------HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHH
Q 040261           82 CFT--PDAVTFTSL------------IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEE  147 (343)
Q Consensus        82 ~~~--~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  147 (343)
                      ...  .+...+..+            ...+...|++++|.+.++++.+.... +...+..+..++...|++++|...+++
T Consensus       101 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~A~~~~~~  179 (359)
T 3ieg_A          101 NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVW-DAELRELRAECFIKEGEPRKAISDLKA  179 (359)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            420  244455444            57888999999999999999987543 778899999999999999999999999


Q ss_pred             HHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHH------------HHHHHHhccCcHH
Q 040261          148 MANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYT------------SLIRGFCYANDWN  215 (343)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~------------~l~~~~~~~~~~~  215 (343)
                      +....       +.+..++..+...+...|++++|...+++..+.. +.+...+.            .+...+...|+++
T Consensus       180 ~~~~~-------~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  251 (359)
T 3ieg_A          180 ASKLK-------SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYT  251 (359)
T ss_dssp             HHTTC-------SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHhC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHH
Confidence            99875       5567889999999999999999999999988754 22333333            2366788999999


Q ss_pred             HHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          216 EAKCLFIEMMDQGVQPNV----VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       216 ~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      +|...++.+.+.. +.+.    ..+..+..++...|++++|...++++.+.. +.+..++..+...+...|++++|...+
T Consensus       252 ~A~~~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~  329 (359)
T 3ieg_A          252 DATSKYESVMKTE-PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDY  329 (359)
T ss_dssp             HHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            9999999999874 2233    235557789999999999999999999875 557889999999999999999999999


Q ss_pred             HHHHhCCCCccHHHHHHHHHHHHh
Q 040261          292 VSMESNGCMRDVFSYGILINGYCK  315 (343)
Q Consensus       292 ~~~~~~~~~~~~~~~~~l~~~~~~  315 (343)
                      +++.+.. +.+...+..+..+...
T Consensus       330 ~~a~~~~-p~~~~~~~~l~~~~~~  352 (359)
T 3ieg_A          330 EAAQEHN-ENDQQIREGLEKAQRL  352 (359)
T ss_dssp             HHHHTTC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHhcC-CCChHHHHHHHHHHHH
Confidence            9999864 2345566666655443

>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=99.92  E-value=2e-21  Score=167.74  Aligned_cols=317  Identities=13%  Similarity=0.093  Sum_probs=235.0

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.|+.+....|.  ++.+|..+..++.+.|++++|++.++++.+.+ +.+..++..+..++...|++++|...|+.+...
T Consensus        46 ~~~~~al~~~p~--~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  122 (537)
T 3fp2_A           46 KYYQYAIELDPN--EPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFDLSVLSLN  122 (537)
T ss_dssp             HHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHC--
T ss_pred             HHHHHHHhhCCC--CcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC
Confidence            467777777764  88899999999999999999999999988765 456778888889999999988888877432100


Q ss_pred             --------------------------------------------------------------------------------
Q 040261           82 --------------------------------------------------------------------------------   81 (343)
Q Consensus        82 --------------------------------------------------------------------------------   81 (343)
                                                                                                      
T Consensus       123 ~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  202 (537)
T 3fp2_A          123 GDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQR  202 (537)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ---------------------------CCCcc--------HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHH
Q 040261           82 ---------------------------CFTPD--------AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYT  126 (343)
Q Consensus        82 ---------------------------~~~~~--------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  126 (343)
                                                 ...|+        ..++..+...+...|++++|.+.+++..+.  .|+...+.
T Consensus       203 ~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~  280 (537)
T 3fp2_A          203 LYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYI  280 (537)
T ss_dssp             HHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHH
T ss_pred             HHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHH
Confidence                                       00111        113444555666677788888888887776  34466777


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHH
Q 040261          127 TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIR  206 (343)
Q Consensus       127 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  206 (343)
                      .+...+...|++++|...++++....       +.+..++..+...+...|++++|...++++.+.. +.+...+..+..
T Consensus       281 ~l~~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~  352 (537)
T 3fp2_A          281 FLALTLADKENSQEFFKFFQKAVDLN-------PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLAC  352 (537)
T ss_dssp             HHHHHTCCSSCCHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHhccC-------CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            77788888888888888888887764       3456778888888888888888888888877654 234667778888


Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC-----CCCHHHHHHHHHHHhcC
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV-----RPDASVYNTLMDGFCLT  281 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~  281 (343)
                      ++...|++++|...++.+.+.. +.+...+..+...+...|++++|...++++.+...     ......+......+...
T Consensus       353 ~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~  431 (537)
T 3fp2_A          353 LLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQ  431 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHH
Confidence            8888888888888888888763 44566777888888888888888888888776421     11122234445566666


Q ss_pred             ----------CchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          282 ----------GRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       282 ----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                                |++++|...++++.+.. +.+...+..+...|...|++++|.+.|+++....
T Consensus       432 ~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          432 SSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             HTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence                      88888888888887753 3467788889999999999999999999988653

>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=99.91  E-value=1.2e-21  Score=158.28  Aligned_cols=277  Identities=11%  Similarity=-0.001  Sum_probs=236.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           48 LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        48 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      .+.+...+..+...+...|++++|.++++++.+..+ .+...+..++.++...|++++|...++++.+.... +...+..
T Consensus        18 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~   95 (330)
T 3hym_B           18 LQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDP-FHASCLPVHIGTLVELNKANELFYLSHKLVDLYPS-NPVSWFA   95 (330)
T ss_dssp             --CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STHHHHH
T ss_pred             chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHH
Confidence            345667788888899999999999999999998753 35667777888999999999999999999987543 6778889


Q ss_pred             HHHHHHhcC-ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHH
Q 040261          128 LINGLCRTG-HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIR  206 (343)
Q Consensus       128 l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  206 (343)
                      +...+...| ++++|...++++....       +.+...+..+..++...|++++|...++++.+.. +.+...+..+..
T Consensus        96 l~~~~~~~~~~~~~A~~~~~~a~~~~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~  167 (330)
T 3hym_B           96 VGCYYLMVGHKNEHARRYLSKATTLE-------KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGL  167 (330)
T ss_dssp             HHHHHHHSCSCHHHHHHHHHHHHTTC-------TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhC-------CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHH
Confidence            999999999 9999999999999875       4567789999999999999999999999988764 235677788999


Q ss_pred             HHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC--------CCCCHHHHHHHHHHH
Q 040261          207 GFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG--------VRPDASVYNTLMDGF  278 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~  278 (343)
                      .+...|++++|...++.+.+.. +.+...+..+...+...|++++|...++++.+..        .+....++..+...+
T Consensus       168 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~  246 (330)
T 3hym_B          168 EYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVC  246 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHH
Confidence            9999999999999999999874 5567889999999999999999999999998752        133457889999999


Q ss_pred             hcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          279 CLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      ...|++++|...+++..+.. +.+...+..+...+...|++++|.+.++++.+.  .|+.
T Consensus       247 ~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~  303 (330)
T 3hym_B          247 RKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGL--RRDD  303 (330)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT--CSCC
T ss_pred             HHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc--CCCc
Confidence            99999999999999998764 446788999999999999999999999998754  4543

>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=99.91  E-value=6.4e-22  Score=162.53  Aligned_cols=293  Identities=11%  Similarity=0.021  Sum_probs=231.8

Q ss_pred             HHHhcCChhHHHH-HHHHhHhCCCC-C--CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           26 CLAKNKHYDTVLS-LFKRLNSIGLF-P--DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        26 ~~~~~~~~~~a~~-~~~~~~~~~~~-~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      ++.-.|++++|.+ .+++....... |  +...+..+...+...|++++|...++++.+.. +.+..++..+..++...|
T Consensus        34 ~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g  112 (368)
T 1fch_A           34 AHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENE  112 (368)
T ss_dssp             ------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCc
Confidence            3445678899998 88876543211 1  34568889999999999999999999999875 347788999999999999


Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH-------------
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST-------------  168 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------  168 (343)
                      ++++|.+.++++.+.... +..++..+..++...|++++|...++++....+       .+...+..             
T Consensus       113 ~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~  184 (368)
T 1fch_A          113 QELLAISALRRCLELKPD-NQTALMALAVSFTNESLQRQACEILRDWLRYTP-------AYAHLVTPAEEGAGGAGLGPS  184 (368)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTST-------TTGGGCC--------------
T ss_pred             CHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-------CcHHHHHHHHHHhhhhcccHH
Confidence            999999999999988543 788899999999999999999999999998753       22222211             


Q ss_pred             --HHHHHHhcCChHHHHHHHHHhhhCCCCC-ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          169 --ITDGLCKEGFVDKAKELFLKMKDENINP-DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       169 --l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                        .+..+...|++++|...++++.+..... +..++..+..++...|++++|...++++.+.. +.+...+..+...+..
T Consensus       185 ~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~  263 (368)
T 1fch_A          185 KRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLAN  263 (368)
T ss_dssp             -CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHH
Confidence              2333348999999999999998764221 47889999999999999999999999999874 4567889999999999


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCc----------cHHHHHHHHHHHHh
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMR----------DVFSYGILINGYCK  315 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----------~~~~~~~l~~~~~~  315 (343)
                      .|++++|...++++.+.. +.+...+..+...|.+.|++++|...++++.+.....          ...+|..+..+|..
T Consensus       264 ~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  342 (368)
T 1fch_A          264 GNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSM  342 (368)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHH
Confidence            999999999999999875 5678899999999999999999999999887642111          16789999999999


Q ss_pred             cCChHHHHHHHHHH
Q 040261          316 NKEIEGALSLYSEM  329 (343)
Q Consensus       316 ~~~~~~a~~~~~~~  329 (343)
                      .|++++|..++++.
T Consensus       343 ~g~~~~A~~~~~~~  356 (368)
T 1fch_A          343 LGQSDAYGAADARD  356 (368)
T ss_dssp             HTCGGGHHHHHTTC
T ss_pred             hCChHhHHHhHHHH
Confidence            99999999887644

>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=99.90  E-value=1.1e-20  Score=163.17  Aligned_cols=303  Identities=9%  Similarity=0.035  Sum_probs=246.3

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ....+..+...+.+.|++++|+..|+++.+.. +.+...+..+..++.+.|++++|.+.++++.+.+ +.+..++..+..
T Consensus        24 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~  101 (537)
T 3fp2_A           24 YAVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRAS  101 (537)
T ss_dssp             HHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHH
Confidence            35678889999999999999999999998865 5578899999999999999999999999999875 336888999999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCC-------------------------------------CCHH---------------
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCK-------------------------------------PDVF---------------  123 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~-------------------------------------~~~~---------------  123 (343)
                      ++...|++++|.+.|+.+ .....                                     |+..               
T Consensus       102 ~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (537)
T 3fp2_A          102 ANESLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEV  180 (537)
T ss_dssp             HHHHHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHH
Confidence            999999999999999643 22111                                     1110               


Q ss_pred             ---------------HHHHHHHHHH--------hcCChHHHHHHHHHHHccCCCCCccccCC-------cchHHHHHHHH
Q 040261          124 ---------------TYTTLINGLC--------RTGHTIVALNLFEEMANGNGEFGVVCKPD-------AITYSTITDGL  173 (343)
Q Consensus       124 ---------------~~~~l~~~~~--------~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~~~  173 (343)
                                     ....+...+.        ..|++++|..+++++.+..       +.+       ..++..+...+
T Consensus       181 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~-------p~~~~~~~~~~~~~~~~g~~~  253 (537)
T 3fp2_A          181 SSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN-------TVDDPLRENAALALCYTGIFH  253 (537)
T ss_dssp             HTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC---------CCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC-------CCcchhhHHHHHHHHHHHHHH
Confidence                           1111111111        1247889999999998865       222       23466777888


Q ss_pred             HhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHH
Q 040261          174 CKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEAS  253 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  253 (343)
                      ...|++++|...++++.+..  |+...+..+...+...|++++|...++.+.+.. +.+..++..+...+...|++++|.
T Consensus       254 ~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~  330 (537)
T 3fp2_A          254 FLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAK  330 (537)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHH
Confidence            99999999999999998864  558889999999999999999999999999874 456788999999999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          254 RLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      ..++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.|+++....
T Consensus       331 ~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  408 (537)
T 3fp2_A          331 EDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLE  408 (537)
T ss_dssp             HHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC
Confidence            9999999875 4467789999999999999999999999998864 4467788999999999999999999999988653

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.90  E-value=6.9e-22  Score=162.18  Aligned_cols=267  Identities=13%  Similarity=0.012  Sum_probs=220.2

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      +...+..+...+.+.|++++|...|+++.+.. +.+..++..+..++...|++++|++.|++..+.... +..++..+..
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPN-NLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-CHHHHHHHHH
Confidence            44568888999999999999999999999875 347889999999999999999999999999987543 6888999999


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcc----------hHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-CChh
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAI----------TYSTITDGLCKEGFVDKAKELFLKMKDENIN-PDVV  199 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~----------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~  199 (343)
                      +|...|++++|...++++....       +.+..          .+..+...+...|++++|...++++.+.... ++..
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  214 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQN-------PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPD  214 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-------HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHH
T ss_pred             HHHccccHHHHHHHHHHHHHhC-------ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHH
Confidence            9999999999999999998864       22222          3344578899999999999999999886422 1578


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      ++..+...+...|++++|...++++.+.. +.+..++..+..++...|++++|...++++.+.. +.+..++..+..+|.
T Consensus       215 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~  292 (365)
T 4eqf_A          215 LQTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCI  292 (365)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHH
Confidence            89999999999999999999999999874 5568899999999999999999999999999875 556889999999999


Q ss_pred             cCCchHHHHHHHHHHHhCCCC-----------ccHHHHHHHHHHHHhcCChHHHHHHHHH
Q 040261          280 LTGRVNRAKELFVSMESNGCM-----------RDVFSYGILINGYCKNKEIEGALSLYSE  328 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~~~~-----------~~~~~~~~l~~~~~~~~~~~~a~~~~~~  328 (343)
                      ..|++++|...++++.+....           .+...|..+..++...|+.+.+.++.++
T Consensus       293 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          293 NLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            999999999999998764210           1367899999999999999988877654

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.89  E-value=2.7e-21  Score=158.64  Aligned_cols=270  Identities=11%  Similarity=-0.024  Sum_probs=220.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...+..+...+.+.|++++|+..|+++.+.. +.+..++..+..++...|++++|...|+++.+.. +.+..++..+.
T Consensus        63 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  140 (365)
T 4eqf_A           63 KDWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALA  140 (365)
T ss_dssp             TTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHH
Confidence            345669999999999999999999999998865 5578899999999999999999999999999875 33688999999


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCC---------CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcch
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKP---------DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAIT  165 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  165 (343)
                      .++...|++++|.+.++++.+.....         ....+..+...+...|++++|...++++....+     ...+..+
T Consensus       141 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-----~~~~~~~  215 (365)
T 4eqf_A          141 VSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNG-----DMIDPDL  215 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSC-----SSCCHHH
T ss_pred             HHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCc-----CccCHHH
Confidence            99999999999999999998763210         112233457889999999999999999998752     1125788


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                      +..+...+...|++++|...++++.+.. +.+..++..+..++...|++++|...++++.+.. +.+..++..+..++..
T Consensus       216 ~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~  293 (365)
T 4eqf_A          216 QTGLGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCIN  293 (365)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHH
Confidence            9999999999999999999999988764 3468899999999999999999999999999874 4458889999999999


Q ss_pred             CCChhHHHHHHHHHHHcCCC-----------CCHHHHHHHHHHHhcCCchHHHHHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVR-----------PDASVYNTLMDGFCLTGRVNRAKELFVS  293 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~-----------~~~~~~~~l~~~~~~~~~~~~a~~~~~~  293 (343)
                      .|++++|...++++.+....           .+..+|..+..++...|+.+.+..+..+
T Consensus       294 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          294 LGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999999999999875211           1357889999999999999988887654

>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=99.89  E-value=7.5e-21  Score=156.14  Aligned_cols=267  Identities=12%  Similarity=0.032  Sum_probs=225.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...+..+...+.+.|++++|...|+++.+.. +.+..++..+..++...|++++|...++++.+.. +.+..++..+..
T Consensus        63 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~  140 (368)
T 1fch_A           63 DHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAV  140 (368)
T ss_dssp             TCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            35678899999999999999999999999865 5577899999999999999999999999999875 347889999999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH---------------HHHHHHhcCChHHHHHHHHHHHccCCCCCcccc
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTT---------------LINGLCRTGHTIVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      .+...|++++|.+.++++...... +...+..               .+..+...|++++|...++++....+.     .
T Consensus       141 ~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~-----~  214 (368)
T 1fch_A          141 SFTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPT-----S  214 (368)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTT-----S
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcC-----c
Confidence            999999999999999999987533 2222211               233444899999999999999987521     1


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM  240 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  240 (343)
                      ++..++..+..++.+.|++++|...++++.... +.+...+..+..++...|++++|...++++.+.. +.+...+..+.
T Consensus       215 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~  292 (368)
T 1fch_A          215 IDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLG  292 (368)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            157788999999999999999999999988764 3467889999999999999999999999999874 45678899999


Q ss_pred             HHHHhCCChhHHHHHHHHHHHcCCCCC-----------HHHHHHHHHHHhcCCchHHHHHHHHH
Q 040261          241 NELCKNGKMDEASRLLELMIQIGVRPD-----------ASVYNTLMDGFCLTGRVNRAKELFVS  293 (343)
Q Consensus       241 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~  293 (343)
                      .++.+.|++++|...++++.+.. +.+           ..+|..+..+|...|++++|..++++
T Consensus       293 ~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          293 ISCINLGAHREAVEHFLEALNMQ-RKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHH-HTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            99999999999999999998753 222           68899999999999999999998764

>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=99.88  E-value=3.4e-20  Score=149.61  Aligned_cols=262  Identities=11%  Similarity=0.012  Sum_probs=177.7

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 040261           57 ILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG  136 (343)
Q Consensus        57 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  136 (343)
                      .+...+...|++++|..+++++.+... .+...+..+..++...|++++|.+.++++.+.... +..++..+...+...|
T Consensus        26 ~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~~  103 (327)
T 3cv0_A           26 EEGLSMLKLANLAEAALAFEAVCQAAP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNEH  103 (327)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcC-CHHHHHHHHHHHHHcC
Confidence            333344444444444444444443321 13334444444444444444444444444443211 3444444445555555


Q ss_pred             ChHHHHHHHHHHHccCCCCCccccCCcchHHH-------------H-HH-HHHhcCChHHHHHHHHHhhhCCCCCChhhH
Q 040261          137 HTIVALNLFEEMANGNGEFGVVCKPDAITYST-------------I-TD-GLCKEGFVDKAKELFLKMKDENINPDVVTY  201 (343)
Q Consensus       137 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------l-~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  201 (343)
                      ++++|.+.++++....       +.+...+..             + .. .+...|++++|...++++.+.. +.+...+
T Consensus       104 ~~~~A~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  175 (327)
T 3cv0_A          104 NANAALASLRAWLLSQ-------PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLH  175 (327)
T ss_dssp             CHHHHHHHHHHHHHTS-------TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             CHHHHHHHHHHHHHhC-------CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHH
Confidence            5555555555544432       111122222             2 22 3778899999999999988764 3467889


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT  281 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  281 (343)
                      ..+...+...|++++|...++.+.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...
T Consensus       176 ~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~  253 (327)
T 3cv0_A          176 ASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNM  253 (327)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHh
Confidence            999999999999999999999999874 4567889999999999999999999999998875 55788999999999999


Q ss_pred             CchHHHHHHHHHHHhCCCCc-----------cHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          282 GRVNRAKELFVSMESNGCMR-----------DVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       282 ~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      |++++|.+.++++.+.....           +...+..+..++...|++++|..++++.+
T Consensus       254 g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          254 SQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             ccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            99999999999988753221           47788999999999999999999887543

>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=99.88  E-value=2.1e-20  Score=150.85  Aligned_cols=268  Identities=11%  Similarity=-0.054  Sum_probs=225.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...+..+...+...|++++|..+|+++.+.. +.+...+..+..++...|++++|.+.++++.+.. +.+..++..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHH
Confidence            45567888999999999999999999998765 4577889999999999999999999999999875 346788899999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHH--------------HH-HHHhcCChHHHHHHHHHHHccCCCCCcccc
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL--------------IN-GLCRTGHTIVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      .+...|++++|.+.++++.+.... +...+..+              .. .+...|++++|...++++....       +
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------~  169 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-------P  169 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-------T
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-------C
Confidence            999999999999999999887433 22233333              22 3778899999999999998875       4


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM  240 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  240 (343)
                      .+..++..+...+...|++++|...++++.+.. +.+...+..+..++...|++++|...++++.+.. +.+...+..+.
T Consensus       170 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~  247 (327)
T 3cv0_A          170 NDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMA  247 (327)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHH
Confidence            567889999999999999999999999988764 3467889999999999999999999999998874 45678899999


Q ss_pred             HHHHhCCChhHHHHHHHHHHHcCCCC-----------CHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          241 NELCKNGKMDEASRLLELMIQIGVRP-----------DASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       241 ~~~~~~~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      ..+...|++++|...++++.+.....           +...+..+..++...|++++|..++++..
T Consensus       248 ~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          248 VSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            99999999999999999998864221           57789999999999999999999987543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.86  E-value=8.3e-19  Score=138.54  Aligned_cols=276  Identities=13%  Similarity=0.094  Sum_probs=216.9

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCH--HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDL--YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES  101 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  101 (343)
                      +......|+++.|+..++......  |+.  .....+.++|...|+++.|+..++.   . -+|+..++..+...+...+
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~--p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~   79 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSS--PERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHS   79 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCS--HHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCC--chhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCC
Confidence            445567899999999998765533  443  4556678999999999999876654   2 3567788888999999999


Q ss_pred             cHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH
Q 040261          102 RIMEAAALFTKLRAFGCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD  180 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  180 (343)
                      +.++|++.++++...+..| +...+..+..++...|++++|++.+++    .        .+..++..++.++.+.|+++
T Consensus        80 ~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~----~--------~~~~~~~~l~~~~~~~g~~~  147 (291)
T 3mkr_A           80 RRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ----G--------DSLECMAMTVQILLKLDRLD  147 (291)
T ss_dssp             THHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT----C--------CSHHHHHHHHHHHHHTTCHH
T ss_pred             cHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC----C--------CCHHHHHHHHHHHHHCCCHH
Confidence            9999999999998876444 566677788999999999999999987    1        35678899999999999999


Q ss_pred             HHHHHHHHhhhCCCCCChhhH---HHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHH
Q 040261          181 KAKELFLKMKDENINPDVVTY---TSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLE  257 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  257 (343)
                      +|...++++.+..  |+....   ..++..+...|++++|..+|+++.+. .+.+...++.+..++.+.|++++|...++
T Consensus       148 ~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~  224 (291)
T 3mkr_A          148 LARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQ  224 (291)
T ss_dssp             HHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999998764  443211   22334445669999999999999988 36678899999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHhcCCchHH-HHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHH
Q 040261          258 LMIQIGVRPDASVYNTLMDGFCLTGRVNR-AKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLY  326 (343)
Q Consensus       258 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  326 (343)
                      ++.+.. +-+..++..++..+...|+.++ +.++++++.+..  |+...   +.+...+.+.++++..-|
T Consensus       225 ~al~~~-p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~--P~~~~---~~d~~~~~~~fd~~~~~~  288 (291)
T 3mkr_A          225 EALDKD-SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH--RSHPF---IKEYRAKENDFDRLVLQY  288 (291)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHH---HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhC-CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC--CCChH---HHHHHHHHHHHHHHHHHc
Confidence            999886 5678899999999999999876 678999988753  54332   233455556666665443

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.85  E-value=1.2e-18  Score=137.72  Aligned_cols=257  Identities=9%  Similarity=-0.004  Sum_probs=206.7

Q ss_pred             HHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH
Q 040261           60 NCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI  139 (343)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  139 (343)
                      +.....|+++.|+..++.+......+.......+.++|...|+++.|+..++.   . -+|+..++..+...+...++.+
T Consensus         7 ~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~~   82 (291)
T 3mkr_A            7 KNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRRD   82 (291)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTHH
T ss_pred             HHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcHH
Confidence            44567799999999988765543222234556678999999999999987654   2 3567778889999999999999


Q ss_pred             HHHHHHHHHHccCCCCCccc-cCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHH
Q 040261          140 VALNLFEEMANGNGEFGVVC-KPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAK  218 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  218 (343)
                      +|++.++++...+      . +.+...+..+..++...|++++|++.+++      +.+...+..++..+.+.|++++|.
T Consensus        83 ~A~~~l~~ll~~~------~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~  150 (291)
T 3mkr_A           83 AIVAELDREMSRS------VDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLAR  150 (291)
T ss_dssp             HHHHHHHHHHHSC------CCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHhcc------cCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            9999999988654      2 33556677778999999999999999987      457888999999999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHH---HHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          219 CLFIEMMDQGVQPNVVTF---NVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      ..++.+.+..  |+....   ...+..+...|++++|..+|+++.+.. +.+...++.+..++.+.|++++|...++++.
T Consensus       151 ~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al  227 (291)
T 3mkr_A          151 KELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEAL  227 (291)
T ss_dssp             HHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999874  553322   123344455689999999999999984 6788999999999999999999999999988


Q ss_pred             hCCCCccHHHHHHHHHHHHhcCChHH-HHHHHHHHHhCCCCCCc
Q 040261          296 SNGCMRDVFSYGILINGYCKNKEIEG-ALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       296 ~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~p~~  338 (343)
                      +.. +.++.++..++..+...|+.++ +.++++++++.  .|+.
T Consensus       228 ~~~-p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~--~P~~  268 (291)
T 3mkr_A          228 DKD-SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA--HRSH  268 (291)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--CTTC
T ss_pred             HhC-CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--CCCC
Confidence            864 4478889999999999999876 57899998865  4543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.83  E-value=3.8e-16  Score=133.04  Aligned_cols=288  Identities=13%  Similarity=0.043  Sum_probs=151.2

Q ss_pred             ChhhHHHHHHHHHh----cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHHcCCCccH
Q 040261           16 PVCSFNILFGCLAK----NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK----MGRVSPGFVVLGRILRSCFTPDA   87 (343)
Q Consensus        16 ~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~   87 (343)
                      ++.++..+...|..    .+++++|...|++..+.|   +...+..+...|..    .+++++|.++|++..+.+   +.
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  111 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LP  111 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            44555555555555    556666666666555533   34455555555555    555666666666555543   33


Q ss_pred             HHHHHHHHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHHccCCCCCccc
Q 040261           88 VTFTSLIKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR----TGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        88 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      ..+..+...|..    .+++++|.+.|++..+.|   +...+..+...|..    .+++++|.++|++..+.+       
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~-------  181 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG-------  181 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT-------
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-------
Confidence            444445555544    455555555555555443   33444444444444    445555555555554432       


Q ss_pred             cCCcchHHHHHHHHHh----------------------------------------cCChHHHHHHHHHhhhCCCCCChh
Q 040261          160 KPDAITYSTITDGLCK----------------------------------------EGFVDKAKELFLKMKDENINPDVV  199 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~----------------------------------------~~~~~~a~~~~~~~~~~~~~~~~~  199 (343)
                        +...+..+...|..                                        .+++++|..+|++..+.+   +..
T Consensus       182 --~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~  256 (490)
T 2xm6_A          182 --NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSI  256 (490)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHH
T ss_pred             --CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHH
Confidence              23344444444443                                        444555555554444432   233


Q ss_pred             hHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-----CChhHHHHHHHHHHHcCCCCCHHH
Q 040261          200 TYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN-----GKMDEASRLLELMIQIGVRPDASV  270 (343)
Q Consensus       200 ~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~  270 (343)
                      .+..+...+..    .+++++|...++...+.+   +...+..+...+...     +++++|...+++..+.+   +...
T Consensus       257 a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a  330 (490)
T 2xm6_A          257 AQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATA  330 (490)
T ss_dssp             HHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHH
Confidence            34444444444    455555555555555443   233444455555544     56666666666665543   3344


Q ss_pred             HHHHHHHHhcCC---chHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh----cCChHHHHHHHHHHHhCC
Q 040261          271 YNTLMDGFCLTG---RVNRAKELFVSMESNGCMRDVFSYGILINGYCK----NKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       271 ~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  333 (343)
                      +..+...|...|   ++++|.+.|++..+.+   ++..+..+...|..    .+++++|...|++..+.|
T Consensus       331 ~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~  397 (490)
T 2xm6_A          331 QANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG  397 (490)
T ss_dssp             HHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC
Confidence            555555555544   5666666666666642   45566666666666    667777777777766654

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.83  E-value=4.8e-16  Score=132.44  Aligned_cols=290  Identities=11%  Similarity=0.018  Sum_probs=207.3

Q ss_pred             ChhhHHHHHHHHHh----cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHHcCCCccH
Q 040261           16 PVCSFNILFGCLAK----NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK----MGRVSPGFVVLGRILRSCFTPDA   87 (343)
Q Consensus        16 ~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~   87 (343)
                      ++.++..|...|..    .+++++|...|++..+.|   +...+..+...|..    .++.++|.++|++..+.+   +.
T Consensus       110 ~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~  183 (490)
T 2xm6_A          110 LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NV  183 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            33444445555544    445555555555554433   33444444444444    445555555555555543   44


Q ss_pred             HHHHHHHHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHHccCCCCCccc
Q 040261           88 VTFTSLIKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR----TGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        88 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      ..+..+...|..    .++.++|.+.|++..+.|   +...+..+...|..    .+++++|..++++..+.+       
T Consensus       184 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-------  253 (490)
T 2xm6_A          184 WSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG-------  253 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT-------
T ss_pred             HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-------
Confidence            455555555555    566666666666666543   44555556666665    667777777777776643       


Q ss_pred             cCCcchHHHHHHHHHh----cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc-----CcHHHHHHHHHHHHHcCCC
Q 040261          160 KPDAITYSTITDGLCK----EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA-----NDWNEAKCLFIEMMDQGVQ  230 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~  230 (343)
                        +...+..+...|..    .++.++|+.+|++..+.+   +...+..+...|...     +++++|...++...+.+  
T Consensus       254 --~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~--  326 (490)
T 2xm6_A          254 --NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG--  326 (490)
T ss_dssp             --CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT--
T ss_pred             --CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC--
Confidence              35567777778877    899999999999998765   566777788888776     89999999999999875  


Q ss_pred             CCHHHHHHHHHHHHhCC---ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchHHHHHHHHHHHhCCCCccH
Q 040261          231 PNVVTFNVIMNELCKNG---KMDEASRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVNRAKELFVSMESNGCMRDV  303 (343)
Q Consensus       231 ~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~  303 (343)
                       +...+..+...+...|   ++++|..+|++..+.+   +...+..+...|..    .+++++|...|++..+.+   ++
T Consensus       327 -~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~  399 (490)
T 2xm6_A          327 -DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LS  399 (490)
T ss_dssp             -CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             -CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CH
Confidence             4567777888887766   8899999999999875   57788888888888    899999999999999875   57


Q ss_pred             HHHHHHHHHHHh----cCChHHHHHHHHHHHhCCCC
Q 040261          304 FSYGILINGYCK----NKEIEGALSLYSEMLSKGIR  335 (343)
Q Consensus       304 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~  335 (343)
                      ..+..+...|..    .+++++|...|++....+..
T Consensus       400 ~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~  435 (490)
T 2xm6_A          400 AAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMN  435 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCC
Confidence            788889999988    89999999999999987643

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.2e-17  Score=129.98  Aligned_cols=225  Identities=11%  Similarity=0.026  Sum_probs=136.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCc--c----HHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTP--D----AVTF   90 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~----~~~~   90 (343)
                      ...+..+...+...|++++|...|+++.+..  .+...+..+..++...|++++|.+.++++.+.....  +    ..++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4567777777777777777777777776655  566677777777777777777777777776542111  1    4566


Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHH
Q 040261           91 TSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTIT  170 (343)
Q Consensus        91 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  170 (343)
                      ..+...+...|++++|.+.+++..+..  |+.       ..+...|++++|...++++....       +.+...+..+.
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~~  146 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKAEAEAYVN-------PEKAEEARLEG  146 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCC-------HHHHHHHHHHH
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHHHHHHHcC-------cchHHHHHHHH
Confidence            666666777777777777777766652  332       23445556666666666666543       33445555666


Q ss_pred             HHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChh
Q 040261          171 DGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMD  250 (343)
Q Consensus       171 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  250 (343)
                      ..+...|++++|...++++.+.. +.+...+..+..++...|++++|...++.+.+.. +.+...+..+..++...|+++
T Consensus       147 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~  224 (258)
T 3uq3_A          147 KEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYA  224 (258)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHH
Confidence            66666666666666666655543 2244555555555666666666666666555542 233455555555555556665


Q ss_pred             HHHHHHHHHHH
Q 040261          251 EASRLLELMIQ  261 (343)
Q Consensus       251 ~a~~~~~~~~~  261 (343)
                      +|...++++.+
T Consensus       225 ~A~~~~~~a~~  235 (258)
T 3uq3_A          225 SALETLDAART  235 (258)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555555544

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.81  E-value=3.4e-17  Score=127.33  Aligned_cols=233  Identities=13%  Similarity=0.018  Sum_probs=192.6

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcch
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAIT  165 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  165 (343)
                      ....+..+...+...|++++|...+++..+..  .+...+..+..++...|++++|...++++....+......+....+
T Consensus         4 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            4 MADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHH
Confidence            34567778888888899999999999988876  5778888889999999999999999998877541100000001578


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                      +..+..++...|++++|...++++....  |+.       ..+...|++++|...++.+.+.. +.+...+..+...+..
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~  151 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFT  151 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHH
Confidence            8899999999999999999999998853  442       45667789999999999998863 3346778889999999


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      .|++++|...++++.+.. +.+..++..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|...
T Consensus       152 ~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (258)
T 3uq3_A          152 KSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALET  229 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            999999999999999876 5678899999999999999999999999998864 44678899999999999999999999


Q ss_pred             HHHHHhC
Q 040261          326 YSEMLSK  332 (343)
Q Consensus       326 ~~~~~~~  332 (343)
                      +++..+.
T Consensus       230 ~~~a~~~  236 (258)
T 3uq3_A          230 LDAARTK  236 (258)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9998765

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.81  E-value=4.2e-20  Score=161.41  Aligned_cols=153  Identities=14%  Similarity=0.193  Sum_probs=125.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhH---hCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLN---SIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+|+++|++|++.|+.++|.++|++|.   ..|+.||..+||++|.+|++.|++++|.++|++|.+.|+.||..||+++|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI  207 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAAL  207 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            479999999999999999999998876   45789999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCc-HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcc--ccCCcchHHHHHH
Q 040261           95 KGLCAESR-IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVV--CKPDAITYSTITD  171 (343)
Q Consensus        95 ~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~  171 (343)
                      .++++.|+ .++|.++|++|.+.|+.||..+|+.++....+.       .+++.+.+..+.+.+.  .++...+...|..
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~-------~vL~~Vrkv~P~f~p~~~~~~~~~t~~LL~d  280 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA-------TVLKAVHKVKPTFSLPPQLPPPVNTSKLLRD  280 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH-------HHHHHHGGGCCCCCCCCCCCCCCCCCTTTHH
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH-------HHHHHHHHhCcccCCCCCCcccccchHHHHH
Confidence            99999998 478999999999999999999999988655442       3344444434333221  1122445556667


Q ss_pred             HHHhcC
Q 040261          172 GLCKEG  177 (343)
Q Consensus       172 ~~~~~~  177 (343)
                      .|.+.+
T Consensus       281 l~s~d~  286 (1134)
T 3spa_A          281 VYAKDG  286 (1134)
T ss_dssp             HHCCCS
T ss_pred             HHccCC
Confidence            777655

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.81  E-value=5.8e-19  Score=142.82  Aligned_cols=267  Identities=13%  Similarity=0.131  Sum_probs=134.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ++.+|..++.++.+.|++++|++.|.+.      +|...|..++.++...|++++|..+++...+.  .+++.+...++.
T Consensus        31 ~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~  102 (449)
T 1b89_A           31 EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIF  102 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHH
Confidence            3458999999999999999999999652      57779999999999999999999988877764  445778888999


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      +|.+.|+++++.++++       .|+..+|..+...|...|.+++|...|..+               ..|..++.++.+
T Consensus       103 ~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------------~n~~~LA~~L~~  160 (449)
T 1b89_A          103 ALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------------SNFGRLASTLVH  160 (449)
T ss_dssp             ------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT---------------TCHHHHHHHHHT
T ss_pred             HHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------------hhHHHHHHHHHH
Confidence            9999999999988874       367779999999999999999999999974               368999999999


Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      .|++++|.+.+.++      .++.+|..++.+|...|+++.|......+     ...+.....++..|.+.|.+++|..+
T Consensus       161 Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L-----~~~ad~l~~lv~~Yek~G~~eEai~l  229 (449)
T 1b89_A          161 LGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEELITM  229 (449)
T ss_dssp             TTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTT-----TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHH-----HhCHhhHHHHHHHHHHCCCHHHHHHH
Confidence            99999999999988      26889999999999999999996655432     23334455788999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhcC--CchHHHHHHHHHHHhCCCCc------cHHHHHHHHHHHHhcCChHHHHHHH
Q 040261          256 LELMIQIGVRPDASVYNTLMDGFCLT--GRVNRAKELFVSMESNGCMR------DVFSYGILINGYCKNKEIEGALSLY  326 (343)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~~~  326 (343)
                      ++...... +-....|+.+.-+|++-  ++..+.++.|..  +-+++|      +...|.-+...|..-++++.|....
T Consensus       230 Le~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~--~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm  305 (449)
T 1b89_A          230 LEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWS--RVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM  305 (449)
T ss_dssp             HHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHST--TSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH
Confidence            99998765 66678888888777765  344444444431  122333      4567888999999999999987743

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.80  E-value=3e-15  Score=128.84  Aligned_cols=188  Identities=11%  Similarity=0.082  Sum_probs=149.7

Q ss_pred             cCChH-------HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCC--hhhHHHHH
Q 040261          135 TGHTI-------VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPD--VVTYTSLI  205 (343)
Q Consensus       135 ~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~  205 (343)
                      .|+++       +|..++++..+..      .+.+...|..++..+.+.|++++|..+|+++.+.  .|+  ...|..++
T Consensus       292 ~g~~~~a~~~~~~A~~~~~~Al~~~------~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~  363 (530)
T 2ooe_A          292 KGDMNNAKLFSDEAANIYERAISTL------LKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYM  363 (530)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTTTT------CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHH
T ss_pred             ccchhhhhhhhHHHHHHHHHHHHHh------CcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHH
Confidence            57776       7888888887632      2456788999999999999999999999999885  343  24788888


Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE-LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV  284 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  284 (343)
                      ..+.+.|++++|..+|++..+.. +.+...|...+.. +...|+.++|..+|+...+.. +.+...|..++..+.+.|+.
T Consensus       364 ~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~  441 (530)
T 2ooe_A          364 KFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNED  441 (530)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCH
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCH
Confidence            88889999999999999998863 2233333333222 346899999999999998874 45688999999999999999


Q ss_pred             HHHHHHHHHHHhCCC-Ccc--HHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          285 NRAKELFVSMESNGC-MRD--VFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       285 ~~a~~~~~~~~~~~~-~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ++|..+|++....+. .|+  ...|...+......|+.+.+..+++++.+.
T Consensus       442 ~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          442 NNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             HHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999988632 222  447888888888899999999999988754

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.80  E-value=2.3e-19  Score=156.82  Aligned_cols=116  Identities=12%  Similarity=0.172  Sum_probs=62.7

Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHH---cCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMD---QGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTL  274 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  274 (343)
                      ..+|+++|.+|++.|++++|..+|..|.+   .|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||+.+
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            34455555555555555555555544432   245555555555555555555555555555555555555555555555


Q ss_pred             HHHHhcCCch-HHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          275 MDGFCLTGRV-NRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       275 ~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      |.++++.|+. ++|.++|++|.+.|+.||..+|+.++.++
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~  246 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEE  246 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChh
Confidence            5555555542 45555555555555555555555555433

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.80  E-value=2e-17  Score=125.09  Aligned_cols=198  Identities=14%  Similarity=-0.005  Sum_probs=110.5

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      |+++..+..+...+.+.|++++|+..|++..+.. +.+...+..+..++.+.|++++|...+++..+..+ .+...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTP-RYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHH
Confidence            4677778888888888888888888888877754 45667777788888888888888888888877642 256667777


Q ss_pred             HHHHhhc-----------CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           94 IKGLCAE-----------SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        94 ~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      ..++...           |++++|+..+++..+..+. +...+..+..++...|++++|...+++..+..        .+
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--------~~  150 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPR-YAPLHLQRGLVYALLGERDKAEASLKQALALE--------DT  150 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------CC
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--------cc
Confidence            7777666           5555555555555544322 34444455555555555555555555554431        23


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIE  223 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  223 (343)
                      ...+..+..++...|++++|...|++..+.. +.+...+..+..++...|++++|...+++
T Consensus       151 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          151 PEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC-------------
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            3444445555555555555555555544432 12344444444455555555555444443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.80  E-value=1.1e-16  Score=135.75  Aligned_cols=318  Identities=10%  Similarity=-0.039  Sum_probs=213.1

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhC-----C--CCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHcCC
Q 040261           13 SPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSI-----G--LFPDLYTYNILINCFCKM--GRVSPGFVVLGRILRSCF   83 (343)
Q Consensus        13 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~   83 (343)
                      .|....+|+.+..+|...|++++|...+++..+.     +  ......++.....++...  +++++|.+.|++..+..+
T Consensus        90 ~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p  169 (472)
T 4g1t_A           90 EIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKP  169 (472)
T ss_dssp             TTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHST
T ss_pred             chHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCC
Confidence            3356778999999999999999999999887542     1  012345666666555554  578999999999998753


Q ss_pred             CccHHHHHHHHHHH---hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHHccCCCCC
Q 040261           84 TPDAVTFTSLIKGL---CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR----TGHTIVALNLFEEMANGNGEFG  156 (343)
Q Consensus        84 ~~~~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~  156 (343)
                      . +...+..+..++   ...++.++|++.+++..+..+. +..++..+...+..    .+++++|.+.+++.....    
T Consensus       170 ~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~-~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~----  243 (472)
T 4g1t_A          170 K-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPD-NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA----  243 (472)
T ss_dssp             T-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSS-CHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC----
T ss_pred             C-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCc-chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC----
Confidence            3 455555555443   3457778899999998877533 55566555555444    467889999999988865    


Q ss_pred             ccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc-------------------CcHHHH
Q 040261          157 VVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA-------------------NDWNEA  217 (343)
Q Consensus       157 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------------------~~~~~a  217 (343)
                         +.+..++..+...|...|++++|...+++..+.. +.+..++..+..+|...                   +.++.|
T Consensus       244 ---~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A  319 (472)
T 4g1t_A          244 ---PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHA  319 (472)
T ss_dssp             ---SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHH
T ss_pred             ---ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHH
Confidence               4567788999999999999999999999988764 23566666666555322                   335678


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHH--HHHHHHH-HHhcCCchHHHHHHHHHH
Q 040261          218 KCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDAS--VYNTLMD-GFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~-~~~~~~~~~~a~~~~~~~  294 (343)
                      ...++...+.. +.+...+..+...+...|++++|...|+++.+....+...  .+..+.. .....|+.++|...+++.
T Consensus       320 ~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~ka  398 (472)
T 4g1t_A          320 VAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEG  398 (472)
T ss_dssp             HHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHH
T ss_pred             HHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            88888887764 4456778889999999999999999999999875333221  2233332 245778999999988877


Q ss_pred             HhCC-----------------------CCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC-CCCCcccc
Q 040261          295 ESNG-----------------------CMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKG-IRPTVVTY  341 (343)
Q Consensus       295 ~~~~-----------------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~t~  341 (343)
                      .+..                       -+.+..+|..+...|...|++++|++.|++.++.+ ..|+..+|
T Consensus       399 l~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          399 VKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC----------------------
T ss_pred             HhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            6532                       13456788999999999999999999999999875 34666555

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.80  E-value=2.3e-17  Score=124.74  Aligned_cols=198  Identities=13%  Similarity=0.055  Sum_probs=109.3

Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA  163 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  163 (343)
                      +++...+..+...+.+.|++++|...|++..+..+. +...+..+..++.+.|++++|...+++..+..       |.+.
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-------P~~~   73 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQ-DPEALYWLARTQLKLGLVNPALENGKTLVART-------PRYL   73 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCcH
Confidence            345666777777777888888888888887776443 56677777778888888888888888877764       3445


Q ss_pred             chHHHHHHHHHhc-----------CChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040261          164 ITYSTITDGLCKE-----------GFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN  232 (343)
Q Consensus       164 ~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  232 (343)
                      ..+..+..++...           |++++|+..+++..+.. +.+...+..+..++...|++++|...+++..+..  .+
T Consensus        74 ~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~  150 (217)
T 2pl2_A           74 GGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DT  150 (217)
T ss_dssp             HHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CC
T ss_pred             HHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cc
Confidence            6666676666665           55555555555554432 1234444445555555555555555555555443  34


Q ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHH
Q 040261          233 VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVS  293 (343)
Q Consensus       233 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  293 (343)
                      ...+..+..++...|++++|...++++.+.. +.+...+..+...+...|++++|...+++
T Consensus       151 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          151 PEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC-------------
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            4444455555555555555555555554443 33344444444555555555555544443

>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=99.79  E-value=9.4e-16  Score=120.35  Aligned_cols=225  Identities=11%  Similarity=-0.035  Sum_probs=165.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHHcCCCccHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK----MGRVSPGFVVLGRILRSCFTPDAVTF   90 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~   90 (343)
                      .++.++..+...+...|++++|...|++..+.   .+...+..+...+..    .+++++|...|++..+.+   +...+
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~   77 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGC   77 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            46777888888888888888888888888773   345677777778888    888888888888887764   56677


Q ss_pred             HHHHHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           91 TSLIKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR----TGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        91 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      ..+...+..    .+++++|++.|++..+.+   +...+..+...|..    .+++++|...+++..+.+         +
T Consensus        78 ~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---------~  145 (273)
T 1ouv_A           78 HLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---------D  145 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---------C
T ss_pred             HHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---------c
Confidence            777777777    888888888888887764   66677777777777    788888888888877653         3


Q ss_pred             cchHHHHHHHHHh----cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHH
Q 040261          163 AITYSTITDGLCK----EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVV  234 (343)
Q Consensus       163 ~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~  234 (343)
                      ...+..+...|..    .+++++|...|++..+.+   +...+..+...+..    .+++++|...+++..+.+   +..
T Consensus       146 ~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~  219 (273)
T 1ouv_A          146 GDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGG  219 (273)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHH
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHH
Confidence            4566666677766    777778877777776653   45566666667766    777777777777777654   245


Q ss_pred             HHHHHHHHHHh----CCChhHHHHHHHHHHHcC
Q 040261          235 TFNVIMNELCK----NGKMDEASRLLELMIQIG  263 (343)
Q Consensus       235 ~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  263 (343)
                      .+..+...+..    .+++++|...+++..+.+
T Consensus       220 a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          220 GCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            56666666766    777777777777777665

>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=99.79  E-value=6.2e-17  Score=132.09  Aligned_cols=217  Identities=5%  Similarity=0.018  Sum_probs=127.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC-cchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR-VSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ..+|..+...+.+.|++++|+..++++++.. +-+..+|+.+..++...|+ +++|+..|+++++.... +...|..+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHHHHH
Confidence            4556666666666777777777777666644 3345566666666666665 77777777776665432 5566666666


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      ++...|++++|+..|+++.+.... +...|..+..++.+.|++++|+..++++.+.+       +.+..+|+.+..++.+
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ldP~-~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-------P~~~~a~~~lg~~l~~  246 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-------VRNNSVWNQRYFVISN  246 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHH
Confidence            666667777777777766666433 55666666666666677777777776666654       3445666666666666


Q ss_pred             -cCChHHH-----HHHHHHhhhCCCCCChhhHHHHHHHHhccC--cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC
Q 040261          176 -EGFVDKA-----KELFLKMKDENINPDVVTYTSLIRGFCYAN--DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN  246 (343)
Q Consensus       176 -~~~~~~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  246 (343)
                       .|..++|     +..+++..... +-+...|..+...+...|  ++++|...+..+ +. .+.+...+..++.++.+.
T Consensus       247 l~~~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~  322 (382)
T 2h6f_A          247 TTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDM  322 (382)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHH
T ss_pred             hcCcchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHH
Confidence             4443555     34555544432 123445555555555544  355555555554 22 122344445555555443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.79  E-value=1.2e-15  Score=129.38  Aligned_cols=307  Identities=12%  Similarity=-0.012  Sum_probs=223.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhC--------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC----
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSI--------GLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC----   82 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----   82 (343)
                      .....||.+...+...|++++|++.|++..+.        .-+....+|+.+..+|...|++++|...+++..+..    
T Consensus        49 ~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~  128 (472)
T 4g1t_A           49 FKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFS  128 (472)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcc
Confidence            45678999999999999999999999887542        112345689999999999999999999999887531    


Q ss_pred             --CC-ccHHHHHHHHHHHhhc--CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH---HHhcCChHHHHHHHHHHHccCCC
Q 040261           83 --FT-PDAVTFTSLIKGLCAE--SRIMEAAALFTKLRAFGCKPDVFTYTTLING---LCRTGHTIVALNLFEEMANGNGE  154 (343)
Q Consensus        83 --~~-~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~a~~~~~~~~~~~~~  154 (343)
                        .. ....++.....++...  +++++|++.|++..+..+. +...+..+..+   +...++.++|++.+++..+..  
T Consensus       129 ~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~--  205 (472)
T 4g1t_A          129 SPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN--  205 (472)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC--
T ss_pred             cccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC--
Confidence              11 1245566555555543  5799999999999987543 45555555544   445678889999999988764  


Q ss_pred             CCccccCCcchHHHHHHHHHh----cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCC
Q 040261          155 FGVVCKPDAITYSTITDGLCK----EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQ  230 (343)
Q Consensus       155 ~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  230 (343)
                           +.+..++..+...+..    .+++++|.+.+++..... +.+...+..+...+...|++++|...+++..+.. +
T Consensus       206 -----p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p  278 (472)
T 4g1t_A          206 -----PDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-P  278 (472)
T ss_dssp             -----SSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-T
T ss_pred             -----CcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-C
Confidence                 3445566655555443    467889999999887764 3467888999999999999999999999999873 3


Q ss_pred             CCHHHHHHHHHHHHhC-------------------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          231 PNVVTFNVIMNELCKN-------------------GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       231 ~~~~~~~~l~~~~~~~-------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      -+..++..+..+|...                   +..+.|...++...+.. +.+...+..+...+...|++++|...|
T Consensus       279 ~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~  357 (472)
T 4g1t_A          279 NNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYF  357 (472)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHH
Confidence            4466666666555322                   23567888888887765 455667888999999999999999999


Q ss_pred             HHHHhCCCCccHH--HHHHHHH-HHHhcCChHHHHHHHHHHHhC
Q 040261          292 VSMESNGCMRDVF--SYGILIN-GYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       292 ~~~~~~~~~~~~~--~~~~l~~-~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ++..+....+...  .+..+.. .....|++++|+..|++.+..
T Consensus       358 ~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i  401 (472)
T 4g1t_A          358 QKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI  401 (472)
T ss_dssp             HHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS
T ss_pred             HHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            9998864333221  2233332 245779999999999998854

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.78  E-value=1.3e-16  Score=125.13  Aligned_cols=244  Identities=9%  Similarity=0.061  Sum_probs=135.1

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHH
Q 040261           56 NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP--DVFTYTTLINGLC  133 (343)
Q Consensus        56 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~  133 (343)
                      ......+...|++++|...++++.+..+ .+...+..+..++...|++++|++.+++..+.+..+  ....+..+...+.
T Consensus         7 ~~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~   85 (272)
T 3u4t_A            7 FRYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILM   85 (272)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHH
Confidence            3344444555555555555555554421 133345555555555555555555555555522111  1223555666666


Q ss_pred             hcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc
Q 040261          134 RTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND  213 (343)
Q Consensus       134 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  213 (343)
                      ..|++++|...+++..+..       +.+..++..+..++...|++++|...+++..+.. +.+...+..+...+...++
T Consensus        86 ~~~~~~~A~~~~~~a~~~~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~  157 (272)
T 3u4t_A           86 KKGQDSLAIQQYQAAVDRD-------TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKE  157 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-------TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTC
T ss_pred             HcccHHHHHHHHHHHHhcC-------cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHH
Confidence            6666666666666666543       3344566666666666666666666666665542 2244555555523333447


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC---hhHHHHHHHHHHHcC-CCCC------HHHHHHHHHHHhcCCc
Q 040261          214 WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK---MDEASRLLELMIQIG-VRPD------ASVYNTLMDGFCLTGR  283 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~~~~~  283 (343)
                      +++|...++.+.+.. +.+...+..+..++...|+   +++|...++++.+.. -.|+      ..++..+...|...|+
T Consensus       158 ~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  236 (272)
T 3u4t_A          158 YVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRD  236 (272)
T ss_dssp             HHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCC
Confidence            777777777766653 3335555566666666666   666777776666541 1122      2456667777777777


Q ss_pred             hHHHHHHHHHHHhCCCCccHHHHHHHH
Q 040261          284 VNRAKELFVSMESNGCMRDVFSYGILI  310 (343)
Q Consensus       284 ~~~a~~~~~~~~~~~~~~~~~~~~~l~  310 (343)
                      +++|...+++..+.. +.+...+..+.
T Consensus       237 ~~~A~~~~~~al~~~-p~~~~a~~~l~  262 (272)
T 3u4t_A          237 KVKADAAWKNILALD-PTNKKAIDGLK  262 (272)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHC
T ss_pred             HHHHHHHHHHHHhcC-ccHHHHHHHhh
Confidence            777777777776653 22344444433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.77  E-value=4.3e-16  Score=122.18  Aligned_cols=247  Identities=13%  Similarity=0.105  Sum_probs=160.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc--HHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD--AVTFTSLI   94 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~   94 (343)
                      +..+......+.+.|++++|+..|++..+.. +.+...+..+..++...|++++|.+.++++.+....++  ...|..+.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg   81 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYG   81 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHH
Confidence            3455666777777778888888877777654 33445677777777777788888777777776321111  23366777


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      ..+...|++++|++.+++..+.... +...+..+..++...|++++|...+++..+..       +.+...+..+...+.
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-------~~~~~~~~~l~~~~~  153 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRDTT-RLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-------TTDPKVFYELGQAYY  153 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-------CCCHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-------CCcHHHHHHHHHHHH
Confidence            7777777788888777777776433 45677777777777788888877777776653       344555666662333


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc---HHHHHHHHHHHHHcC-CCCC------HHHHHHHHHHHH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND---WNEAKCLFIEMMDQG-VQPN------VVTFNVIMNELC  244 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~  244 (343)
                      ..+++++|...|+++.+.. +.+...+..+..++...|+   +++|...++++.+.. -.|+      ...|..+...+.
T Consensus       154 ~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  232 (272)
T 3u4t_A          154 YNKEYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYT  232 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHH
Confidence            4457777877777776653 2235566666666666666   666777777766541 1122      145666777777


Q ss_pred             hCCChhHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          245 KNGKMDEASRLLELMIQIGVRPDASVYNTL  274 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  274 (343)
                      ..|++++|...++++.+.. +.+......+
T Consensus       233 ~~~~~~~A~~~~~~al~~~-p~~~~a~~~l  261 (272)
T 3u4t_A          233 INRDKVKADAAWKNILALD-PTNKKAIDGL  261 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhcC-ccHHHHHHHh
Confidence            7778888888777777764 3344444443

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.77  E-value=4.9e-18  Score=137.47  Aligned_cols=248  Identities=13%  Similarity=0.109  Sum_probs=107.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      .+.+.|+.   +.|+.++|.+.++++.      +..+|..++.++.+.|++++|++.|.+.      +|...|..++.++
T Consensus         7 ~a~~~ll~---~~~~ld~A~~fae~~~------~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~a   71 (449)
T 1b89_A            7 SAVQVLIE---HIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAA   71 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHH---HccCHHHHHHHHHhCC------ChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHH
Confidence            34444444   6788999999999883      2359999999999999999999999653      4777999999999


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      ...|++++|+++++..++.  .+++.+.+.++.+|.+.|+++++.++++             .|+..+|..+...|...|
T Consensus        72 e~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------------~pn~~a~~~IGd~~~~~g  136 (449)
T 1b89_A           72 NTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------------GPNNAHIQQVGDRCYDEK  136 (449)
T ss_dssp             ---------------------------------------CHHHHTTTTT-------------CC----------------
T ss_pred             HhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------------CCcHHHHHHHHHHHHHcC
Confidence            9999999999988887764  4467788899999999999999887774             255679999999999999


Q ss_pred             ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHH
Q 040261          178 FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLE  257 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  257 (343)
                      .+++|...|..+         ..|..++.++.+.|++++|.+.+.++      .+..+|..++.+|...|+++.|.....
T Consensus       137 ~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l  201 (449)
T 1b89_A          137 MYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGL  201 (449)
T ss_dssp             CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTT
T ss_pred             CHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHH
Confidence            999999999977         36999999999999999999999988      278999999999999999999966554


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhc
Q 040261          258 LMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKN  316 (343)
Q Consensus       258 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  316 (343)
                      .+     ...+.-...++..|.+.|++++|..+++...... +-....|+.+...|++-
T Consensus       202 ~L-----~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky  254 (449)
T 1b89_A          202 HI-----VVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF  254 (449)
T ss_dssp             TT-----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT
T ss_pred             HH-----HhCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhc
Confidence            42     2344445578899999999999999999988754 44567777777777654

>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=99.77  E-value=5.1e-16  Score=126.68  Aligned_cols=249  Identities=11%  Similarity=0.009  Sum_probs=203.6

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc-HHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           52 LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR-IMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        52 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      ...|..+..++...|++++|+..++++++.... +...|+.+..++...|+ +++|+..|++..+.... +...|..+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~-~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHHHHH
Confidence            457888888899999999999999999987533 68889999999999996 99999999999998655 7889999999


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY  210 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (343)
                      ++...|++++|+..++++...+       +.+..+|..+..++.+.|++++|+..++++.+.. +-+...|+.+..++..
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld-------P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~  246 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD-------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISN  246 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-------ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            9999999999999999999876       5677899999999999999999999999998875 3367889989888888


Q ss_pred             -cCcHHHH-----HHHHHHHHHcCCCCCHHHHHHHHHHHHhCC--ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCC
Q 040261          211 -ANDWNEA-----KCLFIEMMDQGVQPNVVTFNVIMNELCKNG--KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTG  282 (343)
Q Consensus       211 -~~~~~~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  282 (343)
                       .|..++|     +..+++.++.. +-+...|..+..++...|  ++++|...+.++ +.. +.+...+..+...|.+.|
T Consensus       247 l~~~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~-p~~~~al~~La~~~~~~~  323 (382)
T 2h6f_A          247 TTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPS-HSSPYLIAFLVDIYEDML  323 (382)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTT-CCCHHHHHHHHHHHHHHH
T ss_pred             hcCcchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccC-CCCHHHHHHHHHHHHHHh
Confidence             5654666     58888888763 445778888888888888  689999999887 433 556788888888888864


Q ss_pred             ---------chHHHHHHHHHH-HhCCCCccHHHHHHHHHHHH
Q 040261          283 ---------RVNRAKELFVSM-ESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       283 ---------~~~~a~~~~~~~-~~~~~~~~~~~~~~l~~~~~  314 (343)
                               ..++|.++++++ .+.. +.....|..+...+.
T Consensus       324 ~~~~~~~~~~~~~A~~~~~~l~~~~D-P~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          324 ENQCDNKEDILNKALELCEILAKEKD-TIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HTTCSSHHHHHHHHHHHHHHHHHTTC-GGGHHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHHHHHHHHhC-chhHHHHHHHHHHHH
Confidence                     358999999999 6642 223455665555544

>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=99.76  E-value=1.1e-15  Score=118.53  Aligned_cols=203  Identities=13%  Similarity=-0.010  Sum_probs=148.0

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040261           52 LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING  131 (343)
Q Consensus        52 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  131 (343)
                      ...+..+...+...|++++|.+.++++.+.. +.+...+..+...+...|++++|.+.++++.+.... +...+..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHH
Confidence            4566777777777888888888888777654 235667777777788888888888888887776433 56677777778


Q ss_pred             HHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          132 LCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       132 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                      +...|++++|.+.++++...+.     .+.+...+..+..++...|++++|...++++.+.. +.+...+..+...+...
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~-----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~  188 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTL-----YPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKE  188 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTT-----CTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHT
T ss_pred             HHHHhHHHHHHHHHHHHHhCcc-----CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHc
Confidence            8888888888888888776210     13345667777778888888888888888776653 23566777777888888


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      |++++|...++.+.+.. +.+...+..+...+...|++++|..+++++.+..
T Consensus       189 g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          189 REYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             TCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            88888888888877653 4456667777777888888888888888887763

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.76  E-value=8.6e-17  Score=126.37  Aligned_cols=245  Identities=12%  Similarity=-0.055  Sum_probs=133.2

Q ss_pred             CCcchHHHHHHHHHHcCC---CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHH
Q 040261           66 GRVSPGFVVLGRILRSCF---TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVAL  142 (343)
Q Consensus        66 ~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  142 (343)
                      |++++|...++++.+...   +.+..++..+...+...|++++|.+.|++..+.... +..++..+..++...|++++|.
T Consensus        19 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~A~   97 (275)
T 1xnf_A           19 LQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAY   97 (275)
T ss_dssp             HHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHH
T ss_pred             chHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHccCHHHHH
Confidence            445555555555554321   112344555555555556666666666655554322 4555555666666666666666


Q ss_pred             HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHH
Q 040261          143 NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFI  222 (343)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  222 (343)
                      ..++++....       +.+..++..+..++...|++++|...++++.+..  |+.......+..+...|++++|...++
T Consensus        98 ~~~~~al~~~-------~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~  168 (275)
T 1xnf_A           98 EAFDSVLELD-------PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYLAEQKLDEKQAKEVLK  168 (275)
T ss_dssp             HHHHHHHHHC-------TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHHHHHhcC-------ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHhcCHHHHHHHHH
Confidence            6666665543       2344556666666666666666666666655532  333333333334445566666666666


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC---CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCC
Q 040261          223 EMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR---PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGC  299 (343)
Q Consensus       223 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  299 (343)
                      ...... +++...+ .++..+...++.++|...++.+.+....   .+...+..+...|...|++++|...+++..+.. 
T Consensus       169 ~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-  245 (275)
T 1xnf_A          169 QHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN-  245 (275)
T ss_dssp             HHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-
Confidence            655542 2333333 2555555666666666666665443210   114566777777777788888888877777653 


Q ss_pred             CccHHHHHHHHHHHHhcCChHHHHHHH
Q 040261          300 MRDVFSYGILINGYCKNKEIEGALSLY  326 (343)
Q Consensus       300 ~~~~~~~~~l~~~~~~~~~~~~a~~~~  326 (343)
                       |+.  +.....++...|++++|++.+
T Consensus       246 -p~~--~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          246 -VHN--FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             -CTT--CHHHHHHHHHHHHHHHC----
T ss_pred             -chh--HHHHHHHHHHHHHHHhhHHHH
Confidence             321  223344566667777776655

>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=99.76  E-value=8.1e-15  Score=115.00  Aligned_cols=224  Identities=16%  Similarity=-0.019  Sum_probs=150.8

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYT  126 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  126 (343)
                      +..++..+...+...|++++|.+.|++..+.+   +...+..+...+..    .+++++|.+.|++..+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            45566667777777777777777777777632   44566667777777    777777777777777664   566666


Q ss_pred             HHHHHHHh----cCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh----cCChHHHHHHHHHhhhCCCCCCh
Q 040261          127 TLINGLCR----TGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK----EGFVDKAKELFLKMKDENINPDV  198 (343)
Q Consensus       127 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~  198 (343)
                      .+...|..    .+++++|...+++..+.+         +..++..+...|..    .+++++|+..+++..+.+   +.
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---------~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~  146 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---------YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DG  146 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---------CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cH
Confidence            77777777    777777777777776643         45566667777776    777777777777776654   45


Q ss_pred             hhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHHHHHHHHHHHcCCCCCHHH
Q 040261          199 VTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEASRLLELMIQIGVRPDASV  270 (343)
Q Consensus       199 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  270 (343)
                      ..+..+...+..    .+++++|...+++..+.+   +...+..+...+..    .+++++|...+++..+.+   +...
T Consensus       147 ~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a  220 (273)
T 1ouv_A          147 DGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGG  220 (273)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHH
Confidence            556666666665    677777777777766653   34555666666666    677777777777766654   2455


Q ss_pred             HHHHHHHHhc----CCchHHHHHHHHHHHhCC
Q 040261          271 YNTLMDGFCL----TGRVNRAKELFVSMESNG  298 (343)
Q Consensus       271 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  298 (343)
                      +..+...|..    .+++++|...+++..+.+
T Consensus       221 ~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          221 CFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            5666666666    667777777777666654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.76  E-value=9.3e-16  Score=116.59  Aligned_cols=204  Identities=10%  Similarity=-0.051  Sum_probs=119.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++.++..+...+...|++++|...++++.+.. +.+...+..+..++...|++++|.+.++++.+.. +.+..++..+.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~   83 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYG   83 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            355666777777777777777777777766543 3345566666666677777777777777666553 22455566666


Q ss_pred             HHHhhc-CcHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHH
Q 040261           95 KGLCAE-SRIMEAAALFTKLRAFGCKPD-VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDG  172 (343)
Q Consensus        95 ~~~~~~-~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  172 (343)
                      ..+... |++++|.+.++++.+.+..|+ ...+..+..++...|++++|...++++.+..       +.+...+..+..+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~la~~  156 (225)
T 2vq2_A           84 WFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-------PQFPPAFKELART  156 (225)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHH
T ss_pred             HHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCCchHHHHHHHH
Confidence            666666 666666666666665221222 3455556666666666666666666665543       2334455555555


Q ss_pred             HHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          173 LCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      +.+.|++++|...++++.+.....+...+..+...+...|+.+++..+++.+.+.
T Consensus       157 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          157 KMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            6666666666666655544321123444445555555555555555555555443

>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=99.75  E-value=3.3e-15  Score=115.71  Aligned_cols=201  Identities=11%  Similarity=0.019  Sum_probs=138.1

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...+..+...+...|++++|.+.++++.+.... +...+..+...+...|++++|.+.++++.+..       +.+...+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-------~~~~~~~  108 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPS-SADAHAALAVVFQTEMEPKLADEEYRKALASD-------SRNARVL  108 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCC-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-------cCcHHHH
Confidence            455666667777777777777777777765422 56667777777777777777777777776654       3345667


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCCCC-ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENINP-DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                      ..+...+...|++++|.+.++++...+..| +...+..+..++...|++++|...++++.+.. +.+...+..+...+..
T Consensus       109 ~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  187 (252)
T 2ho1_A          109 NNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYK  187 (252)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHH
Confidence            777777777777777777777776622223 35566666777777777777777777777653 3346666777777777


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .|++++|...++++.+.. +.+...+..+...+...|++++|.+.++++.+.
T Consensus       188 ~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          188 EREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             TTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            777777777777776654 445666677777777777777777777777665

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.75  E-value=2.8e-15  Score=113.91  Aligned_cols=200  Identities=11%  Similarity=-0.035  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...+..+...+...|++++|.+.++++.+.... +...+..+...+...|++++|...++++....       +.+..++
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-------~~~~~~~   79 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSDPK-NELAWLVRAEIYQYLKVNDKAQESFRQALSIK-------PDSAEIN   79 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-------CCChHHH
Confidence            334444455555555555555555555444221 34445555555555555555555555554432       2234445


Q ss_pred             HHHHHHHHhc-CChHHHHHHHHHhhhCCCCC-ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040261          167 STITDGLCKE-GFVDKAKELFLKMKDENINP-DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC  244 (343)
Q Consensus       167 ~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  244 (343)
                      ..+...+... |++++|...++++.+.+..| +...+..+..++...|++++|...++.+.+.. +.+...+..+...+.
T Consensus        80 ~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~  158 (225)
T 2vq2_A           80 NNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKM  158 (225)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHH
Confidence            5555555555 55555555555554421111 13444455555555555555555555555442 223444555555555


Q ss_pred             hCCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          245 KNGKMDEASRLLELMIQIGVR-PDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      ..|++++|...++++.+.. + .+...+..+...+...|+.+.|..+++.+.+
T Consensus       159 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          159 LAGQLGDADYYFKKYQSRV-EVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHTCHHHHHHHHHHHHHHH-CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            5555555555555555543 2 3444455555555555555555555555543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.74  E-value=2.5e-16  Score=123.66  Aligned_cols=249  Identities=9%  Similarity=-0.039  Sum_probs=193.2

Q ss_pred             HHhcCChhHHHHHHHHhHhCCC---CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGL---FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      +...|++++|+..|+++.+...   +.+..++..+..++...|++++|...|+++.+.. +.+..++..+...+...|++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~   93 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNF   93 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCH
Confidence            3456889999999999987532   1245678889999999999999999999999875 33688899999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                      ++|.+.+++..+.... +...+..+..++...|++++|...++++....        |+.......+..+...|++++|.
T Consensus        94 ~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--------~~~~~~~~~~~~~~~~~~~~~A~  164 (275)
T 1xnf_A           94 DAAYEAFDSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--------PNDPFRSLWLYLAEQKLDEKQAK  164 (275)
T ss_dssp             HHHHHHHHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------TTCHHHHHHHHHHHHHHCHHHHH
T ss_pred             HHHHHHHHHHHhcCcc-ccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--------CCChHHHHHHHHHHHhcCHHHHH
Confidence            9999999999987543 57788999999999999999999999999864        44444555556667789999999


Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCC--C-CHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQ--P-NVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      ..+++..... +++...+ .++..+...++.++|...+....+....  | +...+..+...+...|++++|...++++.
T Consensus       165 ~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  242 (275)
T 1xnf_A          165 EVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAV  242 (275)
T ss_dssp             HHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9998877653 3344444 4677778888889999999887654211  1 15778889999999999999999999998


Q ss_pred             HcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          261 QIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       261 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      +.. +.+.   .....++...|++++|.+.+
T Consensus       243 ~~~-p~~~---~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          243 ANN-VHNF---VEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             TTC-CTTC---HHHHHHHHHHHHHHHC----
T ss_pred             hCC-chhH---HHHHHHHHHHHHHHhhHHHH
Confidence            864 2232   23345667778888887766

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.74  E-value=4.3e-16  Score=119.99  Aligned_cols=197  Identities=14%  Similarity=0.060  Sum_probs=85.8

Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTI  169 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  169 (343)
                      |..+...+...|++++|...++++.+.... +...+..+...+...|++++|...++++....       +.+..++..+
T Consensus        26 ~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~l   97 (243)
T 2q7f_A           26 GGQQMGRGSEFGDYEKAAEAFTKAIEENKE-DAIPYINFANLLSSVNELERALAFYDKALELD-------SSAATAYYGA   97 (243)
T ss_dssp             ----------------CCTTHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHH
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------CcchHHHHHH
Confidence            333444444444444444444444443211 33444444444444444444444444444432       2233444444


Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCh
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM  249 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  249 (343)
                      ...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++
T Consensus        98 a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  175 (243)
T 2q7f_A           98 GNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGML  175 (243)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCH
Confidence            444444555555555544444332 1233444444455555555555555555554442 22344455555555555555


Q ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          250 DEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ++|...++++.+.. +.+..++..+...|...|++++|...++++.+.
T Consensus       176 ~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          176 DEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc
Confidence            55555555555443 333445555555555555555555555555543

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.74  E-value=5.1e-16  Score=119.58  Aligned_cols=199  Identities=14%  Similarity=0.091  Sum_probs=103.7

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLC  133 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  133 (343)
                      .|..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|.+.+++..+.... +...+..+...+.
T Consensus        25 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~  102 (243)
T 2q7f_A           25 TGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSS-AATAYYGAGNVYV  102 (243)
T ss_dssp             -----------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCc-chHHHHHHHHHHH
Confidence            44444455555555555555555555432 223445555555555555555555555555544322 4455555555566


Q ss_pred             hcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc
Q 040261          134 RTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAND  213 (343)
Q Consensus       134 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  213 (343)
                      ..|++++|.+.++++.+..       +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|+
T Consensus       103 ~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~  174 (243)
T 2q7f_A          103 VKEMYKEAKDMFEKALRAG-------MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGM  174 (243)
T ss_dssp             HTTCHHHHHHHHHHHHHHT-------CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HhccHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCC
Confidence            6666666666666555543       2344455555566666666666666666655432 2245555666666666666


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          214 WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      +++|...++.+.+.. +.+..++..+..++...|++++|...++++.+..
T Consensus       175 ~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          175 LDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            666666666666552 3345566666667777777777777777766653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.73  E-value=2.8e-16  Score=130.56  Aligned_cols=304  Identities=13%  Similarity=0.026  Sum_probs=227.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHc----CCCc-
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD----LYTYNILINCFCKMGRVSPGFVVLGRILRS----CFTP-   85 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-   85 (343)
                      .....+......+.+.|++++|...|+++.+.+ +.+    ..++..+...+...|++++|...+++....    +..| 
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            566678889999999999999999999998764 223    357888899999999999999999987653    1112 


Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC-CC----HHHHHHHHHHHHhcCC--------------------hHH
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK-PD----VFTYTTLINGLCRTGH--------------------TIV  140 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~  140 (343)
                      ...++..+...+...|++++|...+++..+.... ++    ..++..+...+...|+                    +++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            2557788889999999999999999987654110 11    3477888899999999                    999


Q ss_pred             HHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC-CCC----hhhHHHHHHHHhccCcHH
Q 040261          141 ALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENI-NPD----VVTYTSLIRGFCYANDWN  215 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~  215 (343)
                      |...+++........+. .+....++..+...+...|++++|...+++..+... .++    ..++..+...+...|+++
T Consensus       166 A~~~~~~al~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  244 (406)
T 3sf4_A          166 AVDFYEENLSLVTALGD-RAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  244 (406)
T ss_dssp             HHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHhccC-cHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChH
Confidence            99999887653210000 112245788888999999999999999998764310 011    347888889999999999


Q ss_pred             HHHHHHHHHHHcC----CCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC----C-CCHHHHHHHHHHHhcCCchH
Q 040261          216 EAKCLFIEMMDQG----VQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQIGV----R-PDASVYNTLMDGFCLTGRVN  285 (343)
Q Consensus       216 ~a~~~~~~~~~~~----~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~-~~~~~~~~l~~~~~~~~~~~  285 (343)
                      +|...+++..+..    ..+. ..++..+...+...|++++|...+++..+...    . ....++..+...|...|+++
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  324 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHD  324 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            9999999887541    1111 45778889999999999999999998876421    1 11557788899999999999


Q ss_pred             HHHHHHHHHHhC----CCC-ccHHHHHHHHHHHHhcCChH
Q 040261          286 RAKELFVSMESN----GCM-RDVFSYGILINGYCKNKEIE  320 (343)
Q Consensus       286 ~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~  320 (343)
                      +|...+++..+.    +.. ....++..+...+...|+..
T Consensus       325 ~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  364 (406)
T 3sf4_A          325 QAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSY  364 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhH
Confidence            999999987643    211 22456777778888777653

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.71  E-value=7.2e-16  Score=128.41  Aligned_cols=278  Identities=13%  Similarity=0.060  Sum_probs=208.0

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH----HHHHHHHHHHhhcCcHHHHHHHHHHHHhc----CC-CCCHH
Q 040261           53 YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA----VTFTSLIKGLCAESRIMEAAALFTKLRAF----GC-KPDVF  123 (343)
Q Consensus        53 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~  123 (343)
                      ..+..+...+...|++++|...|+++.+.... +.    ..+..+...+...|++++|.+.+++..+.    +. .....
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  127 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAK  127 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHH
Confidence            34556677788899999999999999886433 32    46778888899999999999999887653    11 12345


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC-----------------hHHHHHHH
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF-----------------VDKAKELF  186 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~  186 (343)
                      .+..+...|...|++++|...+++........+. .+....++..+...|...|+                 +++|...+
T Consensus       128 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~  206 (411)
T 4a1s_A          128 SSGNLGNTLKVMGRFDEAAICCERHLTLARQLGD-RLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFY  206 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-HHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc-hHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHH
Confidence            6778888999999999999999887664210000 12234578888899999999                 99999998


Q ss_pred             HHhhhC----CC-CCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhCCChhHHHHHH
Q 040261          187 LKMKDE----NI-NPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQ-PN----VVTFNVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       187 ~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~  256 (343)
                      ++..+.    +. +.....+..+...+...|++++|...+++..+.... ++    ...+..+...+...|++++|...+
T Consensus       207 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  286 (411)
T 4a1s_A          207 QENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHY  286 (411)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            876442    11 112457788889999999999999999988764210 11    237788899999999999999999


Q ss_pred             HHHHHcCCC-----CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CC-CccHHHHHHHHHHHHhcCChHHHHHHH
Q 040261          257 ELMIQIGVR-----PDASVYNTLMDGFCLTGRVNRAKELFVSMESN----GC-MRDVFSYGILINGYCKNKEIEGALSLY  326 (343)
Q Consensus       257 ~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~  326 (343)
                      +++.+....     ....++..+...+...|++++|...+++..+.    +. .....++..+...|...|++++|.+.+
T Consensus       287 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  366 (411)
T 4a1s_A          287 KRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYA  366 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHH
Confidence            988764211     12567888999999999999999999987653    10 112457788889999999999999999


Q ss_pred             HHHHhC
Q 040261          327 SEMLSK  332 (343)
Q Consensus       327 ~~~~~~  332 (343)
                      ++....
T Consensus       367 ~~al~~  372 (411)
T 4a1s_A          367 EQHLQL  372 (411)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.71  E-value=6.7e-15  Score=121.37  Aligned_cols=301  Identities=11%  Similarity=-0.037  Sum_probs=211.2

Q ss_pred             HHhcCChhHHHHHHHHhHhC--CCCCC--HHHHHHHHHH--HHhcCCcchHH-----------HHHHHHHHcCCCccHHH
Q 040261           27 LAKNKHYDTVLSLFKRLNSI--GLFPD--LYTYNILINC--FCKMGRVSPGF-----------VVLGRILRSCFTPDAVT   89 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~--~~~~~--~~~~~~l~~~--~~~~~~~~~a~-----------~~~~~~~~~~~~~~~~~   89 (343)
                      +.+.+++++|..+++++.+.  .+..|  ...|..++..  ..-.++++.+.           +.++.+....  .+...
T Consensus        22 ~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~--~~~~~   99 (383)
T 3ulq_A           22 YIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQ--ARLTG   99 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHT--HHHHH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcC--CCchh
Confidence            45789999999999998652  22233  3334444332  22223344444           6777765432  12121


Q ss_pred             ------HHHHHHHHhhcCcHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcc
Q 040261           90 ------FTSLIKGLCAESRIMEAAALFTKLRAF----GCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVV  158 (343)
Q Consensus        90 ------~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  158 (343)
                            +......+...|++++|...+++..+.    +-.+ ...++..+...|...|+++.|...+++........+..
T Consensus       100 ~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~  179 (383)
T 3ulq_A          100 LLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAY  179 (383)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTT
T ss_pred             HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccc
Confidence                  222556678889999999999998764    1111 24578889999999999999999999987653211000


Q ss_pred             ccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCC-CChhhHHHHHHHHhccCcHHHHHHHHHHHHHc----CC
Q 040261          159 CKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NIN-PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ----GV  229 (343)
Q Consensus       159 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~  229 (343)
                      .+....++..+..+|...|++++|...+++..+.    +.. ....++..+..+|...|++++|...+++..+.    +.
T Consensus       180 ~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~  259 (383)
T 3ulq_A          180 NIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNI  259 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcc
Confidence            0112357888899999999999999999887643    111 11247888999999999999999999998873    22


Q ss_pred             -CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCCHHHHHHHHHHHhcCCc---hHHHHHHHHHHHhCCCCc
Q 040261          230 -QPNVVTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPDASVYNTLMDGFCLTGR---VNRAKELFVSMESNGCMR  301 (343)
Q Consensus       230 -~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~  301 (343)
                       +....++..+...+...|++++|...+++..+.    +-+.....+..+...+...|+   +++|..++++..   ..|
T Consensus       260 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~---~~~  336 (383)
T 3ulq_A          260 LPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKM---LYA  336 (383)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTT---CHH
T ss_pred             chhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCc---CHH
Confidence             333667888999999999999999999988764    212223345678888899998   777777776652   223


Q ss_pred             -cHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          302 -DVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       302 -~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                       ....+..+...|...|++++|...+++....
T Consensus       337 ~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          337 DLEDFAIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             3456778889999999999999999998754

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.71  E-value=1.1e-15  Score=126.97  Aligned_cols=283  Identities=11%  Similarity=0.046  Sum_probs=213.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc---HHHHHHHHHHHhhcCcHHHHHHHHHHHHhc----CCCC-
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD---AVTFTSLIKGLCAESRIMEAAALFTKLRAF----GCKP-  120 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-  120 (343)
                      ......+......+...|++++|...|+++.+......   ..++..+...+...|++++|...+++....    +..| 
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            34566777888899999999999999999998743311   357888889999999999999999987543    1111 


Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC--------------------hH
Q 040261          121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF--------------------VD  180 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------------------~~  180 (343)
                      ...++..+...+...|++++|...+++........+. ......++..+...+...|+                    ++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~  164 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELND-KVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQ  164 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-HHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhccc-ccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHH
Confidence            2456778889999999999999999988764310000 01113478888899999999                    99


Q ss_pred             HHHHHHHHhhhC----CCC-CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhCCChh
Q 040261          181 KAKELFLKMKDE----NIN-PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGV-QPN----VVTFNVIMNELCKNGKMD  250 (343)
Q Consensus       181 ~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~  250 (343)
                      +|...+++....    +.. ....++..+...+...|++++|...+++..+... .++    ..++..+...+...|+++
T Consensus       165 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  244 (406)
T 3sf4_A          165 AAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  244 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChH
Confidence            999998876442    111 1245678888999999999999999998875410 112    237788899999999999


Q ss_pred             HHHHHHHHHHHcC----CCC-CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCc-cHHHHHHHHHHHHhcCChH
Q 040261          251 EASRLLELMIQIG----VRP-DASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMR-DVFSYGILINGYCKNKEIE  320 (343)
Q Consensus       251 ~a~~~~~~~~~~~----~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~  320 (343)
                      +|...+++..+..    ..+ ...++..+...|...|++++|...+++..+.    +..+ ...++..+...|...|+++
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  324 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHD  324 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            9999999887642    111 1567788899999999999999999987653    1111 1557788889999999999


Q ss_pred             HHHHHHHHHHhC
Q 040261          321 GALSLYSEMLSK  332 (343)
Q Consensus       321 ~a~~~~~~~~~~  332 (343)
                      +|.+.+++....
T Consensus       325 ~A~~~~~~al~~  336 (406)
T 3sf4_A          325 QAMHFAEKHLEI  336 (406)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999987643

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.71  E-value=1.1e-15  Score=127.36  Aligned_cols=279  Identities=14%  Similarity=0.052  Sum_probs=212.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHHc----C-CCccH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL----YTYNILINCFCKMGRVSPGFVVLGRILRS----C-FTPDA   87 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~   87 (343)
                      ...+..+...+...|++++|+..|+++.+.+ +.+.    ..+..+...+...|++++|...+++..+.    + .....
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  126 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEA  126 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHH
Confidence            3445667888899999999999999998864 2233    47888899999999999999999988753    1 12245


Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcC-----CCCCHHHHHHHHHHHHhcCC-----------------hHHHHHHH
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFG-----CKPDVFTYTTLINGLCRTGH-----------------TIVALNLF  145 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~  145 (343)
                      .++..+...+...|++++|.+.+++..+..     ......++..+...|...|+                 +++|...+
T Consensus       127 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~  206 (411)
T 4a1s_A          127 KSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFY  206 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHH
Confidence            678888899999999999999999876541     11134477888899999999                 99999998


Q ss_pred             HHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-CC----hhhHHHHHHHHhccCcHHHHHHH
Q 040261          146 EEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENIN-PD----VVTYTSLIRGFCYANDWNEAKCL  220 (343)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~  220 (343)
                      ++.......... .+....++..+...+...|++++|...+++..+.... ++    ...+..+..++...|++++|...
T Consensus       207 ~~al~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  285 (411)
T 4a1s_A          207 QENLKLMRDLGD-RGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEH  285 (411)
T ss_dssp             HHHHHHHHHHTC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHHHcCC-HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            887553210000 1122357888889999999999999999987653110 11    23788889999999999999999


Q ss_pred             HHHHHHcCC--C---CCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC----C-CCCHHHHHHHHHHHhcCCchHHHHHH
Q 040261          221 FIEMMDQGV--Q---PNVVTFNVIMNELCKNGKMDEASRLLELMIQIG----V-RPDASVYNTLMDGFCLTGRVNRAKEL  290 (343)
Q Consensus       221 ~~~~~~~~~--~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~l~~~~~~~~~~~~a~~~  290 (343)
                      +++..+...  .   ....++..+...+...|++++|...+++..+..    . .....++..+...|...|++++|...
T Consensus       286 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  365 (411)
T 4a1s_A          286 YKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKY  365 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence            998876421  0   114677888999999999999999999887641    1 11245778889999999999999999


Q ss_pred             HHHHHhC
Q 040261          291 FVSMESN  297 (343)
Q Consensus       291 ~~~~~~~  297 (343)
                      +++..+.
T Consensus       366 ~~~al~~  372 (411)
T 4a1s_A          366 AEQHLQL  372 (411)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998774

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.70  E-value=1.1e-13  Score=110.35  Aligned_cols=219  Identities=10%  Similarity=0.019  Sum_probs=175.5

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHH-------hcCCh-------HHHHHHHHHHHccCCCCCccccCCcchHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLC-------RTGHT-------IVALNLFEEMANGNGEFGVVCKPDAITYSTI  169 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~-------~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  169 (343)
                      ++|..+|++.....+. +...|..++..+.       +.|++       ++|..+|++....-      .+.+...|..+
T Consensus        33 ~~a~~~~~~al~~~p~-~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~------~p~~~~~~~~~  105 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGH-HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTL------LKKNMLLYFAY  105 (308)
T ss_dssp             HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTT------TTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHh------CcccHHHHHHH
Confidence            6777788887775332 6667777776665       35776       89999999999841      13456689999


Q ss_pred             HHHHHhcCChHHHHHHHHHhhhCCCCCC-hh-hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-hC
Q 040261          170 TDGLCKEGFVDKAKELFLKMKDENINPD-VV-TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC-KN  246 (343)
Q Consensus       170 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~  246 (343)
                      +..+.+.|++++|..+|+++.+.  .|+ .. .|..++..+.+.|++++|..+|++..+.. +++...|........ ..
T Consensus       106 ~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~  182 (308)
T 2ond_A          106 ADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCS  182 (308)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTS
T ss_pred             HHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHc
Confidence            99999999999999999999885  343 33 79999999999999999999999999874 344555544433322 37


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC-CCc--cHHHHHHHHHHHHhcCChHHHH
Q 040261          247 GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG-CMR--DVFSYGILINGYCKNKEIEGAL  323 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~~~~~~a~  323 (343)
                      |++++|..+|+++++.. +.+...|..++..+.+.|++++|..+|++..... .+|  ....|..++....+.|+.++|.
T Consensus       183 ~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~  261 (308)
T 2ond_A          183 KDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASIL  261 (308)
T ss_dssp             CCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999998874 4578899999999999999999999999999863 344  4678888999999999999999


Q ss_pred             HHHHHHHhCC
Q 040261          324 SLYSEMLSKG  333 (343)
Q Consensus       324 ~~~~~~~~~~  333 (343)
                      .+++++.+..
T Consensus       262 ~~~~~a~~~~  271 (308)
T 2ond_A          262 KVEKRRFTAF  271 (308)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHc
Confidence            9999998663

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.69  E-value=2.2e-15  Score=121.74  Aligned_cols=273  Identities=12%  Similarity=0.064  Sum_probs=173.5

Q ss_pred             HHHHHhcCCcchHHHHHHHHHHcCCCcc---HHHHHHHHHHHhhcCcHHHHHHHHHHHHhc----CCC-CCHHHHHHHHH
Q 040261           59 INCFCKMGRVSPGFVVLGRILRSCFTPD---AVTFTSLIKGLCAESRIMEAAALFTKLRAF----GCK-PDVFTYTTLIN  130 (343)
Q Consensus        59 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~  130 (343)
                      ...+...|++++|...++++.+......   ...+..+...+...|++++|.+.+++..+.    +.. ....++..+..
T Consensus        12 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~   91 (338)
T 3ro2_A           12 GERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGN   91 (338)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHH
Confidence            3344444444444444444444321100   233444445555555555555555443321    101 11334556666


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC--------------------hHHHHHHHHHhh
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF--------------------VDKAKELFLKMK  190 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~  190 (343)
                      .+...|++++|...+++........+. ......++..+...+...|+                    +++|...+++..
T Consensus        92 ~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~  170 (338)
T 3ro2_A           92 TLKVLGNFDEAIVCCQRHLDISRELND-KVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENL  170 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHH
Confidence            677777777777777666543210000 01113367777788888888                    888888887764


Q ss_pred             hC----CC-CCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC----CCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHH
Q 040261          191 DE----NI-NPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG----VQP-NVVTFNVIMNELCKNGKMDEASRLLELMI  260 (343)
Q Consensus       191 ~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  260 (343)
                      ..    +. +.....+..+...+...|++++|...+++..+..    ..+ ...++..+...+...|++++|...+++..
T Consensus       171 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  250 (338)
T 3ro2_A          171 SLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTL  250 (338)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            32    11 1124567888889999999999999999887541    111 13377888899999999999999999887


Q ss_pred             HcCCC-CC----HHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CC-CccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          261 QIGVR-PD----ASVYNTLMDGFCLTGRVNRAKELFVSMESN----GC-MRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       261 ~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      +.... .+    ..++..+...+...|++++|...+++..+.    +. .....++..+...|...|++++|...+++..
T Consensus       251 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  330 (338)
T 3ro2_A          251 LLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  330 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            64111 11    557788889999999999999999987653    11 1124477788999999999999999999998


Q ss_pred             hC
Q 040261          331 SK  332 (343)
Q Consensus       331 ~~  332 (343)
                      ..
T Consensus       331 ~~  332 (338)
T 3ro2_A          331 EI  332 (338)
T ss_dssp             HC
T ss_pred             HH
Confidence            65

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.67  E-value=1.1e-14  Score=123.19  Aligned_cols=212  Identities=8%  Similarity=-0.090  Sum_probs=165.0

Q ss_pred             cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCh-HHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH
Q 040261          102 RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT-IVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD  180 (343)
Q Consensus       102 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  180 (343)
                      .++++++.+++...... .+...+..+...+...|++ ++|.+.|++..+..       +.+..++..+..+|...|+++
T Consensus        83 ~~~~al~~l~~~~~~~~-~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-------p~~~~a~~~lg~~~~~~g~~~  154 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSAQ-VEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-------PELVEAWNQLGEVYWKKGDVT  154 (474)
T ss_dssp             HHHHHHHHHHHHHTTCC-CCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHhccCc-hhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-------CCCHHHHHHHHHHHHHcCCHH
Confidence            35666677776665432 3677788888888888888 88888888888765       345678888888888888888


Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhcc---------CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-----
Q 040261          181 KAKELFLKMKDENINPDVVTYTSLIRGFCYA---------NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN-----  246 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----  246 (343)
                      +|...|++..+..  |+...+..+..++...         |++++|...+++..+.. +.+...|..+..++...     
T Consensus       155 ~A~~~~~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~  231 (474)
T 4abn_A          155 SAHTCFSGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTG  231 (474)
T ss_dssp             HHHHHHHHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhc
Confidence            8888888887764  5667788888888888         88888888888888764 44577788888888877     


Q ss_pred             ---CChhHHHHHHHHHHHcCCC---CCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChH
Q 040261          247 ---GKMDEASRLLELMIQIGVR---PDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIE  320 (343)
Q Consensus       247 ---~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  320 (343)
                         |++++|...|+++.+.. +   .+...+..+..+|...|++++|...|++..+.. +.+...+..+...+...|+++
T Consensus       232 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~  309 (474)
T 4abn_A          232 QNPKISQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLT  309 (474)
T ss_dssp             CCHHHHHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHH
Confidence               88888888888888864 3   477888888888888888888888888887753 335667777888888888888


Q ss_pred             HHHHHH
Q 040261          321 GALSLY  326 (343)
Q Consensus       321 ~a~~~~  326 (343)
                      +|++.+
T Consensus       310 eAi~~~  315 (474)
T 4abn_A          310 SLLESK  315 (474)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            887654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.67  E-value=1.3e-13  Score=110.06  Aligned_cols=218  Identities=10%  Similarity=0.049  Sum_probs=96.9

Q ss_pred             hHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh-------cCCc-------chHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           34 DTVLSLFKRLNSIGLFPDLYTYNILINCFCK-------MGRV-------SPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        34 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~-------~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      ++|..+|++..... +.+...|..++..+..       .|++       ++|..+|++.++.-.+.+...|..++..+.+
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            45556666655532 3345555555555432       3444       4555555555542111133445555555555


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH-hcC
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVF-TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC-KEG  177 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~  177 (343)
                      .|++++|.++|++..+..+. +.. .|..++..+.+.|++++|..+|++..+..       +.+...|........ ..|
T Consensus       112 ~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-------p~~~~~~~~~a~~~~~~~~  183 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-------RTRHHVYVTAALMEYYCSK  183 (308)
T ss_dssp             TTCHHHHHHHHHHHHTSSSS-CTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-------TCCTHHHHHHHHHHHHTSC
T ss_pred             cCCHHHHHHHHHHHHhcccc-CccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-------CCCHHHHHHHHHHHHHHcC
Confidence            55555555555555543211 121 44555555555555555555555555432       122222322222211 134


Q ss_pred             ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC-CCC--CHHHHHHHHHHHHhCCChhHHHH
Q 040261          178 FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG-VQP--NVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      ++++|..+|++..+.. +.+...|..++..+.+.|++++|..+|++..+.. .+|  ....|..++....+.|+.+.|..
T Consensus       184 ~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~  262 (308)
T 2ond_A          184 DKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILK  262 (308)
T ss_dssp             CHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            4555555544443321 1233444444444444444444444444444431 122  12334444444444444444444


Q ss_pred             HHHHHHH
Q 040261          255 LLELMIQ  261 (343)
Q Consensus       255 ~~~~~~~  261 (343)
                      +++++.+
T Consensus       263 ~~~~a~~  269 (308)
T 2ond_A          263 VEKRRFT  269 (308)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444444

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.67  E-value=3.6e-15  Score=120.45  Aligned_cols=279  Identities=13%  Similarity=0.053  Sum_probs=210.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHc----CCC-ccH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD----LYTYNILINCFCKMGRVSPGFVVLGRILRS----CFT-PDA   87 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~   87 (343)
                      ...+......+...|++++|...|+++.+.. +.+    ...+..+...+...|++++|.+.+++....    +.. ...
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   83 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   83 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHH
Confidence            4456677888999999999999999998764 223    357888899999999999999999987653    111 235


Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCC-CCC----HHHHHHHHHHHHhcCC--------------------hHHHH
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFGC-KPD----VFTYTTLINGLCRTGH--------------------TIVAL  142 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~--------------------~~~a~  142 (343)
                      .++..+...+...|++++|...+++..+... .++    ..++..+...+...|+                    +++|.
T Consensus        84 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~  163 (338)
T 3ro2_A           84 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAV  163 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHH
Confidence            6778888999999999999999998765311 112    3367788889999999                    99999


Q ss_pred             HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CC-CCChhhHHHHHHHHhccCcHHHH
Q 040261          143 NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NI-NPDVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a  217 (343)
                      ..+++......... ..+....++..+...+...|++++|...+++..+.    +. .....++..+...+...|++++|
T Consensus       164 ~~~~~a~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  242 (338)
T 3ro2_A          164 DLYEENLSLVTALG-DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  242 (338)
T ss_dssp             HHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHhcC-CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHH
Confidence            99888754311000 01122457788889999999999999999887643    11 11133778888999999999999


Q ss_pred             HHHHHHHHHcCC-CCC----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcC----CC-CCHHHHHHHHHHHhcCCchHHH
Q 040261          218 KCLFIEMMDQGV-QPN----VVTFNVIMNELCKNGKMDEASRLLELMIQIG----VR-PDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       218 ~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~-~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      ...+++..+... ..+    ..++..+...+...|++++|...++++.+..    .+ ....++..+...|...|++++|
T Consensus       243 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  322 (338)
T 3ro2_A          243 SEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQA  322 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            999998875411 111    4577788899999999999999999887641    11 1244777889999999999999


Q ss_pred             HHHHHHHHhC
Q 040261          288 KELFVSMESN  297 (343)
Q Consensus       288 ~~~~~~~~~~  297 (343)
                      ...+++..+.
T Consensus       323 ~~~~~~a~~~  332 (338)
T 3ro2_A          323 MHFAEKHLEI  332 (338)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHHH
Confidence            9999998874

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.67  E-value=2.6e-14  Score=105.09  Aligned_cols=168  Identities=14%  Similarity=0.062  Sum_probs=132.1

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++.+|..+...+.+.|++++|+..|++..+.. |-+..++..+..++.+.|++++|...+......... +...+..+.
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~   80 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT-SAEAYYILG   80 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch-hHHHHHHHH
Confidence            367788888888888888888888888887765 446778888888888888888888888888776433 566677777


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      ..+...++++.+.+.+.+....... +...+..+..++.+.|++++|++.+++..+..       +.+..++..+..+|.
T Consensus        81 ~~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-------p~~~~~~~~lg~~~~  152 (184)
T 3vtx_A           81 SANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-------PGFIRAYQSIGLAYE  152 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-------chhhhHHHHHHHHHH
Confidence            7788888888888888888776433 66777788888888888888888888888764       445677888888888


Q ss_pred             hcCChHHHHHHHHHhhhC
Q 040261          175 KEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~  192 (343)
                      +.|++++|+..|++..+.
T Consensus       153 ~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          153 GKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             HTTCHHHHHHHHHHHHHT
T ss_pred             HCCCHHHHHHHHHHHHhC
Confidence            888888888888887764

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.66  E-value=2.6e-13  Score=123.06  Aligned_cols=253  Identities=13%  Similarity=0.191  Sum_probs=177.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      +...+...|.+++|..+|++..     -.....+.++.   ..+++++|.++.++.      -+..+|..+..++...|+
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~ 1120 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGM 1120 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCC
Confidence            4566667777777777777642     11222233322   556777777777654      246677888888888888


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  182 (343)
                      +++|++.|.+.      -|...|..++.++.+.|++++|.+++....+..        +++...+.++.+|.+.+++++.
T Consensus      1121 ~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--------~e~~Idt~LafaYAKl~rleel 1186 (1630)
T 1xi4_A         1121 VKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--------RESYVETELIFALAKTNRLAEL 1186 (1630)
T ss_pred             HHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--------ccccccHHHHHHHHhhcCHHHH
Confidence            88888888653      267777888888888888888888888777643        3333444578888888887754


Q ss_pred             HHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          183 KELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       183 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ....    .   .++...|..+...|...|++++|..+|...         ..|..+...+.+.|++++|.+.+++.   
T Consensus      1187 e~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA--- 1247 (1630)
T 1xi4_A         1187 EEFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA--- 1247 (1630)
T ss_pred             HHHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh---
Confidence            4332    1   245566777888888888888888888874         36778888888888888888888776   


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                         .+..+|..+..+|...|++..|......+     ..++..+..++..|.+.|.+++|+.+++..+
T Consensus      1248 ---~n~~aWkev~~acve~~Ef~LA~~cgl~I-----iv~~deLeeli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1248 ---NSTRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             ---CCHHHHHHHHHHHhhhhHHHHHHHHHHhh-----hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence               24567777777777777777777665543     2355566677888888888888888887766

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.64  E-value=2.4e-13  Score=111.84  Aligned_cols=314  Identities=11%  Similarity=-0.021  Sum_probs=214.3

Q ss_pred             CChhhHHHHHHHH--HhcCChhHHHHHHHHhHhC--CCCCC--HHHHHHHHHH--HHhcCCcchHH---------HHHHH
Q 040261           15 PPVCSFNILFGCL--AKNKHYDTVLSLFKRLNSI--GLFPD--LYTYNILINC--FCKMGRVSPGF---------VVLGR   77 (343)
Q Consensus        15 ~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~--~~~~~--~~~~~~l~~~--~~~~~~~~~a~---------~~~~~   77 (343)
                      |+..+=+.+-..|  ...+++++|.++++++...  .+..|  ...|..++..  ..-.+.+..+.         +.++.
T Consensus         8 ~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l~~   87 (378)
T 3q15_A            8 PSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLET   87 (378)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHHHH
Confidence            4455555555555  7899999999999987542  22223  3344444432  22224444444         67777


Q ss_pred             HHHcCCCccH--H--HHHHHHHHHhhcCcHHHHHHHHHHHHhcCC-CCC----HHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261           78 ILRSCFTPDA--V--TFTSLIKGLCAESRIMEAAALFTKLRAFGC-KPD----VFTYTTLINGLCRTGHTIVALNLFEEM  148 (343)
Q Consensus        78 ~~~~~~~~~~--~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~  148 (343)
                      +.....+.+.  .  .+......+...|++++|+..+++..+... .++    ..++..+...|...|+++.|...+++.
T Consensus        88 i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~a  167 (378)
T 3q15_A           88 IETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQA  167 (378)
T ss_dssp             HHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence            6543211111  1  223344556788999999999999876421 122    446778899999999999999999988


Q ss_pred             HccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCC-CChhhHHHHHHHHhccCcHHHHHHHHHH
Q 040261          149 ANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NIN-PDVVTYTSLIRGFCYANDWNEAKCLFIE  223 (343)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~  223 (343)
                      ................++..+..+|...|++++|.+.+++..+.    +.+ ....++..+..+|...|++++|...+++
T Consensus       168 l~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~  247 (378)
T 3q15_A          168 LDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQK  247 (378)
T ss_dssp             HHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            76431100000112457788899999999999999999887652    111 1235678888999999999999999999


Q ss_pred             HHHc----CCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC----CCCCHHHHHHHHHHHhcCCc---hHHHHHHHH
Q 040261          224 MMDQ----GVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG----VRPDASVYNTLMDGFCLTGR---VNRAKELFV  292 (343)
Q Consensus       224 ~~~~----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~  292 (343)
                      ..+.    +.+....++..+..++.+.|++++|...+++..+..    -+.....+..+...+...++   +.+|...++
T Consensus       248 al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~  327 (378)
T 3q15_A          248 AAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFE  327 (378)
T ss_dssp             HHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            8872    223336778889999999999999999999998752    12224456667777888888   777777776


Q ss_pred             HHHhCCCCc-cHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          293 SMESNGCMR-DVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       293 ~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      +.   +..+ ....+..+...|...|++++|...|++...
T Consensus       328 ~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          328 KK---NLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hC---CChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            53   2223 344667788999999999999999998864

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.64  E-value=1.5e-13  Score=100.92  Aligned_cols=165  Identities=13%  Similarity=0.060  Sum_probs=84.7

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhH
Q 040261          122 VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTY  201 (343)
Q Consensus       122 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  201 (343)
                      ...|..+...|...|++++|++.|++..+..       |.+..++..+..++.+.|++++|...+....... +.+...+
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~   76 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-------PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAY   76 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHH
Confidence            4445555555555555555555555555543       2334455555555555555555555555554432 1234444


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT  281 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  281 (343)
                      ..+...+...++++.+...+....+.. +.+...+..+..++.+.|++++|+..|++..+.. +.+..++..+..+|.+.
T Consensus        77 ~~~~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~  154 (184)
T 3vtx_A           77 YILGSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGK  154 (184)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHC
Confidence            444455555555555555555555442 2234445555555555555555555555555543 33444555555555555


Q ss_pred             CchHHHHHHHHHHHh
Q 040261          282 GRVNRAKELFVSMES  296 (343)
Q Consensus       282 ~~~~~a~~~~~~~~~  296 (343)
                      |++++|.+.|++..+
T Consensus       155 g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          155 GLRDEAVKYFKKALE  169 (184)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh
Confidence            555555555555554

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.64  E-value=2.6e-14  Score=120.88  Aligned_cols=213  Identities=8%  Similarity=-0.027  Sum_probs=172.1

Q ss_pred             hhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCc-chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHH
Q 040261           33 YDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRV-SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFT  111 (343)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  111 (343)
                      +++++..++...... +.+...+..+..++...|++ ++|.+.|++.++... .+...|..+..+|...|++++|.+.|+
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~  161 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEP-ELVEAWNQLGEVYWKKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            556666777665533 45788899999999999999 999999999998753 368899999999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhc---------CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc------
Q 040261          112 KLRAFGCKPDVFTYTTLINGLCRT---------GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE------  176 (343)
Q Consensus       112 ~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~------  176 (343)
                      +..+..  |+...+..+..++...         |++++|...+++..+..       +.+...|..+..+|...      
T Consensus       162 ~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~lg~~~~~~~~~~~~  232 (474)
T 4abn_A          162 GALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-------VLDGRSWYILGNAYLSLYFNTGQ  232 (474)
T ss_dssp             HHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHHHhhcc
Confidence            999874  6678899999999999         99999999999999875       45677888888888888      


Q ss_pred             --CChHHHHHHHHHhhhCCCC--CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHH
Q 040261          177 --GFVDKAKELFLKMKDENIN--PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEA  252 (343)
Q Consensus       177 --~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  252 (343)
                        |++++|+..|++..+....  .+...|..+..++...|++++|...+++..+.. +.+...+..+..++...|++++|
T Consensus       233 ~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eA  311 (474)
T 4abn_A          233 NPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSL  311 (474)
T ss_dssp             CHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence              8888888888888775310  367778888888888888888888888887763 33456677777777777777777


Q ss_pred             HHHHH
Q 040261          253 SRLLE  257 (343)
Q Consensus       253 ~~~~~  257 (343)
                      ...+.
T Consensus       312 i~~~~  316 (474)
T 4abn_A          312 LESKG  316 (474)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            66543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.63  E-value=9.1e-15  Score=116.84  Aligned_cols=246  Identities=13%  Similarity=0.039  Sum_probs=163.0

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc-------CCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCC-Cc
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLRAF-------GCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEF-GV  157 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~  157 (343)
                      +..++..+...+...|++++|..+++++.+.       ........+..+...|...|++++|...+++........ +.
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3455666777777777777777777776652       122234566677777888888888888887776541000 00


Q ss_pred             cccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC------C-CCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc---
Q 040261          158 VCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE------N-INPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ---  227 (343)
Q Consensus       158 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  227 (343)
                      ..+....++..+...+...|++++|...++++.+.      + .+.....+..+...+...|++++|..+++++.+.   
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  185 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQT  185 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            01334567888999999999999999999987653      1 1224566888899999999999999999998765   


Q ss_pred             ---CCCC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC-------CCCC-------HHHHHHHHHHHhcCCchHHHHH
Q 040261          228 ---GVQP-NVVTFNVIMNELCKNGKMDEASRLLELMIQIG-------VRPD-------ASVYNTLMDGFCLTGRVNRAKE  289 (343)
Q Consensus       228 ---~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------~~~~-------~~~~~~l~~~~~~~~~~~~a~~  289 (343)
                         +..| ...++..+...+...|++++|...++++.+..       ..+.       ...+..+...+...+.+.++..
T Consensus       186 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  265 (311)
T 3nf1_A          186 KLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGG  265 (311)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC-
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHH
Confidence               2123 24577888999999999999999999988631       1111       1222333334445566667777


Q ss_pred             HHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          290 LFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .++...... +....++..+...|.+.|++++|.+.+++.++.
T Consensus       266 ~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  307 (311)
T 3nf1_A          266 WYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMRS  307 (311)
T ss_dssp             --------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            777766542 345678889999999999999999999998754

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.62  E-value=1.6e-15  Score=121.25  Aligned_cols=177  Identities=15%  Similarity=0.045  Sum_probs=137.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhC-------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc------
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSI-------GLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS------   81 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------   81 (343)
                      ....++..+...+...|++++|..+++++.+.       ..+....++..+...+...|++++|...+++....      
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            45678899999999999999999999998763       22334567888999999999999999999998864      


Q ss_pred             CC-CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc------CCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCC
Q 040261           82 CF-TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF------GCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNG  153 (343)
Q Consensus        82 ~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  153 (343)
                      +- +....++..+...+...|++++|.+.+++..+.      +..| ....+..+...+...|++++|...++++.....
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            21 224667888999999999999999999998765      2222 345678889999999999999999999877510


Q ss_pred             CC-CccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhh
Q 040261          154 EF-GVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       154 ~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  191 (343)
                      .. +...+....++..+..++...|++++|...++++.+
T Consensus       185 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          185 TKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            00 000122345678888899999999999999988765

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.62  E-value=3.2e-12  Score=116.18  Aligned_cols=266  Identities=14%  Similarity=0.134  Sum_probs=188.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .++.+|..+..++.+.|++++|++.|.+.      .|...|..++.++.+.|++++|.+++....+..  ++......++
T Consensus      1103 n~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~La 1174 (1630)
T 1xi4_A         1103 NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELI 1174 (1630)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHH
Confidence            45667778888888888888888887553      356677777888888888888888887766653  2322333477


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      .+|++.+++++...+.    +   .++...+..+...|...|++++|..+|...               ..|..+..++.
T Consensus      1175 faYAKl~rleele~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------------~ny~rLA~tLv 1232 (1630)
T 1xi4_A         1175 FALAKTNRLAELEEFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------------SNFGRLASTLV 1232 (1630)
T ss_pred             HHHHhhcCHHHHHHHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------------hHHHHHHHHHH
Confidence            7777777776533332    1   245566667778888888888888887773               25777888888


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      +.|++++|.+.+++..      +..+|..+..+|...|++..|......     +..+...+..++..|.+.|.+++|+.
T Consensus      1233 kLge~q~AIEaarKA~------n~~aWkev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~ 1301 (1630)
T 1xi4_A         1233 HLGEYQAAVDGARKAN------STRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELIT 1301 (1630)
T ss_pred             HhCCHHHHHHHHHHhC------CHHHHHHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHH
Confidence            8888888888887662      457788888888888888877776553     23456667788999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhcC--CchHHHHHHHHHHHhCCCCc------cHHHHHHHHHHHHhcCChHHHHH
Q 040261          255 LLELMIQIGVRPDASVYNTLMDGFCLT--GRVNRAKELFVSMESNGCMR------DVFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                      +++...... +-....|+.+...|++.  ++..++.+.|..-..  ++|      +...|.-++..|.+.|+++.|..
T Consensus      1302 LlE~aL~Le-raH~gmftELaiLyaKy~peklmEhlk~f~~rin--i~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1302 MLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVN--IPKVLRAAEQAHLWAELVFLYDKYEEYDNAII 1376 (1630)
T ss_pred             HHHHHhccC-hhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc--cchHhHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence            998887765 45566777777777664  345555555543222  222      45678889999999999999884

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.62  E-value=9.6e-13  Score=110.57  Aligned_cols=220  Identities=9%  Similarity=-0.013  Sum_probs=158.0

Q ss_pred             HHHHHHHHHhhcCcH----HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC---ChHHHHHHHHHHHccCCCCCccccC
Q 040261           89 TFTSLIKGLCAESRI----MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG---HTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      ....+...|...+.+    +.+..++......    ++..+..+...|...|   +.++|+++|++..+.+       ++
T Consensus       143 a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~----~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-------~~  211 (452)
T 3e4b_A          143 AGLAQVLLYRTQGTYDQHLDDVERICKAALNT----TDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-------TV  211 (452)
T ss_dssp             HHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTT----CTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-------CS
T ss_pred             HHHHHHHHHHcCCCcccCHHHHHHHHHHHHcC----CHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-------CH
Confidence            344445555555533    3333344333322    3337788888888899   8999999999998876       44


Q ss_pred             CcchHHHHHHHHHhc----CChHHHHHHHHHhhhCCCCCChhhHHHHHHH-H--hccCcHHHHHHHHHHHHHcCCCCCHH
Q 040261          162 DAITYSTITDGLCKE----GFVDKAKELFLKMKDENINPDVVTYTSLIRG-F--CYANDWNEAKCLFIEMMDQGVQPNVV  234 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~  234 (343)
                      +...+..+..+|...    +++++|..+|++.. .|   +...+..+... +  ...+++++|...+++..+.|   +..
T Consensus       212 ~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~  284 (452)
T 3e4b_A          212 TAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPR  284 (452)
T ss_dssp             CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHH
T ss_pred             HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHH
Confidence            555556777777655    78999999999987 33   56666666666 4  56889999999999998876   566


Q ss_pred             HHHHHHHHHHhCC-----ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchHHHHHHHHHHHhCCCCccHHH
Q 040261          235 TFNVIMNELCKNG-----KMDEASRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVNRAKELFVSMESNGCMRDVFS  305 (343)
Q Consensus       235 ~~~~l~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  305 (343)
                      .+..+...|. .|     ++++|..+|++.. .|   +......|...|..    ..++++|...|++..+.|   +...
T Consensus       285 A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A  356 (452)
T 3e4b_A          285 AELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GR---EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSA  356 (452)
T ss_dssp             HHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TT---CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTH
T ss_pred             HHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHH
Confidence            7777777776 45     8999999999887 43   56677777777766    348999999999998876   3445


Q ss_pred             HHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 040261          306 YGILINGYCK----NKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       306 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~  334 (343)
                      ...|...|..    .+++++|..+|+...+.|.
T Consensus       357 ~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          357 DFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             HHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC
Confidence            5566666654    4588899999888877663

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.60  E-value=4.8e-12  Score=108.86  Aligned_cols=218  Identities=10%  Similarity=0.054  Sum_probs=167.7

Q ss_pred             hHHHHHHHHHHcCCCccHHHHHHHHHHHhh-------cCcHH-------HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 040261           70 PGFVVLGRILRSCFTPDAVTFTSLIKGLCA-------ESRIM-------EAAALFTKLRAFGCKPDVFTYTTLINGLCRT  135 (343)
Q Consensus        70 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  135 (343)
                      .+..+|++.+... +.+...|..++..+.+       .|+++       +|..++++..+.-.+.+...|..++..+.+.
T Consensus       256 ~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~  334 (530)
T 2ooe_A          256 RVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR  334 (530)
T ss_dssp             HHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhc
Confidence            3445566665543 2356677777777765       68876       8999999998621233688899999999999


Q ss_pred             CChHHHHHHHHHHHccCCCCCccccCCc-chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHH-HhccCc
Q 040261          136 GHTIVALNLFEEMANGNGEFGVVCKPDA-ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG-FCYAND  213 (343)
Q Consensus       136 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~  213 (343)
                      |++++|..+|+++.+..       +.+. ..|..++..+.+.|+.++|..+|++..+.. +.+...|...... +...|+
T Consensus       335 g~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~  406 (530)
T 2ooe_A          335 MKYEKVHSIYNRLLAIE-------DIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKD  406 (530)
T ss_dssp             TCHHHHHHHHHHHHHSS-------SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHhCcc-------ccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCC
Confidence            99999999999999854       2232 478888999999999999999999998753 2233333332222 335899


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC-CC--CHHHHHHHHHHHhcCCchHHHHHH
Q 040261          214 WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV-RP--DASVYNTLMDGFCLTGRVNRAKEL  290 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~  290 (343)
                      .++|..+|+...+.. +-+...|..++..+.+.|+.++|..+|+++...+. .|  ....|...+......|+.+.+..+
T Consensus       407 ~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~  485 (530)
T 2ooe_A          407 KSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKV  485 (530)
T ss_dssp             HHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999999998873 44578899999999999999999999999998642 23  255888888888899999999999


Q ss_pred             HHHHHhC
Q 040261          291 FVSMESN  297 (343)
Q Consensus       291 ~~~~~~~  297 (343)
                      .+++.+.
T Consensus       486 ~~r~~~~  492 (530)
T 2ooe_A          486 EKRRFTA  492 (530)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988774

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.59  E-value=1.4e-13  Score=115.69  Aligned_cols=286  Identities=14%  Similarity=0.029  Sum_probs=166.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCc---chHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRV---SPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      +...+.+.|++++|.++|++..+.|   +...+..+...+...|+.   ++|..+|++..+.    ++..+..+...+..
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~~   81 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLAA   81 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC--------------------------------CHHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHHh
Confidence            4455556666666666666655544   222333344444445555   5666666655532    33334444443333


Q ss_pred             cC-----cHHHHHHHHHHHHhcCCCC--------------------------------CHHHHHHHHHHHHhcCChHHHH
Q 040261          100 ES-----RIMEAAALFTKLRAFGCKP--------------------------------DVFTYTTLINGLCRTGHTIVAL  142 (343)
Q Consensus       100 ~~-----~~~~a~~~~~~~~~~~~~~--------------------------------~~~~~~~l~~~~~~~~~~~~a~  142 (343)
                      .+     ++++|++.|++..+.|...                                +......+...|...+.++++.
T Consensus        82 ~~~~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~  161 (452)
T 3e4b_A           82 KPGATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHL  161 (452)
T ss_dssp             C--CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGH
T ss_pred             CCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCH
Confidence            32     5556666666655543221                                1222333444444444333333


Q ss_pred             HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC---ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc----CcHH
Q 040261          143 NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG---FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA----NDWN  215 (343)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~  215 (343)
                      .....+....      ...++..+..+..+|...|   +.++|+..|++..+.|. ++...+..+...|...    ++++
T Consensus       162 ~~a~~~~~~a------~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~  234 (452)
T 3e4b_A          162 DDVERICKAA------LNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEK  234 (452)
T ss_dssp             HHHHHHHHHH------TTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHH
T ss_pred             HHHHHHHHHH------HcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHH
Confidence            2222221111      1223448888888898899   89999999999988873 4555556677777655    7899


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHH-H--HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCC-----chHHH
Q 040261          216 EAKCLFIEMMDQGVQPNVVTFNVIMNE-L--CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTG-----RVNRA  287 (343)
Q Consensus       216 ~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~a  287 (343)
                      +|...|+... .|   +...+..+... +  ...+++++|..+|++..+.|   +...+..|...|. .|     ++++|
T Consensus       235 ~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A  306 (452)
T 3e4b_A          235 TAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAA  306 (452)
T ss_dssp             HHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHH
T ss_pred             HHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHH
Confidence            9999999987 33   45566666666 4  56889999999999999876   5667777777776 44     99999


Q ss_pred             HHHHHHHHhCCCCccHHHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 040261          288 KELFVSMESNGCMRDVFSYGILINGYCK----NKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~  334 (343)
                      ...|++.. .   -++.....|...|..    ..++++|..+|++..+.|.
T Consensus       307 ~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  353 (452)
T 3e4b_A          307 EAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ  353 (452)
T ss_dssp             HHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh
Confidence            99999887 4   366777777777766    3489999999999887764

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.59  E-value=8.1e-14  Score=122.56  Aligned_cols=169  Identities=12%  Similarity=0.040  Sum_probs=150.8

Q ss_pred             CCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHH
Q 040261           13 SPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTS   92 (343)
Q Consensus        13 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   92 (343)
                      .|.++.+|+.+...+.+.|++++|++.|++..+.. +-+..+|..+..++.+.|++++|++.|++.++.... +...|..
T Consensus         5 ~P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~-~~~a~~n   82 (723)
T 4gyw_A            5 CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSN   82 (723)
T ss_dssp             -CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHH
Confidence            35678899999999999999999999999998865 446789999999999999999999999999987533 6889999


Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHH
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDG  172 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  172 (343)
                      +..++.+.|++++|++.|++..+.... +..++..+..+|...|++++|++.|++..+..       +.+...+..+..+
T Consensus        83 Lg~~l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-------P~~~~a~~~L~~~  154 (723)
T 4gyw_A           83 MGNTLKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALKLK-------PDFPDAYCNLAHC  154 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------SCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCChHHHhhhhhH
Confidence            999999999999999999999988544 68899999999999999999999999999875       4567889999999


Q ss_pred             HHhcCChHHHHHHHHHhhh
Q 040261          173 LCKEGFVDKAKELFLKMKD  191 (343)
Q Consensus       173 ~~~~~~~~~a~~~~~~~~~  191 (343)
                      +...|++++|.+.++++.+
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            9999999999999887654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.59  E-value=3e-13  Score=111.46  Aligned_cols=235  Identities=9%  Similarity=-0.067  Sum_probs=176.7

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHHc----CCCc-cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC-C-----CHHHHH
Q 040261           58 LINCFCKMGRVSPGFVVLGRILRS----CFTP-DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK-P-----DVFTYT  126 (343)
Q Consensus        58 l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-----~~~~~~  126 (343)
                      ....+...|++++|...+++..+.    +-.+ ...++..+...+...|++++|...+++..+.-.. +     ...++.
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            566778899999999999999864    1111 3467888999999999999999999987754111 1     234678


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CC-CCChhhH
Q 040261          127 TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NI-NPDVVTY  201 (343)
Q Consensus       127 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~  201 (343)
                      .+..+|...|++++|...+++........+. .+....++..+..+|...|++++|...+++..+.    +. +....++
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  267 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQ-PQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAY  267 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCC-hHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHH
Confidence            8889999999999999999998764310000 0111247888999999999999999999988662    22 3346778


Q ss_pred             HHHHHHHhccCcHHHHHHHHHHHHHc----CCCCCHHHHHHHHHHHHhCCC---hhHHHHHHHHHHHcCCCC-CHHHHHH
Q 040261          202 TSLIRGFCYANDWNEAKCLFIEMMDQ----GVQPNVVTFNVIMNELCKNGK---MDEASRLLELMIQIGVRP-DASVYNT  273 (343)
Q Consensus       202 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~-~~~~~~~  273 (343)
                      ..+..++...|++++|...+++..+.    +.+.....+..+...+...|+   .++|..++++.   +..| ....+..
T Consensus       268 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~  344 (383)
T 3ulq_A          268 FLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAID  344 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHH
Confidence            88999999999999999999988754    212223345677888888998   66677776665   2222 3456778


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHh
Q 040261          274 LMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      +...|...|++++|...+++..+
T Consensus       345 la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          345 VAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHH
Confidence            89999999999999999998765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.58  E-value=2.3e-12  Score=105.81  Aligned_cols=276  Identities=11%  Similarity=-0.002  Sum_probs=196.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHH----HHHHHHHHHHhcCCcchHHHHHHHHHHcCCC-cc----HHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLY----TYNILINCFCKMGRVSPGFVVLGRILRSCFT-PD----AVT   89 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~   89 (343)
                      ........+...|++++|...+++........+..    ++..+...+...|+++.|...+++....... .+    ..+
T Consensus        16 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   95 (373)
T 1hz4_A           16 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   95 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            44556667778999999999999987654222222    4666777888999999999999988753211 11    233


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhc----CCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAF----GCK--P-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      +..+...+...|++++|.+.+++..+.    +..  | ....+..+...+...|++++|...+++........+.  +..
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~--~~~  173 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQP--QQQ  173 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCG--GGG
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCc--HHH
Confidence            566778888999999999999987653    221  2 2345667888899999999999999998876532211  112


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCC-hhhHH-----HHHHHHhccCcHHHHHHHHHHHHHcCCCCC---H
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPD-VVTYT-----SLIRGFCYANDWNEAKCLFIEMMDQGVQPN---V  233 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~  233 (343)
                      ..++..+...+...|++++|...+++.......++ ...+.     ..+..+...|++++|...++........+.   .
T Consensus       174 ~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~  253 (373)
T 1hz4_A          174 LQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQ  253 (373)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhH
Confidence            34677788899999999999999998764311111 11121     233447789999999999988775432111   2


Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPDA-SVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      ..+..+...+...|++++|...++.+...    +..++. ..+..+..++...|+.++|...+++...
T Consensus       254 ~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          254 GQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            34567788899999999999999988653    212222 3666777888999999999999988765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.56  E-value=4.3e-12  Score=104.17  Aligned_cols=277  Identities=12%  Similarity=0.010  Sum_probs=194.3

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHH----HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC-CC----HHHH
Q 040261           55 YNILINCFCKMGRVSPGFVVLGRILRSCFTPDAV----TFTSLIKGLCAESRIMEAAALFTKLRAFGCK-PD----VFTY  125 (343)
Q Consensus        55 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~  125 (343)
                      .......+...|++++|...+++........+..    .++.+...+...|++++|.+.+++....... .+    ..++
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   96 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSL   96 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            3444556778899999999999988764322222    4566777888899999999999987653111 12    2235


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC-CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCC----CChhh
Q 040261          126 TTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP-DAITYSTITDGLCKEGFVDKAKELFLKMKDENIN----PDVVT  200 (343)
Q Consensus       126 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~  200 (343)
                      ..+...+...|++++|...+++........+....| ....+..+...+...|++++|...+++.......    ....+
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            667788999999999999999887643110000001 2345667788899999999999999987653211    12356


Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC--HHHHH----HHHHHHHhCCChhHHHHHHHHHHHcCCCC---CHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN--VVTFN----VIMNELCKNGKMDEASRLLELMIQIGVRP---DASVY  271 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~  271 (343)
                      +..+...+...|++++|...+++..+....++  .....    ..+..+...|++++|...+++.......+   ....+
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence            77788889999999999999999876421221  11111    23344778999999999999887643211   13356


Q ss_pred             HHHHHHHhcCCchHHHHHHHHHHHhC----CCCccH-HHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          272 NTLMDGFCLTGRVNRAKELFVSMESN----GCMRDV-FSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       272 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ..+...+...|++++|...+++....    |..++. ..+..+..++...|++++|...+++...
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            77888999999999999999887542    222222 3666777889999999999999988764

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.55  E-value=1.2e-12  Score=95.93  Aligned_cols=167  Identities=17%  Similarity=0.048  Sum_probs=141.4

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ....+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~   84 (186)
T 3as5_A            7 RQVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGL   84 (186)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            35678888999999999999999999987754 4567788889999999999999999999998874 336778888889


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+...|++++|.+.++++.+... .+...+..+...+...|++++|...++++....       +.+..++..+...+..
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~la~~~~~  156 (186)
T 3as5_A           85 TYVQVQKYDLAVPLLIKVAEANP-INFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-------PNEGKVHRAIAFSYEQ  156 (186)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHhcCc-HhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-------ccchHHHHHHHHHHHH
Confidence            99999999999999999888743 367788888999999999999999999988864       4456788888899999


Q ss_pred             cCChHHHHHHHHHhhhC
Q 040261          176 EGFVDKAKELFLKMKDE  192 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~  192 (343)
                      .|++++|...+++..+.
T Consensus       157 ~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          157 MGRHEEALPHFKKANEL  173 (186)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHc
Confidence            99999999999887654

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.55  E-value=1.8e-12  Score=98.69  Aligned_cols=208  Identities=9%  Similarity=-0.025  Sum_probs=161.0

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      +.++..+......+.+.|++++|+..|++..+...+++...+..+..++...|++++|.+.+++..+..+. +...+..+
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l   82 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIGK   82 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHHH
Confidence            45778999999999999999999999999988763377888888999999999999999999999987533 67888999


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCH-------HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC--Ccc
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDV-------FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP--DAI  164 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~~~  164 (343)
                      ..++...|++++|++.+++..+..+. +.       ..|..+...+...|++++|...+++..+..       +.  +..
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~  154 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAVPG-NATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVT-------SKKWKTD  154 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSS-------CHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcC-------CCcccHH
Confidence            99999999999999999999987533 44       457788889999999999999999999864       33  456


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040261          165 TYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVI  239 (343)
Q Consensus       165 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  239 (343)
                      .+..+..++...|     ...++++...+ ..+...|....  ....+.+++|...+++..+.. +-+..+...+
T Consensus       155 ~~~~l~~~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~-p~~~~~~~~l  220 (228)
T 4i17_A          155 ALYSLGVLFYNNG-----ADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLS-PNRTEIKQMQ  220 (228)
T ss_dssp             HHHHHHHHHHHHH-----HHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHHHHH-----HHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcC-CCCHHHHHHH
Confidence            7777777776544     34455554443 22344444433  344577899999999999873 2234444433

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.54  E-value=2.2e-12  Score=94.61  Aligned_cols=167  Identities=17%  Similarity=0.061  Sum_probs=146.4

Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      ...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+.. +.+...+..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            4567778888999999999999999987754 3467888999999999999999999999998874 4567888889999


Q ss_pred             HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHH
Q 040261          243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGA  322 (343)
Q Consensus       243 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  322 (343)
                      +...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHH
Confidence            999999999999999999875 5678889999999999999999999999988764 44678899999999999999999


Q ss_pred             HHHHHHHHhCC
Q 040261          323 LSLYSEMLSKG  333 (343)
Q Consensus       323 ~~~~~~~~~~~  333 (343)
                      ...++++....
T Consensus       164 ~~~~~~~~~~~  174 (186)
T 3as5_A          164 LPHFKKANELD  174 (186)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHcC
Confidence            99999988653

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.53  E-value=9.9e-13  Score=115.73  Aligned_cols=169  Identities=14%  Similarity=0.044  Sum_probs=149.8

Q ss_pred             ccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          159 CKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV  238 (343)
Q Consensus       159 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  238 (343)
                      .|.+..+++.+..++.+.|++++|++.|++..+.. +-+..++..+..++.+.|++++|...+++.++.. +-+...|..
T Consensus         5 ~P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~n   82 (723)
T 4gyw_A            5 CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSN   82 (723)
T ss_dssp             -CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHH
Confidence            34567899999999999999999999999998864 3357889999999999999999999999999874 345789999


Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                      +..++...|++++|++.|+++++.. +-+...+..+..+|...|++++|...|++..+.. +.+...+..+..++...|+
T Consensus        83 Lg~~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~  160 (723)
T 4gyw_A           83 MGNTLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCD  160 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhccc
Confidence            9999999999999999999999985 5578899999999999999999999999998864 3467889999999999999


Q ss_pred             hHHHHHHHHHHHh
Q 040261          319 IEGALSLYSEMLS  331 (343)
Q Consensus       319 ~~~a~~~~~~~~~  331 (343)
                      +++|.+.++++++
T Consensus       161 ~~~A~~~~~kal~  173 (723)
T 4gyw_A          161 WTDYDERMKKLVS  173 (723)
T ss_dssp             CTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999888764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.50  E-value=9.7e-12  Score=94.58  Aligned_cols=208  Identities=13%  Similarity=0.014  Sum_probs=160.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      .|+..+......+...|++++|...|++..+...+++...+..+..++...|++++|++.+++..+.... +...+..+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHHHH
Confidence            4567888899999999999999999999998865467778878999999999999999999999987544 667888999


Q ss_pred             HHHHhcCChHHHHHHHHHHHccCCCCCccccCCc-------chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCC---hh
Q 040261          130 NGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA-------ITYSTITDGLCKEGFVDKAKELFLKMKDENINPD---VV  199 (343)
Q Consensus       130 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~  199 (343)
                      .++...|++++|...+++..+..       +.+.       ..|..+...+...|++++|+..|++..+..  |+   ..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~  154 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAV-------PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVT--SKKWKTD  154 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSS--CHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC-------CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcC--CCcccHH
Confidence            99999999999999999999865       3334       457888889999999999999999998863  43   56


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD  276 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  276 (343)
                      .+..+..++...|     ...++.+...+ ..+...|....  ....+.+++|...+++..+.. +-+..+...+..
T Consensus       155 ~~~~l~~~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~-p~~~~~~~~l~~  222 (228)
T 4i17_A          155 ALYSLGVLFYNNG-----ADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLS-PNRTEIKQMQDQ  222 (228)
T ss_dssp             HHHHHHHHHHHHH-----HHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-----HHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcC-CCCHHHHHHHHH
Confidence            6777777775544     34455555443 33344444433  334577899999999999875 444555544433

>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=99.46  E-value=1.5e-12  Score=102.30  Aligned_cols=200  Identities=13%  Similarity=0.032  Sum_probs=146.3

Q ss_pred             HhcCChHHHHHHHHHHHccCCCCC-ccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC------C-CCCChhhHHHH
Q 040261          133 CRTGHTIVALNLFEEMANGNGEFG-VVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE------N-INPDVVTYTSL  204 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~~~~l  204 (343)
                      ...|++++|...+++..+...... ...+....++..+...+...|++++|...++++.+.      + .+....++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            345666666666665544210000 001334567888899999999999999999887653      1 12345678888


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHc------CC-CCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc------C-CCCCHHH
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQ------GV-QPNVVTFNVIMNELCKNGKMDEASRLLELMIQI------G-VRPDASV  270 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~  270 (343)
                      ..++...|++++|...++++.+.      .. +.....+..+...+...|++++|...++++.+.      + .+....+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            99999999999999999988764      11 223567788889999999999999999988775      1 1223567


Q ss_pred             HHHHHHHHhcCCchHHHHHHHHHHHhC------------------------------------------------CCCcc
Q 040261          271 YNTLMDGFCLTGRVNRAKELFVSMESN------------------------------------------------GCMRD  302 (343)
Q Consensus       271 ~~~l~~~~~~~~~~~~a~~~~~~~~~~------------------------------------------------~~~~~  302 (343)
                      +..+...|...|++++|...+++..+.                                                ..+..
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTV  251 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHH
Confidence            888899999999999999999887653                                                11223


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          303 VFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       303 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ..++..+...|...|++++|...+++.++.
T Consensus       252 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          252 NTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            457788899999999999999999998753

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.46  E-value=1.2e-11  Score=101.68  Aligned_cols=230  Identities=10%  Similarity=0.021  Sum_probs=146.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCC-CC----CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC-----Cc-cHHHH
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGL-FP----DLYTYNILINCFCKMGRVSPGFVVLGRILRSCF-----TP-DAVTF   90 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~-~~~~~   90 (343)
                      .....+...|++++|+..|++..+... .+    ...++..+..++...|+++.|...+++..+...     .+ ...++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            345566778888888888888765311 12    234677788888888888888888888765311     11 24567


Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHhc----CCC-CCHHHHHHHHHHHHhcCChHHHHHHHHHHHc-----cCCCCCcccc
Q 040261           91 TSLIKGLCAESRIMEAAALFTKLRAF----GCK-PDVFTYTTLINGLCRTGHTIVALNLFEEMAN-----GNGEFGVVCK  160 (343)
Q Consensus        91 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  160 (343)
                      +.+...+...|++++|.+.+++..+.    +.. ....++..+..+|...|++++|...+++...     ..       +
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~-------~  258 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVP-------D  258 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCG-------G
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC-------h
Confidence            77788888888888888888876653    111 1134566777788888888888888887766     32       2


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC----CCCChhhHHHHHHHHhccCc---HHHHHHHHHHHHHcCCCCC-
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDEN----INPDVVTYTSLIRGFCYAND---WNEAKCLFIEMMDQGVQPN-  232 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-  232 (343)
                      ....++..+..++.+.|++++|...+++..+..    .+.....+..+...+...++   +.+|...++.   .+..|+ 
T Consensus       259 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~  335 (378)
T 3q15_A          259 LLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYI  335 (378)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHH
Confidence            235667777777888888888888887765431    11122334555555556666   5555555544   221222 


Q ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          233 VVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       233 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      ...+..+...|...|++++|...+++..+
T Consensus       336 ~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          336 EACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            23445566666677777777777666654

>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=99.45  E-value=1.8e-12  Score=101.89  Aligned_cols=234  Identities=13%  Similarity=0.021  Sum_probs=157.6

Q ss_pred             HhcCChhHHHHHHHHhHhC-------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc------CC-CccHHHHHHH
Q 040261           28 AKNKHYDTVLSLFKRLNSI-------GLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS------CF-TPDAVTFTSL   93 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l   93 (343)
                      ...|++++|+..+++..+.       ..+....++..+...+...|++++|...++++.+.      +- +....++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            3467777777777766541       22234567888999999999999999999998864      21 2245678889


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhc------CC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCC-CccccCCcch
Q 040261           94 IKGLCAESRIMEAAALFTKLRAF------GC-KPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEF-GVVCKPDAIT  165 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~  165 (343)
                      ...+...|++++|.+.+++..+.      .. +....++..+...+...|++++|...++++....... +...+....+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            99999999999999999998765      11 2235678889999999999999999999987751000 0001223567


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhC-------CCCCC-hhhHHHHHHHHhccCc------HHHHHHHHHHHHHcCCCC
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDE-------NINPD-VVTYTSLIRGFCYAND------WNEAKCLFIEMMDQGVQP  231 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~-~~~~~~l~~~~~~~~~------~~~a~~~~~~~~~~~~~~  231 (343)
                      +..+..++...|++++|...+++..+.       ...+. ...+..+...+...+.      +..+...++.... ..+.
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-DSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-CCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-CCHH
Confidence            888999999999999999999987653       11222 2233333333332222      2223222222111 1122


Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ...++..+...+...|++++|..++++..+.
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3567888999999999999999999988764

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.44  E-value=3e-10  Score=88.40  Aligned_cols=249  Identities=10%  Similarity=0.034  Sum_probs=171.1

Q ss_pred             HHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           24 FGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        24 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      +.-..-.|++..++.-...+..   ......-.-+.+++...|++...         ....|....+..+...+ ..+  
T Consensus        20 ikn~fy~G~yq~~i~e~~~~~~---~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~~-~~~--   84 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQEIEKFSK---VTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQFL-DTK--   84 (310)
T ss_dssp             HHHHHTTTCHHHHTHHHHTSSC---CCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHHH-TTT--
T ss_pred             HHHHHHhhHHHHHHHHHHhcCc---cchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHHh-ccc--
Confidence            3444567999988884333321   22233444466888888887752         12234444444444443 322  


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                        |+..+++..+.+ .++..++..+..++...|++++|++++.+....+.     ...+...+...+.++.+.|+.+.|.
T Consensus        85 --a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~-----~~~~lea~~l~vqi~L~~~r~d~A~  156 (310)
T 3mv2_B           85 --NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDE-----AEGTTELLLLAIEVALLNNNVSTAS  156 (310)
T ss_dssp             --CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSC-----STTHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             --HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCC-----CcCcHHHHHHHHHHHHHCCCHHHHH
Confidence              778888887765 44666667888999999999999999999876541     0135677888899999999999999


Q ss_pred             HHHHHhhhCCCCC-----ChhhHHHHHHHH--hc--cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHH
Q 040261          184 ELFLKMKDENINP-----DVVTYTSLIRGF--CY--ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASR  254 (343)
Q Consensus       184 ~~~~~~~~~~~~~-----~~~~~~~l~~~~--~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  254 (343)
                      +.+++|.+.  .|     +..+...++.++  ..  .+++.+|..+|+++.+.  .|+..+...++.++.+.|++++|..
T Consensus       157 k~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~  232 (310)
T 3mv2_B          157 TIFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQG  232 (310)
T ss_dssp             HHHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHH
Confidence            999999875  35     355556666553  22  34899999999998765  4553444445558889999999999


Q ss_pred             HHHHHHHcC---------CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH
Q 040261          255 LLELMIQIG---------VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV  303 (343)
Q Consensus       255 ~~~~~~~~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  303 (343)
                      .++.+.+..         -+.++.++..++......|+  +|.++++++.+..  |+.
T Consensus       233 ~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~--P~h  286 (310)
T 3mv2_B          233 IVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLD--HEH  286 (310)
T ss_dssp             HHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTT--CCC
T ss_pred             HHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhC--CCC
Confidence            999766531         13466677566666666776  8899999999863  543

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.39  E-value=2.9e-09  Score=92.89  Aligned_cols=205  Identities=11%  Similarity=0.024  Sum_probs=151.0

Q ss_pred             CHHHHHHHHHHHHhcCChHHHH-HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC------
Q 040261          121 DVFTYTTLINGLCRTGHTIVAL-NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN------  193 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------  193 (343)
                      ....|...+..+...|+.++|. +++++....       +|.+...|...+....+.|+++.|..+|+++....      
T Consensus       342 ~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-------~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~  414 (679)
T 4e6h_A          342 APEIWFNMANYQGEKNTDSTVITKYLKLGQQC-------IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAA  414 (679)
T ss_dssp             CHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhh
Confidence            4455556666667788888886 999988875       35556667778888889999999999999876531      


Q ss_pred             ---CCCC------------hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-CChhHHHHHHH
Q 040261          194 ---INPD------------VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN-GKMDEASRLLE  257 (343)
Q Consensus       194 ---~~~~------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~  257 (343)
                         ..|+            ...|...+....+.|+.+.|..+|..+.+....+....|...+..-.+. ++.+.|.++|+
T Consensus       415 ~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife  494 (679)
T 4e6h_A          415 LMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLE  494 (679)
T ss_dssp             HHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHH
T ss_pred             hhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence               0121            2357777787788889999999999998761122344444433333344 45899999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCC--ccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          258 LMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM--RDVFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       258 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      ..++. .+-+...+...+......|+.+.|..+|++.......  .....|...+..-.+.|+.+.+.++.+++...-
T Consensus       495 ~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          495 LGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             HHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            98887 3556777778888888889999999999999886422  134678888888888999999999999998763

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.38  E-value=6.4e-11  Score=92.03  Aligned_cols=174  Identities=9%  Similarity=-0.077  Sum_probs=136.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--ccHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD---LYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PDAV   88 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~   88 (343)
                      |.++..+..+...+.+.|++++|+..|+++.+.. +.+   ...+..+..++.+.|++++|...|+++++..+.  ....
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~   90 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQ   90 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHH
Confidence            4678889999999999999999999999998754 223   568888999999999999999999999986432  2245


Q ss_pred             HHHHHHHHHhh--------cCcHHHHHHHHHHHHhcCCCCCHHHH-----------------HHHHHHHHhcCChHHHHH
Q 040261           89 TFTSLIKGLCA--------ESRIMEAAALFTKLRAFGCKPDVFTY-----------------TTLINGLCRTGHTIVALN  143 (343)
Q Consensus        89 ~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~-----------------~~l~~~~~~~~~~~~a~~  143 (343)
                      .+..+..++..        .|++++|+..|+++.+..+. +....                 ..+...|.+.|++++|..
T Consensus        91 a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  169 (261)
T 3qky_A           91 AEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPN-HELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAV  169 (261)
T ss_dssp             HHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTT-CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcC-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            67778888888        99999999999999987433 22233                 456788999999999999


Q ss_pred             HHHHHHccCCCCCccccCCcchHHHHHHHHHhc----------CChHHHHHHHHHhhhCC
Q 040261          144 LFEEMANGNGEFGVVCKPDAITYSTITDGLCKE----------GFVDKAKELFLKMKDEN  193 (343)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~  193 (343)
                      .|+++....+.    .+.....+..+..+|...          |++++|...++++.+..
T Consensus       170 ~~~~~l~~~p~----~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~  225 (261)
T 3qky_A          170 TYEAVFDAYPD----TPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF  225 (261)
T ss_dssp             HHHHHHHHCTT----STTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCC----CchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC
Confidence            99999886521    011234677777777766          78888888888887753

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.36  E-value=2.2e-11  Score=107.54  Aligned_cols=174  Identities=8%  Similarity=-0.107  Sum_probs=136.1

Q ss_pred             HhcCChhHHHHHHHHhH--------hCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           28 AKNKHYDTVLSLFKRLN--------SIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        28 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      ...|++++|++.+++..        +.. +.+...+..+..++...|++++|.+.++++.+... .+...|..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVG-WRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc-chHHHHHHHHHHHHH
Confidence            67889999999999887        432 44567788888889999999999999999888643 367788888888899


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCCh
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFV  179 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  179 (343)
                      .|++++|++.|++..+.... +...+..+..++.+.|++++ ...|+++.+.+       +.+...+..+..++.+.|++
T Consensus       480 ~g~~~~A~~~~~~al~l~P~-~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-------P~~~~a~~~lg~~~~~~g~~  550 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPG-ELAPKLALAATAELAGNTDE-HKFYQTVWSTN-------DGVISAAFGLARARSAEGDR  550 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCH
T ss_pred             cCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-------CchHHHHHHHHHHHHHcCCH
Confidence            99999999999998887543 56778888888999999999 99999988865       45667888888999999999


Q ss_pred             HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCc
Q 040261          180 DKAKELFLKMKDENINPDVVTYTSLIRGFCYAND  213 (343)
Q Consensus       180 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  213 (343)
                      ++|...|++..+.+ +.+...+..+..++...++
T Consensus       551 ~~A~~~~~~al~l~-P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          551 VGAVRTLDEVPPTS-RHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHHHHHTSCTTS-TTHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHhhcccC-cccHHHHHHHHHHHHccCC
Confidence            99999998887754 1235667777777766554

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.35  E-value=1.4e-10  Score=79.93  Aligned_cols=129  Identities=18%  Similarity=0.270  Sum_probs=82.3

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL  280 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  280 (343)
                      +..+...+...|++++|..+++.+.+.. +.+...+..+...+...|++++|..+++++.+.+ +.+...+..+...+..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            4455556666666666666666666543 3345555666666666677777777776666654 3455566666667777


Q ss_pred             CCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          281 TGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       281 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .|++++|.+.++++.+.. +.+...+..+...+...|++++|...++++...
T Consensus        82 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            777777777777666543 234556666777777777777777777776654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.34  E-value=5.3e-10  Score=87.01  Aligned_cols=245  Identities=10%  Similarity=-0.015  Sum_probs=166.1

Q ss_pred             HHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHH
Q 040261           61 CFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIV  140 (343)
Q Consensus        61 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  140 (343)
                      -..-.|++..++.-...+   ........-.-+.+++...|++...         ....|....+..+...+ ..+    
T Consensus        22 n~fy~G~yq~~i~e~~~~---~~~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~~-~~~----   84 (310)
T 3mv2_B           22 QNYYTGNFVQCLQEIEKF---SKVTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQFL-DTK----   84 (310)
T ss_dssp             HHHTTTCHHHHTHHHHTS---SCCCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHHH-TTT----
T ss_pred             HHHHhhHHHHHHHHHHhc---CccchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHHh-ccc----
Confidence            344568888777633322   1121223333455777777776532         12234444444444333 322    


Q ss_pred             HHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC-CCChhhHHHHHHHHhccCcHHHHHH
Q 040261          141 ALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENI-NPDVVTYTSLIRGFCYANDWNEAKC  219 (343)
Q Consensus       141 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~  219 (343)
                      +...+++....+       +++..++..+..++...|++++|++++.+....+. .-+...+..++..+.+.|+.+.|.+
T Consensus        85 a~~~l~~l~~~~-------~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k  157 (310)
T 3mv2_B           85 NIEELENLLKDK-------QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTAST  157 (310)
T ss_dssp             CCHHHHHTTTTS-------CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhcC-------CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            677788776653       34455666888999999999999999999876653 2367788889999999999999999


Q ss_pred             HHHHHHHcCCCC-----CHHHHHHHHHHH--HhCC--ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHH
Q 040261          220 LFIEMMDQGVQP-----NVVTFNVIMNEL--CKNG--KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKEL  290 (343)
Q Consensus       220 ~~~~~~~~~~~~-----~~~~~~~l~~~~--~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  290 (343)
                      .++.|.+.  .|     +..+...++.++  ...|  ++.+|..+|+++.+.  .|+..+...++.++.+.|++++|.+.
T Consensus       158 ~l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~  233 (310)
T 3mv2_B          158 IFDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGI  233 (310)
T ss_dssp             HHHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHH
Confidence            99999886  56     355566666553  3334  899999999998765  45533334445589999999999999


Q ss_pred             HHHHHhCC---------CCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCC
Q 040261          291 FVSMESNG---------CMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPT  337 (343)
Q Consensus       291 ~~~~~~~~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  337 (343)
                      ++.+.+..         -+.++.+...++......|+  +|.++++++...  .|+
T Consensus       234 L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~--~P~  285 (310)
T 3mv2_B          234 VELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL--DHE  285 (310)
T ss_dssp             HHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT--TCC
T ss_pred             HHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh--CCC
Confidence            99776531         13466777566666666776  889999999865  454

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.33  E-value=7e-09  Score=81.49  Aligned_cols=237  Identities=7%  Similarity=-0.008  Sum_probs=171.9

Q ss_pred             HHhcCCc-chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC--cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH----Hh
Q 040261           62 FCKMGRV-SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES--RIMEAAALFTKLRAFGCKPDVFTYTTLINGL----CR  134 (343)
Q Consensus        62 ~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~  134 (343)
                      ..+.|.. ++|++.++.++..++. +...|+.--..+...+  +++++++.++.+...+++ +..+|+.-...+    ..
T Consensus        42 ~~~~~e~s~~aL~~t~~~L~~nP~-~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk-~y~aW~~R~~iL~~~~~~  119 (306)
T 3dra_A           42 LMKAEEYSERALHITELGINELAS-HYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEK-NYQIWNYRQLIIGQIMEL  119 (306)
T ss_dssp             HHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHHHHHCcH-HHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHHHHHHh
Confidence            3344444 5788888888876533 5667777777777777  889999999888887655 455565544444    44


Q ss_pred             c---CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH--HHHHHHHHhhhCCCCCChhhHHHHHHHHh
Q 040261          135 T---GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD--KAKELFLKMKDENINPDVVTYTSLIRGFC  209 (343)
Q Consensus       135 ~---~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  209 (343)
                      .   +++++++.+++++.+.+       +.+..+|+.-.-++.+.|.++  ++++.++++.+.+. -+...|+.-.....
T Consensus       120 l~~~~~~~~EL~~~~~~l~~~-------pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~  191 (306)
T 3dra_A          120 NNNDFDPYREFDILEAMLSSD-------PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLF  191 (306)
T ss_dssp             TTTCCCTHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            4   78999999999999876       567788888888888888888  99999999988764 37777877776666


Q ss_pred             ccCc------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhH-HHHHHHHHHHcC--CCCCHHHHHHHHHHHhc
Q 040261          210 YAND------WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDE-ASRLLELMIQIG--VRPDASVYNTLMDGFCL  280 (343)
Q Consensus       210 ~~~~------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~  280 (343)
                      +.+.      ++++++.++.+.... +-|...|+.+...+.+.|+... +..+..++.+.+  -+.+...+..+...|.+
T Consensus       192 ~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~  270 (306)
T 3dra_A          192 SKKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQ  270 (306)
T ss_dssp             SSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHH
T ss_pred             hccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHc
Confidence            6666      888888888888874 5577888888888888777444 555666655432  13467788888888888


Q ss_pred             CCchHHHHHHHHHHHhCCCCccHHHHHHH
Q 040261          281 TGRVNRAKELFVSMESNGCMRDVFSYGIL  309 (343)
Q Consensus       281 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  309 (343)
                      .|+.++|.++++.+.+.--+.....|+..
T Consensus       271 ~~~~~~A~~~~~~l~~~~Dpir~~yW~~~  299 (306)
T 3dra_A          271 QKKYNESRTVYDLLKSKYNPIRSNFWDYQ  299 (306)
T ss_dssp             TTCHHHHHHHHHHHHHTTCGGGHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhccChHHHHHHHHH
Confidence            89999999999988763113334444433

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.33  E-value=1.6e-08  Score=88.32  Aligned_cols=164  Identities=10%  Similarity=0.005  Sum_probs=116.6

Q ss_pred             HHHHHHHHhcCChHHHH-HHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC---------CCCC----
Q 040261          167 STITDGLCKEGFVDKAK-ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG---------VQPN----  232 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------~~~~----  232 (343)
                      ...+..+...|+.++|. .+|++.... .+.+...|...+....+.|+++.|..+|+.+.+..         ..|+    
T Consensus       347 ~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~  425 (679)
T 4e6h_A          347 FNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESA  425 (679)
T ss_dssp             HHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhh
Confidence            33344445667778886 888888764 34456667777888888899999999999887641         0132    


Q ss_pred             --------HHHHHHHHHHHHhCCChhHHHHHHHHHHHc-CCCCCHHHHHHHHHHHhcC-CchHHHHHHHHHHHhCCCCcc
Q 040261          233 --------VVTFNVIMNELCKNGKMDEASRLLELMIQI-GVRPDASVYNTLMDGFCLT-GRVNRAKELFVSMESNGCMRD  302 (343)
Q Consensus       233 --------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~  302 (343)
                              ..+|...+....+.|+.+.|..+|.++.+. + ......|...+..-.+. ++.+.|..+|+...+. .+.+
T Consensus       426 ~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~-~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~  503 (679)
T 4e6h_A          426 INQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKK-LVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATD  503 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGG-GSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTC
T ss_pred             hhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCc
Confidence                    235777777777888999999999999876 2 22333444333333333 4589999999988876 3456


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 040261          303 VFSYGILINGYCKNKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       303 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  333 (343)
                      ...|...++.....|+.+.|..+|++.+...
T Consensus       504 ~~~w~~y~~fe~~~~~~~~AR~lferal~~~  534 (679)
T 4e6h_A          504 GEYINKYLDFLIYVNEESQVKSLFESSIDKI  534 (679)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHTTTS
T ss_pred             hHHHHHHHHHHHhCCCHHHHHHHHHHHHHhc
Confidence            6777788888888899999999999988664

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.32  E-value=3.2e-10  Score=88.09  Aligned_cols=186  Identities=11%  Similarity=0.003  Sum_probs=105.5

Q ss_pred             cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCC----HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC
Q 040261           86 DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPD----VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        86 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      +...+..+...+.+.|++++|+..|+++.+.  .|+    ...+..+..++.+.|++++|...|+++....+.    .+.
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~----~~~   87 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTY--GRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQI----DPR   87 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGG--CSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----CTT
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCC----Cch
Confidence            3445555556666666666666666666654  343    345556666666666666666666666664311    011


Q ss_pred             CcchHHHHHHHHHh--------cCChHHHHHHHHHhhhCCCCCC-hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC
Q 040261          162 DAITYSTITDGLCK--------EGFVDKAKELFLKMKDENINPD-VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN  232 (343)
Q Consensus       162 ~~~~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  232 (343)
                      ...++..+..++..        .|++++|+..|+++.+..  |+ ......+..              +..+...    .
T Consensus        88 ~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~--------------~~~~~~~----~  147 (261)
T 3qky_A           88 VPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQK--------------IRELRAK----L  147 (261)
T ss_dssp             HHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHH--------------HHHHHHH----H
T ss_pred             hHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHH--------------HHHHHHH----H
Confidence            12344455555555        666666666666655532  22 111111100              0000000    0


Q ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhcC----------CchHHHHHHHHHHHhC
Q 040261          233 VVTFNVIMNELCKNGKMDEASRLLELMIQIGVR--PDASVYNTLMDGFCLT----------GRVNRAKELFVSMESN  297 (343)
Q Consensus       233 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~  297 (343)
                      ...+..+...+.+.|++++|...|+++++....  .....+..+..+|...          |++++|...++++.+.
T Consensus       148 ~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          148 ARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            011345677888889999999999888876311  1345667777777755          8888999999888875

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.32  E-value=2.1e-10  Score=79.03  Aligned_cols=132  Identities=14%  Similarity=0.149  Sum_probs=115.2

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      .+|..+...+...|++++|..+++++.+.+ +.+...+..+...+...|++++|...++++.+.+ +.+...+..+...+
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~   79 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHH
Confidence            467889999999999999999999998765 4567788889999999999999999999998875 33677888899999


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ...|++++|.+.++++.+.... +...+..+...+...|++++|...++++....
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  133 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD  133 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHS
T ss_pred             HHhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHccHHHHHHHHHHHHccC
Confidence            9999999999999999887533 67788889999999999999999999987753

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.32  E-value=1.6e-10  Score=86.40  Aligned_cols=190  Identities=9%  Similarity=0.017  Sum_probs=97.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      ++..+......+.+.|++++|+..|++..+..  |+ ...|...     .....              ..........+.
T Consensus         3 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~-----~~~~~--------------~~~~~~~~~~lg   61 (208)
T 3urz_A            3 SVDEMLQKVSAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYWT-----NVDKN--------------SEISSKLATELA   61 (208)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHHH-----HSCTT--------------SHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHh-----hhcch--------------hhhhHHHHHHHH
Confidence            44556666777788889999999988887743  33 3333330     00000              001112223355


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      .++.+.|++++|+..|++..+..+. +...+..+..++...|++++|...|+++.+..       |.+..++..+..+|.
T Consensus        62 ~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------P~~~~a~~~lg~~~~  133 (208)
T 3urz_A           62 LAYKKNRNYDKAYLFYKELLQKAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQLE-------ADNLAANIFLGNYYY  133 (208)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-------CCCHHHHHHHHHHHH
Confidence            5566666666666666666655332 45556666666666666666666666666543       334455555555554


Q ss_pred             hcCC--hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH
Q 040261          175 KEGF--VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV  238 (343)
Q Consensus       175 ~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  238 (343)
                      ..|+  .+.+...++....  ..|....+.....++...|++++|...|++..+.  .|+......
T Consensus       134 ~~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~  195 (208)
T 3urz_A          134 LTAEQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKT  195 (208)
T ss_dssp             HHHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHH
Confidence            4432  2333444433322  1122222333344445556666666666666553  455443333

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.31  E-value=2e-10  Score=85.86  Aligned_cols=139  Identities=10%  Similarity=0.013  Sum_probs=105.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHH
Q 040261          126 TTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLI  205 (343)
Q Consensus       126 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  205 (343)
                      ..+..++.+.|++++|...+++..+..       |.+...+..+..++...|++++|...|++..+.. +.+..++..+.
T Consensus        58 ~~lg~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg  129 (208)
T 3urz_A           58 TELALAYKKNRNYDKAYLFYKELLQKA-------PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLG  129 (208)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHH
Confidence            348889999999999999999999875       4567899999999999999999999999998865 34678888888


Q ss_pred             HHHhccCc--HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          206 RGFCYAND--WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMD  276 (343)
Q Consensus       206 ~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  276 (343)
                      .++...|.  ...+...++....  ..|....+.....++...|++++|...|+++++.  .|+......+.+
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~l~~  198 (208)
T 3urz_A          130 NYYYLTAEQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKTLDK  198 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHHHHH
Confidence            88766654  4455556655532  2333334445666777889999999999999885  577665555443

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.31  E-value=3.5e-09  Score=83.21  Aligned_cols=235  Identities=6%  Similarity=-0.031  Sum_probs=182.9

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC--CcchHHHHHHHHHHcCCCccHHHHHHHHHHH----hhc--
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG--RVSPGFVVLGRILRSCFTPDAVTFTSLIKGL----CAE--  100 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~--  100 (343)
                      +....++|+.+++.++..+ +-+..+|+.--.++...|  +++++++.++.++..+++ +..+|+.....+    ...  
T Consensus        45 ~~e~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk-~y~aW~~R~~iL~~~~~~l~~  122 (306)
T 3dra_A           45 AEEYSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEK-NYQIWNYRQLIIGQIMELNNN  122 (306)
T ss_dssp             TTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHHHHHHhccc
Confidence            3444579999999999865 345667888888888888  999999999999987644 666777665555    444  


Q ss_pred             -CcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH--HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261          101 -SRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI--VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus       101 -~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                       +++++++++++++.+...+ +..+|..-.-++.+.|.++  ++++.++++.+.+       +.+..+|+.-.....+.+
T Consensus       123 ~~~~~~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-------~~N~sAW~~R~~ll~~l~  194 (306)
T 3dra_A          123 DFDPYREFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-------LKNNSAWSHRFFLLFSKK  194 (306)
T ss_dssp             CCCTHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHSSG
T ss_pred             cCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHhcc
Confidence             7899999999999998665 8888988888888889888  9999999999876       567788888777777777


Q ss_pred             C------hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHH-HHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhCCC
Q 040261          178 F------VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWN-EAKCLFIEMMDQG--VQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       178 ~------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~  248 (343)
                      .      ++++++.++++.... +-|...|+.....+.+.|+.. ++..+...+.+.+  -+.+...+..++.++.+.|+
T Consensus       195 ~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~  273 (306)
T 3dra_A          195 HLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKK  273 (306)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTC
T ss_pred             ccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCC
Confidence            6      899999999988765 347888888887777777643 3555666555432  13467888899999999999


Q ss_pred             hhHHHHHHHHHHH-cCCCCCHHHHHHHH
Q 040261          249 MDEASRLLELMIQ-IGVRPDASVYNTLM  275 (343)
Q Consensus       249 ~~~a~~~~~~~~~-~~~~~~~~~~~~l~  275 (343)
                      .++|.++++.+.+ .+ +.....|+...
T Consensus       274 ~~~A~~~~~~l~~~~D-pir~~yW~~~~  300 (306)
T 3dra_A          274 YNESRTVYDLLKSKYN-PIRSNFWDYQI  300 (306)
T ss_dssp             HHHHHHHHHHHHHTTC-GGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC-hHHHHHHHHHH
Confidence            9999999999987 33 44555555443

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.31  E-value=4.2e-10  Score=88.90  Aligned_cols=201  Identities=12%  Similarity=0.003  Sum_probs=146.4

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhC----CCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC---Cc--cH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSI----GLFPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSCF---TP--DA   87 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~   87 (343)
                      ..|...+..+...|++++|.+.|++..+.    |-+++ ..+|+.+..+|.+.|++++|+..+++.++...   .+  -.
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            46888888999999999999999987653    31222 46889999999999999999999999876421   11  14


Q ss_pred             HHHHHHHHHHhhc-CcHHHHHHHHHHHHhcCCCC-C----HHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC
Q 040261           88 VTFTSLIKGLCAE-SRIMEAAALFTKLRAFGCKP-D----VFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP  161 (343)
Q Consensus        88 ~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  161 (343)
                      .+++.+...|... |++++|+..|++..+..... +    ..++..+...+.+.|++++|...+++.....+.     .+
T Consensus       118 ~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~-----~~  192 (292)
T 1qqe_A          118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMG-----NR  192 (292)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSS-----CT
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhc-----CC
Confidence            5788889999996 99999999999987642110 1    346788899999999999999999999986521     11


Q ss_pred             Cc-----chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCCh------hhHHHHHHHHh--ccCcHHHHHHHHHHHH
Q 040261          162 DA-----ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDV------VTYTSLIRGFC--YANDWNEAKCLFIEMM  225 (343)
Q Consensus       162 ~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~--~~~~~~~a~~~~~~~~  225 (343)
                      ..     ..+..+..++...|++++|...+++..+..  |+.      ..+..++.++.  ..+++++|...++.+.
T Consensus       193 ~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          193 LSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSED--PNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             TTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             cccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence            11     156777888999999999999999987642  321      12333444443  3456777776665543

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.30  E-value=7.1e-11  Score=104.33  Aligned_cols=173  Identities=11%  Similarity=-0.016  Sum_probs=145.8

Q ss_pred             HhcCChHHHHHHHHHHH--------ccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHH
Q 040261          133 CRTGHTIVALNLFEEMA--------NGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSL  204 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  204 (343)
                      ...|++++|++.+++..        +..       +.+...+..+..++...|++++|+..++++.+.+ +.+...|..+
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-------p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~l  473 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-------SESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYR  473 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-------TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-------ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHH
Confidence            78899999999999998        432       4567788999999999999999999999998764 3367889999


Q ss_pred             HHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch
Q 040261          205 IRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV  284 (343)
Q Consensus       205 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  284 (343)
                      ..++...|++++|...|++..+.. +-+...+..+..++.+.|++++ ...|+++.+.+ +.+...+..+..++.+.|++
T Consensus       474 g~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~  550 (681)
T 2pzi_A          474 AVAELLTGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDR  550 (681)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCH
Confidence            999999999999999999999874 4457788899999999999999 99999999876 56788999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCcc-HHHHHHHHHHHHhcCC
Q 040261          285 NRAKELFVSMESNGCMRD-VFSYGILINGYCKNKE  318 (343)
Q Consensus       285 ~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~  318 (343)
                      ++|...|++..+..  |+ ...+..+..++...++
T Consensus       551 ~~A~~~~~~al~l~--P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          551 VGAVRTLDEVPPTS--RHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHHHHHTSCTTS--TTHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHhhcccC--cccHHHHHHHHHHHHccCC
Confidence            99999999998763  54 5677777777766554

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.30  E-value=1.5e-09  Score=81.41  Aligned_cols=175  Identities=14%  Similarity=-0.046  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC----ChHHHHHHHH
Q 040261           71 GFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG----HTIVALNLFE  146 (343)
Q Consensus        71 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~  146 (343)
                      |+++|++..+.|   ++..+..+...+...+++++|++.|++..+.|   +...+..+...|.. +    ++++|.++|+
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAE   77 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHH
Confidence            444444444432   34444444555555555555555555554442   33444444444444 3    4555555555


Q ss_pred             HHHccCCCCCccccCCcchHHHHHHHHHh----cCChHHHHHHHHHhhhCCCC-CChhhHHHHHHHHhc----cCcHHHH
Q 040261          147 EMANGNGEFGVVCKPDAITYSTITDGLCK----EGFVDKAKELFLKMKDENIN-PDVVTYTSLIRGFCY----ANDWNEA  217 (343)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a  217 (343)
                      +..+.+         +..++..+...|..    .+++++|+.+|++..+.+.. .....+..+...|..    .+++++|
T Consensus        78 ~A~~~g---------~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A  148 (212)
T 3rjv_A           78 KAVEAG---------SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKA  148 (212)
T ss_dssp             HHHHTT---------CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHH
T ss_pred             HHHHCC---------CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            554332         33444444444444    45555555555555544310 013444444444444    4455555


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhC-C-----ChhHHHHHHHHHHHcC
Q 040261          218 KCLFIEMMDQGVQPNVVTFNVIMNELCKN-G-----KMDEASRLLELMIQIG  263 (343)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~~~~~~  263 (343)
                      ...+++..+.  ..+...+..|...|..- |     ++++|..+|+...+.|
T Consensus       149 ~~~~~~A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          149 SEYFKGSSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHHHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            5555555443  11223334444444321 1     4555555555555544

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.29  E-value=1e-09  Score=82.27  Aligned_cols=177  Identities=16%  Similarity=0.062  Sum_probs=146.5

Q ss_pred             HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccC----cHH
Q 040261          140 VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAN----DWN  215 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~  215 (343)
                      +|+++|++..+.+         ++..+..+...|...+++++|+.+|++..+.+   +...+..+...|.. +    +++
T Consensus         4 eA~~~~~~aa~~g---------~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~   70 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---------DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYP   70 (212)
T ss_dssp             CTTHHHHHHHHTT---------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHH
T ss_pred             hHHHHHHHHHHCC---------CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHH
Confidence            4677788877754         67788889999999999999999999998876   67778888888888 7    899


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhc----CCchHH
Q 040261          216 EAKCLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEASRLLELMIQIGVR-PDASVYNTLMDGFCL----TGRVNR  286 (343)
Q Consensus       216 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~  286 (343)
                      +|...+++..+.+   +...+..+...|..    .+++++|..+|++..+.+.. .+...+..|...|..    .+++++
T Consensus        71 ~A~~~~~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~  147 (212)
T 3rjv_A           71 QARQLAEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVK  147 (212)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHH
Confidence            9999999998865   56777888888877    88999999999999987621 126788888888888    789999


Q ss_pred             HHHHHHHHHhCCCCccHHHHHHHHHHHHhc-C-----ChHHHHHHHHHHHhCCC
Q 040261          287 AKELFVSMESNGCMRDVFSYGILINGYCKN-K-----EIEGALSLYSEMLSKGI  334 (343)
Q Consensus       287 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~~~~~~~  334 (343)
                      |...|++..+.  ..+...+..|...|... |     ++++|...|++..+.|.
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  24555777788887654 3     89999999999988774

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.29  E-value=7.7e-11  Score=85.67  Aligned_cols=167  Identities=13%  Similarity=-0.007  Sum_probs=128.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...+..+...+.+.|++++|...|++..+.. +.+...+..+..++...|++++|...++++.....  +...+.....
T Consensus         5 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~   81 (176)
T 2r5s_A            5 PDEQLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAK   81 (176)
T ss_dssp             -CTTHHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHH
Confidence            34567788889999999999999999987654 44677899999999999999999999999877643  4443332221


Q ss_pred             H-HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           96 G-LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        96 ~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      . +...+...+|...+++..+..+. +...+..+..++...|++++|...++++.+..+.     ..+...+..+..++.
T Consensus        82 ~~~~~~~~~~~a~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~-----~~~~~a~~~l~~~~~  155 (176)
T 2r5s_A           82 LELHQQAAESPELKRLEQELAANPD-NFELACELAVQYNQVGRDEEALELLWNILKVNLG-----AQDGEVKKTFMDILS  155 (176)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-----TTTTHHHHHHHHHHH
T ss_pred             HHHHhhcccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcc-----cChHHHHHHHHHHHH
Confidence            2 12222334578889888887443 6788889999999999999999999999987521     123558889999999


Q ss_pred             hcCChHHHHHHHHHhhh
Q 040261          175 KEGFVDKAKELFLKMKD  191 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~  191 (343)
                      ..|+.++|...|++...
T Consensus       156 ~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          156 ALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             HHCSSCHHHHHHHHHHH
T ss_pred             HhCCCCcHHHHHHHHHH
Confidence            99999999999987653

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.28  E-value=2.3e-11  Score=85.80  Aligned_cols=146  Identities=10%  Similarity=-0.065  Sum_probs=115.6

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      |...+...|++++|+..++...... +.+...+..+...|.+.|++++|.+.|++.++..+. +..+|..+..++.+.|+
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCc
Confidence            5566677889999999999876632 223446677889999999999999999999987533 78899999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHH-HHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALN-LFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      +++|+..|++..+..+. +..++..+..+|.+.|+++++.+ ++++..+..       |.++.+|......+...|+
T Consensus        81 ~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~-------P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           81 TDKAVECYRRSVELNPT-QKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF-------PGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS-------TTCHHHHHHHHHHHHTCCC
T ss_pred             hHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC-------cCCHHHHHHHHHHHHHhCc
Confidence            99999999999988544 67889999999999999877655 468888764       4456777777777776664

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.28  E-value=5e-10  Score=88.49  Aligned_cols=180  Identities=9%  Similarity=-0.039  Sum_probs=125.8

Q ss_pred             ChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc----CCCcc-HHHHHHHHHHHhhcCcHHHH
Q 040261           32 HYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS----CFTPD-AVTFTSLIKGLCAESRIMEA  106 (343)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a  106 (343)
                      ++++|...|++.               ...+...|++++|...|.+....    +-.+. ..+|+.+..+|.+.|++++|
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A   96 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNA   96 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            477777777765               44677889999999999988763    21122 56888999999999999999


Q ss_pred             HHHHHHHHhcCC---CC--CHHHHHHHHHHHHhc-CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH
Q 040261          107 AALFTKLRAFGC---KP--DVFTYTTLINGLCRT-GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD  180 (343)
Q Consensus       107 ~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  180 (343)
                      +..+++..+...   .+  ...++..+..+|... |++++|+..+++.....+..+. ......++..+...+.+.|+++
T Consensus        97 ~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~-~~~~~~~~~~lg~~~~~~g~~~  175 (292)
T 1qqe_A           97 VDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQS-VALSNKCFIKCADLKALDGQYI  175 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCC-hHHHHHHHHHHHHHHHHhCCHH
Confidence            999998875421   11  134778888999996 9999999999998775310000 0000345777788888888888


Q ss_pred             HHHHHHHHhhhCCCCCChh------hHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          181 KAKELFLKMKDENINPDVV------TYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~------~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      +|+..|++..+........      .|..+..++...|++++|...+++..+.
T Consensus       176 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  228 (292)
T 1qqe_A          176 EASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (292)
T ss_dssp             HHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            8888888877653222111      3555666677777777777777776553

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.26  E-value=1.9e-10  Score=90.64  Aligned_cols=165  Identities=16%  Similarity=0.026  Sum_probs=82.1

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHH-HHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTF-TSLI   94 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~   94 (343)
                      +...+..+...+.+.|++++|...|++..+.. +.+...+..+..++...|++++|...++++....  |+.... ....
T Consensus       116 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~  192 (287)
T 3qou_A          116 EEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQ  192 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHH
T ss_pred             chhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHH
Confidence            44445555555555556666655555555433 2344455555555555555555555555554432  222211 1112


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      ..+...++.++|.+.+++.....+. +...+..+...+...|++++|...+.++....+.     ..+...+..++..+.
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~P~-~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~-----~~~~~a~~~l~~~~~  266 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAENPE-DAALATQLALQLHQVGRNEEALELLFGHLRXDLT-----AADGQTRXTFQEILA  266 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-----GGGGHHHHHHHHHHH
T ss_pred             HHHHhhcccCccHHHHHHHHhcCCc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccc-----cccchHHHHHHHHHH
Confidence            2233444455555555555554322 4455555555555555555555555555554310     111345555555555


Q ss_pred             hcCChHHHHHHHHHh
Q 040261          175 KEGFVDKAKELFLKM  189 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~  189 (343)
                      ..|+.++|...+++.
T Consensus       267 ~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          267 ALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHCTTCHHHHHHHHH
T ss_pred             HcCCCCcHHHHHHHH
Confidence            555555555555443

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.25  E-value=2.8e-10  Score=82.69  Aligned_cols=165  Identities=13%  Similarity=0.020  Sum_probs=130.2

Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      ...+......+...|++++|...+++..+.. +.+...+..+..++...|++++|...++.+.+..  |+...+..+...
T Consensus         6 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~   82 (176)
T 2r5s_A            6 DEQLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKL   82 (176)
T ss_dssp             CTTHHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHH
Confidence            4456777888999999999999999987653 3367888999999999999999999999987763  344433332222


Q ss_pred             -HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCc-cHHHHHHHHHHHHhcCChH
Q 040261          243 -LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMR-DVFSYGILINGYCKNKEIE  320 (343)
Q Consensus       243 -~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~  320 (343)
                       +...++...|...+++..+.. +.+...+..+...+...|++++|...|+++.+....+ +...+..+...+...|+.+
T Consensus        83 ~~~~~~~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  161 (176)
T 2r5s_A           83 ELHQQAAESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGN  161 (176)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSC
T ss_pred             HHHhhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCC
Confidence             223334455788999998875 5568899999999999999999999999999874322 3568889999999999999


Q ss_pred             HHHHHHHHHHh
Q 040261          321 GALSLYSEMLS  331 (343)
Q Consensus       321 ~a~~~~~~~~~  331 (343)
                      +|...|++.+.
T Consensus       162 ~A~~~y~~al~  172 (176)
T 2r5s_A          162 AIASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            99999998764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.25  E-value=2e-09  Score=81.55  Aligned_cols=187  Identities=11%  Similarity=-0.006  Sum_probs=116.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCC-C-CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH--HHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLF-P-DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA--VTFT   91 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~   91 (343)
                      ++..+..+...+.+.|++++|+..|+++.+.... | ....+..+..++.+.|++++|...|+++.+..+....  ..+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            5567778888999999999999999999875311 1 1357888899999999999999999999986433111  2344


Q ss_pred             HHHHHHhh------------------cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCC
Q 040261           92 SLIKGLCA------------------ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNG  153 (343)
Q Consensus        92 ~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  153 (343)
                      .+..++..                  .|++++|...|+++.+..+. +...+......          ..+...+     
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l----------~~~~~~~-----  146 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRL----------VFLKDRL-----  146 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHH----------HHHHHHH-----
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHH----------HHHHHHH-----
Confidence            44444443                  56888899999888876322 22222111100          0000000     


Q ss_pred             CCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCC--ChhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          154 EFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINP--DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       154 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                               ......+...+.+.|++++|+..|+++.+.....  ....+..+..++.+.|++++|...++.+...
T Consensus       147 ---------~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          147 ---------AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             ---------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             ---------HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence                     0112234556666777777777777666542110  1244666666777777777777777766654

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.23  E-value=1.4e-10  Score=81.83  Aligned_cols=112  Identities=6%  Similarity=0.035  Sum_probs=50.8

Q ss_pred             HhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHH
Q 040261          174 CKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEAS  253 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  253 (343)
                      ...|++++|+..++...... +-+...+..+...|.+.|++++|...+++.++.. +-+..+|..+..++...|++++|.
T Consensus         8 ~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~   85 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAV   85 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHH
Confidence            34444445554444443321 1122333344444555555555555555544442 223444444555555555555555


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHH
Q 040261          254 RLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAK  288 (343)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  288 (343)
                      ..|+++++.. +-+...+..+...|.+.|++++|.
T Consensus        86 ~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa  119 (150)
T 4ga2_A           86 ECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRA  119 (150)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHH
Confidence            5555554443 223444445555555555544433

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.21  E-value=7.5e-10  Score=87.17  Aligned_cols=158  Identities=15%  Similarity=0.033  Sum_probs=66.3

Q ss_pred             HHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhC
Q 040261          168 TITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFN-VIMNELCKN  246 (343)
Q Consensus       168 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~  246 (343)
                      .+...+...|++++|...|+++.+.. +.+...+..+..++...|++++|...++++.+.  .|+..... .....+...
T Consensus       122 ~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~l~~~  198 (287)
T 3qou_A          122 QQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIELLXQ  198 (287)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHHHHhh
Confidence            33333444444444444444443322 112333444444444444444444444443332  12221111 111123334


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCC-ccHHHHHHHHHHHHhcCChHHHHHH
Q 040261          247 GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCM-RDVFSYGILINGYCKNKEIEGALSL  325 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~  325 (343)
                      ++.+.|...+++..+.. +.+...+..+...+...|++++|...++++.+.... .+...+..++..+...|+.++|...
T Consensus       199 ~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~  277 (287)
T 3qou_A          199 AADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASX  277 (287)
T ss_dssp             HTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             cccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHH
Confidence            44444455555444443 334444555555555555555555555555443211 0133445555555555555555555


Q ss_pred             HHHH
Q 040261          326 YSEM  329 (343)
Q Consensus       326 ~~~~  329 (343)
                      |++.
T Consensus       278 ~r~a  281 (287)
T 3qou_A          278 YRRQ  281 (287)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.20  E-value=6.5e-10  Score=96.45  Aligned_cols=153  Identities=12%  Similarity=0.004  Sum_probs=91.6

Q ss_pred             CChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHH
Q 040261           31 KHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALF  110 (343)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  110 (343)
                      |++++|...+++..+.. +.+...+..+...+...|++++|.+.+++..+... .+...+..+..++...|++++|.+.+
T Consensus         3 g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHP-GHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTST-TCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            56677777777766543 33456677777777777777777777777776542 24666667777777777777777777


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc---CChHHHHHHHH
Q 040261          111 TKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE---GFVDKAKELFL  187 (343)
Q Consensus       111 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~  187 (343)
                      ++..+.... +...+..+..++...|++++|.+.+++..+..       +.+...+..+..++...   |+.++|.+.++
T Consensus        81 ~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~  152 (568)
T 2vsy_A           81 QQASDAAPE-HPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-------PEEPYITAQLLNWRRRLCDWRALDVLSAQVR  152 (568)
T ss_dssp             HHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHH
T ss_pred             HHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence            777666433 45666777777777777777777777776654       33455666677777777   77777777777


Q ss_pred             HhhhCC
Q 040261          188 KMKDEN  193 (343)
Q Consensus       188 ~~~~~~  193 (343)
                      +..+.+
T Consensus       153 ~al~~~  158 (568)
T 2vsy_A          153 AAVAQG  158 (568)
T ss_dssp             HHHHHT
T ss_pred             HHHhcC
Confidence            766543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.20  E-value=4.6e-09  Score=79.53  Aligned_cols=186  Identities=9%  Similarity=-0.006  Sum_probs=133.4

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCc--cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH--HHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTP--DAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV--FTYT  126 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~  126 (343)
                      +...+..+...+.+.|++++|...|+++.+..+..  ....+..+..++.+.|++++|+..|+++.+..+....  .++.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            34556667778899999999999999999864321  2357778889999999999999999999987443211  2444


Q ss_pred             HHHHHHHh------------------cCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040261          127 TLINGLCR------------------TGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK  188 (343)
Q Consensus       127 ~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  188 (343)
                      .+..++..                  .|++++|...|+++.+..       |.+..++.......          .+...
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-------P~~~~a~~a~~~l~----------~~~~~  145 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-------PNSQYTTDATKRLV----------FLKDR  145 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-------TTCTTHHHHHHHHH----------HHHHH
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-------cCChhHHHHHHHHH----------HHHHH
Confidence            44555543                  578999999999999875       22333333221111          01111


Q ss_pred             hhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          189 MKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN----VVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       189 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      +        ......+...+.+.|++++|...++.+.+..  |+    ...+..+..++.+.|+.++|...++.+...+
T Consensus       146 ~--------~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          146 L--------AKYEYSVAEYYTERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             H--------HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             H--------HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            1        1112345678889999999999999999873  33    2567888999999999999999999988764

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.18  E-value=1.3e-09  Score=94.50  Aligned_cols=131  Identities=10%  Similarity=-0.019  Sum_probs=63.4

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNEL  243 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  243 (343)
                      ..+..+...+...|++++|.+.+++..+.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+..++
T Consensus        24 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~  101 (568)
T 2vsy_A           24 VAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHAL  101 (568)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            344444455555555555555555544432 1234444445555555555555555555554442 22344444455555


Q ss_pred             HhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC---CchHHHHHHHHHHHhC
Q 040261          244 CKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT---GRVNRAKELFVSMESN  297 (343)
Q Consensus       244 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~  297 (343)
                      ...|++++|...++++.+.. +.+...+..+...+...   |+.++|.+.+++..+.
T Consensus       102 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A          102 EDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            55555555555555554443 23344444455555555   5555555555554443

>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=99.14  E-value=1.8e-07  Score=74.42  Aligned_cols=224  Identities=11%  Similarity=0.016  Sum_probs=151.8

Q ss_pred             HhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC-cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc-C-ChH
Q 040261           63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES-RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRT-G-HTI  139 (343)
Q Consensus        63 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-~~~  139 (343)
                      .+.+..++|++++++++..++. +..+|+..-..+...+ .+++++++++.+....++ +..+|+.-..++.+. + +++
T Consensus        65 ~~~e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL~~l~~~~~~  142 (349)
T 3q7a_A           65 AKEEKSERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLLDRISPQDPV  142 (349)
T ss_dssp             HTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHHHHHCCSCCH
T ss_pred             HhCCCCHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhcCCChH
Confidence            3344456788999988887533 5677777777777777 589999999999988665 777887777777766 6 888


Q ss_pred             HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChH--------HHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          140 VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVD--------KAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                      +++++++++.+.+       +.+..+|+.-..++.+.|.++        ++++.++++.+.+. -|...|+.....+.+.
T Consensus       143 ~EL~~~~k~L~~d-------pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~l  214 (349)
T 3q7a_A          143 SEIEYIHGSLLPD-------PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVSR  214 (349)
T ss_dssp             HHHHHHHHHTSSC-------TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhc
Confidence            9999999998875       556777776666666656555        88888888877653 3777788777777776


Q ss_pred             Cc-------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCh--------------------hHHHHHHHHHHHcC-
Q 040261          212 ND-------WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKM--------------------DEASRLLELMIQIG-  263 (343)
Q Consensus       212 ~~-------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~~~~~~~~~-  263 (343)
                      +.       ++++++.++++.... +-|...|+.+-..+.+.|..                    .........+...+ 
T Consensus       215 ~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  293 (349)
T 3q7a_A          215 PGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPL  293 (349)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CC
T ss_pred             cccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhccc
Confidence            65       678888888887763 45677777766666666554                    11222222221111 


Q ss_pred             ----CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          264 ----VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       264 ----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                          -.++...+..++..|...|+.++|.++++.+.+.
T Consensus       294 ~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          294 PEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             CSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             ccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence                0245566666667777777777777777776543

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.11  E-value=6.8e-09  Score=82.59  Aligned_cols=229  Identities=11%  Similarity=-0.004  Sum_probs=154.4

Q ss_pred             hcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh-cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHH
Q 040261           64 KMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA-ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVAL  142 (343)
Q Consensus        64 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  142 (343)
                      ..|++++|.+++++..+.... .          +.. .+++++|...|.+.               ...|...|++++|.
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~-~----------~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~   56 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKT-S----------FMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAK   56 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCC-C----------SSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHccc-c----------ccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHH
Confidence            356778888888877654211 1          112 46777777777664               45677889999999


Q ss_pred             HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCCC-ChhhHHHHHHHHhccCcHHHH
Q 040261          143 NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NINP-DVVTYTSLIRGFCYANDWNEA  217 (343)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a  217 (343)
                      ..+.+........+. ......+|..+..+|.+.|++++|+..+++....    |-+. ...++..+..+|.. |++++|
T Consensus        57 ~~~~~al~~~~~~~~-~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A  134 (307)
T 2ifu_A           57 DAYLQEAEAHANNRS-LFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKA  134 (307)
T ss_dssp             HHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHH
T ss_pred             HHHHHHHHHHHHcCC-HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHH
Confidence            988887654310000 0111357788888999999999999999886542    2111 13567788888888 999999


Q ss_pred             HHHHHHHHHcCCC---C--CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHhcCCchHHH
Q 040261          218 KCLFIEMMDQGVQ---P--NVVTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPD-ASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       218 ~~~~~~~~~~~~~---~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a  287 (343)
                      ...+++..+....   +  ...++..+...+...|++++|+..|++..+.    +..+. ...+..+..++...|++++|
T Consensus       135 ~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A  214 (307)
T 2ifu_A          135 VHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAA  214 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999988764111   1  1457788889999999999999999988764    11111 23566677778888999999


Q ss_pred             HHHHHHHHhCCCCcc------HHHHHHHHHHHHhcCChHHHHH
Q 040261          288 KELFVSMESNGCMRD------VFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       288 ~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                      ...|++.. .  .|+      ......++.++ ..|+.+.+.+
T Consensus       215 ~~~~~~al-~--~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          215 QKCVRESY-S--IPGFSGSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             HHHHHHHT-T--STTSTTSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             HHHHHHHh-C--CCCCCCCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence            99999987 4  232      12344455555 5566655544

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=99.11  E-value=1.8e-09  Score=73.49  Aligned_cols=113  Identities=10%  Similarity=-0.025  Sum_probs=94.2

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      |.....+......+.+.|++++|++.|++.++.. +.+...|..+..++.+.|++++|+..+++.++.+. .+...|..+
T Consensus        10 P~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~l   87 (126)
T 4gco_A           10 PELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS-KFIKGYIRK   87 (126)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh-hhhHHHHHH
Confidence            3456788899999999999999999999988765 55788899999999999999999999999998753 367888999


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      ..++...|++++|++.|++..+..+. +......+.
T Consensus        88 g~~~~~~~~~~~A~~~~~~al~l~P~-~~~a~~~l~  122 (126)
T 4gco_A           88 AACLVAMREWSKAQRAYEDALQVDPS-NEEAREGVR  122 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHCcC-CHHHHHHHH
Confidence            99999999999999999999987433 454544443

>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=99.11  E-value=1e-07  Score=75.73  Aligned_cols=246  Identities=9%  Similarity=0.003  Sum_probs=176.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG-RVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      +++.+.....+.+..++|+++++.++..+ +-+..+|+.--.++...| .++++++.++.++...++ +..+|+.....+
T Consensus        56 ~~~~~r~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL  133 (349)
T 3q7a_A           56 AMDYFRAIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLL  133 (349)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHH
Confidence            34444444455666789999999999866 445667888888888888 599999999999988644 788888877777


Q ss_pred             hhc-C-cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChH--------HHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           98 CAE-S-RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTI--------VALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        98 ~~~-~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      .+. + ++++++++++++.+...+ +..+|+--.-++.+.+.++        ++++.++++.+.+       +.|..+|+
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~~dpk-Ny~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-------p~N~SAW~  205 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLLPDPK-NYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-------GRNNSAWG  205 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTSSCTT-CHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-------TTCHHHHH
T ss_pred             HHhcCCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-------CCCHHHHH
Confidence            776 6 889999999999988655 7788877666666666666        8999999999876       56788898


Q ss_pred             HHHHHHHhcCC-------hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcH--------------------HHHHHH
Q 040261          168 TITDGLCKEGF-------VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDW--------------------NEAKCL  220 (343)
Q Consensus       168 ~l~~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~  220 (343)
                      .....+.+.+.       ++++++.+++..... +-|...|+.+-..+.+.|..                    ......
T Consensus       206 ~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (349)
T 3q7a_A          206 WRWYLRVSRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAF  284 (349)
T ss_dssp             HHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC-------------
T ss_pred             HHHHHHHhccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHH
Confidence            88888888876       688899988887764 34677777666555554442                    223333


Q ss_pred             HHHHHHcC-----CCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          221 FIEMMDQG-----VQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM  275 (343)
Q Consensus       221 ~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  275 (343)
                      ...+...+     -.++...+..++..|...|+.++|.++++.+.+.--+....-|+-.+
T Consensus       285 ~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~~dpir~~yw~~~~  344 (349)
T 3q7a_A          285 GFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEYDQMRAGYWEFRR  344 (349)
T ss_dssp             -CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHHHHHHHH
T ss_pred             HHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhChHHHHHHHHHH
Confidence            32232221     13567888899999999999999999999987542233344444333

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.11  E-value=6.5e-07  Score=75.82  Aligned_cols=296  Identities=13%  Similarity=0.030  Sum_probs=174.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC-cchHHHHHHHHHHc-CCC-ccHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR-VSPGFVVLGRILRS-CFT-PDAVTFTS   92 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~-~~~-~~~~~~~~   92 (343)
                      -..+|...+..+-. |+++.+..+|++....  .|+...|...+....+.++ .+....+|+..+.. |.. .+...|..
T Consensus        14 aR~vyer~l~~~P~-~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~   90 (493)
T 2uy1_A           14 PSAIMEHARRLYMS-KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKE   90 (493)
T ss_dssp             HHHHHHHHHHHHHT-TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHH
T ss_pred             HHHHHHHHHHHCCC-CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHH
Confidence            34556666655544 6777777777777663  3677777777766655553 34556666666553 322 24566666


Q ss_pred             HHHHHh----hcCcHHHHHHHHHHHHhcCCCC------------------------------------------------
Q 040261           93 LIKGLC----AESRIMEAAALFTKLRAFGCKP------------------------------------------------  120 (343)
Q Consensus        93 l~~~~~----~~~~~~~a~~~~~~~~~~~~~~------------------------------------------------  120 (343)
                      .+..+.    ..++.+.+.++|++........                                                
T Consensus        91 Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~  170 (493)
T 2uy1_A           91 YIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGW  170 (493)
T ss_dssp             HHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhc
Confidence            666543    2345666777777766531110                                                


Q ss_pred             CHHHHHHHHHHHHhc--CC-----hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          121 DVFTYTTLINGLCRT--GH-----TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~--~~-----~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                      +...|...+..-...  +-     .+.+..+|+++....       +.....|...+..+.+.|+.+.|..++++.... 
T Consensus       171 s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~-------p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~-  242 (493)
T 2uy1_A          171 SVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSF-------YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM-  242 (493)
T ss_dssp             SHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             cHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-
Confidence            011122222111111  00     223456677766643       445677888888888999999999999988776 


Q ss_pred             CCCChhhHH----------------------------------------HHHHHHhccCcHHHHHHHHHHHHHcCCCCCH
Q 040261          194 INPDVVTYT----------------------------------------SLIRGFCYANDWNEAKCLFIEMMDQGVQPNV  233 (343)
Q Consensus       194 ~~~~~~~~~----------------------------------------~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  233 (343)
                       +.+...+.                                        ..+....+.++.+.|..+|+.. +.. ..+.
T Consensus       243 -P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~  319 (493)
T 2uy1_A          243 -SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGP  319 (493)
T ss_dssp             -CCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCH
T ss_pred             -CCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCCh
Confidence             33322221                                        1122222345677778888777 321 2234


Q ss_pred             HHHHHHHHHHHh-CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHH
Q 040261          234 VTFNVIMNELCK-NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILING  312 (343)
Q Consensus       234 ~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  312 (343)
                      ..|...+..-.. .++.+.|..+|+...+.. +-+...+...++...+.|+.+.|..+|+++.     .....|...+..
T Consensus       320 ~v~i~~A~lE~~~~~d~~~ar~ife~al~~~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~f  393 (493)
T 2uy1_A          320 HVFIYCAFIEYYATGSRATPYNIFSSGLLKH-PDSTLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEY  393 (493)
T ss_dssp             HHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHH
Confidence            444332222222 236888888888887753 3334556666777777888888888888872     256677777777


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 040261          313 YCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       313 ~~~~~~~~~a~~~~~~~~~  331 (343)
                      -...|+.+.+.++++++..
T Consensus       394 E~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          394 EFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHSCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            6777888888888887764

>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=99.07  E-value=8.1e-08  Score=75.81  Aligned_cols=165  Identities=10%  Similarity=0.026  Sum_probs=108.3

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc----chHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-CC----
Q 040261          127 TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA----ITYSTITDGLCKEGFVDKAKELFLKMKDENIN-PD----  197 (343)
Q Consensus       127 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----  197 (343)
                      ..+..+...|++++|...+++......     ..++.    ..+..+...+...+++++|+..++++...... ++    
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~-----~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~  154 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEE-----YHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCC-----CCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhcccc-----CChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHH
Confidence            346677888999999999998877542     11221    12334666677778888888888887763222 12    


Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCC
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ-----GVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPD  267 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~  267 (343)
                      ..+++.+..+|...|++++|...++++.+.     +..+. ..++..+..+|.+.|++++|...+++..+.    +..+.
T Consensus       155 ~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~  234 (293)
T 3u3w_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHH
Confidence            225777778888888888888888877642     11111 236667777788888888888887776653    11111


Q ss_pred             -HHHHHHHHHHHhcCCc-hHHHHHHHHHHHh
Q 040261          268 -ASVYNTLMDGFCLTGR-VNRAKELFVSMES  296 (343)
Q Consensus       268 -~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~  296 (343)
                       ..++..+..+|.+.|+ +++|...+++...
T Consensus       235 ~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence             5567777777777774 5777777766543

>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=99.05  E-value=1.1e-07  Score=75.10  Aligned_cols=165  Identities=13%  Similarity=0.027  Sum_probs=125.0

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCC-CCCh----hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCC-CC----HHHH
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENI-NPDV----VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQ-PN----VVTF  236 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~  236 (343)
                      ...+..+...|++++|...+++..+... .|+.    ..+..+...+...+++++|...++.+.+.... ++    ..++
T Consensus        79 ~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 3u3w_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHH
Confidence            3346778899999999999999877421 2221    13345677778888999999999999984322 22    2368


Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHHc-----CCCC-CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCc-cHHH
Q 040261          237 NVIMNELCKNGKMDEASRLLELMIQI-----GVRP-DASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMR-DVFS  305 (343)
Q Consensus       237 ~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~  305 (343)
                      +.+..+|...|++++|...++++.+.     +..+ ...++..+...|.+.|++++|...+++..+.    +..+ -..+
T Consensus       159 ~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~  238 (293)
T 3u3w_A          159 NAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHH
Confidence            89999999999999999999998852     1122 2347888999999999999999999887642    2222 2568


Q ss_pred             HHHHHHHHHhcCC-hHHHHHHHHHHHh
Q 040261          306 YGILINGYCKNKE-IEGALSLYSEMLS  331 (343)
Q Consensus       306 ~~~l~~~~~~~~~-~~~a~~~~~~~~~  331 (343)
                      +..+..+|.+.|+ +++|.+.+++.+.
T Consensus       239 ~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          239 YYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            8889999999995 6999999988764

>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=99.04  E-value=3.9e-08  Score=73.58  Aligned_cols=128  Identities=13%  Similarity=0.020  Sum_probs=110.0

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040261          165 TYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELC  244 (343)
Q Consensus       165 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  244 (343)
                      .+..+...+...|++++|...|++..    .|+...+..+..++...|++++|...++...+.. +.+...+..+..++.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            45566778889999999999998874    4678899999999999999999999999998874 456788889999999


Q ss_pred             hCCChhHHHHHHHHHHHcCCCC----------------CHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          245 KNGKMDEASRLLELMIQIGVRP----------------DASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~~~~~----------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      ..|++++|...++++.+.. +.                ....+..+..++...|++++|...+++..+..
T Consensus        83 ~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQL-RGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTT-TTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HcccHHHHHHHHHHHHHhC-CCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            9999999999999998853 22                23778889999999999999999999998864

>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=99.03  E-value=3.7e-08  Score=73.70  Aligned_cols=133  Identities=11%  Similarity=-0.127  Sum_probs=80.7

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 040261           56 NILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRT  135 (343)
Q Consensus        56 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  135 (343)
                      ..+...+...|++++|...+++..    .|+...+..+...+...|++++|++.+++..+.... +...+..+..++...
T Consensus        10 ~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~lg~~~~~~   84 (213)
T 1hh8_A           10 WNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYYQT   84 (213)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHc
Confidence            334444555555555555555442    334555555666666666666666666666554322 455566666666666


Q ss_pred             CChHHHHHHHHHHHccCCCCC---------ccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          136 GHTIVALNLFEEMANGNGEFG---------VVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       136 ~~~~~a~~~~~~~~~~~~~~~---------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                      |++++|...+++..+..+...         ...+.....+..+..++.+.|++++|...|++..+..
T Consensus        85 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           85 EKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             TCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            666666666666665431100         0011123678888899999999999999999988764

>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=99.03  E-value=3e-08  Score=70.86  Aligned_cols=128  Identities=12%  Similarity=0.040  Sum_probs=80.1

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      .+..+...+...|++++|...++...+.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+..++.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            34555556666666777776666666653 3345666666667777777777777777776654 445666667777777


Q ss_pred             cCCchHHHHHHHHHHHhCCCCccHHHHHH--HHHHHHhcCChHHHHHHHHHHH
Q 040261          280 LTGRVNRAKELFVSMESNGCMRDVFSYGI--LINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      ..|++++|...+++..+.. +.+...+..  .+..+...|++++|++.+.+..
T Consensus        93 ~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            7777777777777766542 223334422  3333666677777777776554

>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=99.02  E-value=3.2e-09  Score=83.28  Aligned_cols=196  Identities=11%  Similarity=-0.008  Sum_probs=122.2

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      |.+...+..+...+.+.|++++|+..|++..+.. +.+...|..+..++.+.|++++|...+++..+... .+...+..+
T Consensus         1 p~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l   78 (281)
T 2c2l_A            1 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFL   78 (281)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCT-TCHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHH
Confidence            3567788888889999999999999999888754 34677888888888899999999999988887642 357778888


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHH
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGL  173 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  173 (343)
                      ..++...|++++|...|++..+.+.. +...+...+....+   ...+..... .....      .+.+......+... 
T Consensus        79 g~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~---~~~~~~~~~-~~~~~------~~~~~~i~~~l~~l-  146 (281)
T 2c2l_A           79 GQCQLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALR---IAKKKRWNS-IEERR------IHQESELHSYLTRL-  146 (281)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHH---HHHHHHHHH-HHHTC------CCCCCHHHHHHHHH-
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHH---HHHHHHHHH-HHHHH------HhhhHHHHHHHHHH-
Confidence            88888889999999888887765211 10011111111111   111111111 22222      23344443333332 


Q ss_pred             HhcCChHHHHHHHHHhhhCCCCCC-hhhHHHHHHHHhcc-CcHHHHHHHHHHHHH
Q 040261          174 CKEGFVDKAKELFLKMKDENINPD-VVTYTSLIRGFCYA-NDWNEAKCLFIEMMD  226 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~  226 (343)
                       ..|+.++|++.++...+..  |+ ......+...+.+. +.++++..+|..+.+
T Consensus       147 -~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          147 -IAAERERELEECQRNHEGH--EDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             -HHHHHHHHHTTTSGGGTTT--SCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             -HHHHHHHHHHHHHhhhccc--cchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence             2577888888887776643  33 33333333333333 557777888776654

>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=99.01  E-value=2.2e-08  Score=71.56  Aligned_cols=131  Identities=8%  Similarity=-0.033  Sum_probs=109.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      ...+..+...+...|++++|...|++..+.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+..+
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4568888999999999999999999988755 4567889999999999999999999999999875 3367888899999


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHH--HHHHHHHHhcCChHHHHHHHHHHHc
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTY--TTLINGLCRTGHTIVALNLFEEMAN  150 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~  150 (343)
                      +...|++++|.+.+++..+.... +...+  ......+...|++++|...+.....
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            99999999999999999887543 44455  3344447788999999999887654

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.01  E-value=2.1e-08  Score=79.73  Aligned_cols=131  Identities=9%  Similarity=-0.009  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCC---CC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC---Cc--cHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGL---FP--DLYTYNILINCFCKMGRVSPGFVVLGRILRSCF---TP--DAV   88 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~   88 (343)
                      .|......|...|++++|...|.+..+...   .+  -..+|+.+..+|...|++++|...+++..+...   .+  ...
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            444445555555555555555555433110   00  122445555555555555555555555443210   11  123


Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHhcCChHHHHHHHHHHHc
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKP-----DVFTYTTLINGLCRTGHTIVALNLFEEMAN  150 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  150 (343)
                      ++..+...|.. |++++|++.|++..+.....     ...++..+...|.+.|++++|...+++...
T Consensus       118 ~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          118 ALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444544 55555555555444321000     022344444445555555555555544443

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=99.01  E-value=3e-08  Score=66.95  Aligned_cols=115  Identities=14%  Similarity=0.126  Sum_probs=95.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      ...+..+...+...|++++|.+.++++.... +.+...+..+...+...|++++|..+++++.+.. +.+..++..+...
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            6788899999999999999999999988754 4567788889999999999999999999998864 3367788889999


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR  134 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  134 (343)
                      +...|++++|...++++.+.... +...+..+...+..
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~  123 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELDPN-NAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHh
Confidence            99999999999999999887533 55555555555544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=99.00  E-value=3.6e-09  Score=74.20  Aligned_cols=99  Identities=7%  Similarity=-0.092  Sum_probs=51.4

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...+..+...+.+.|++++|...|++..... |.+...|..+..++...|++++|...|++..+..+. +...|..+..
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~-~~~~~~~lg~  112 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN-DYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS-CCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC-CcHHHHHHHH
Confidence            44445555555555555555555555555433 234445555555555555555555555555554322 3444555555


Q ss_pred             HHhhcCcHHHHHHHHHHHHhc
Q 040261           96 GLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      ++...|++++|.+.|++..+.
T Consensus       113 ~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          113 CQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh
Confidence            555555555555555555544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.99  E-value=1.6e-08  Score=69.34  Aligned_cols=120  Identities=9%  Similarity=-0.013  Sum_probs=99.0

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSL   93 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l   93 (343)
                      |.+...+..+...+.+.|++++|...|++..+.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l   90 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRK   90 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHH
Confidence            4567889999999999999999999999988754 4477889999999999999999999999998875 3367888889


Q ss_pred             HHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 040261           94 IKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG  136 (343)
Q Consensus        94 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  136 (343)
                      ..++.+.|++++|.+.+++..+.... +...+..+..++...|
T Consensus        91 a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           91 AAALEAMKDYTKAMDVYQKALDLDSS-CKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCGG-GTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHhc
Confidence            99999999999999999998876432 3455666666665544

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.98  E-value=2.2e-07  Score=73.31  Aligned_cols=170  Identities=9%  Similarity=0.015  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCC---CCC--h
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENI---NPD--V  198 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~--~  198 (343)
                      .+...+..+...|++++|.+.+++..+....... .......+..+...+...|++++|+..+++......   .+.  .
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPE-FQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHH-HHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChh-HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            3444555666666666666666665554310000 000001122334445555666666666665543211   111  2


Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHc-CCCCC-----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC----C-C
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQ-GVQPN-----VVTFNVIMNELCKNGKMDEASRLLELMIQIGVR----P-D  267 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~-~  267 (343)
                      .+++.+...|...|++++|...+++..+. ...|+     ..++..+..+|...|++++|...+++..+....    . -
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            34555555555566666666666555421 00111     134555555555556666666555555543100    0 0


Q ss_pred             HHHHHHHHHHHhcCCchHHH-HHHHHHH
Q 040261          268 ASVYNTLMDGFCLTGRVNRA-KELFVSM  294 (343)
Q Consensus       268 ~~~~~~l~~~~~~~~~~~~a-~~~~~~~  294 (343)
                      ..++..+...|...|++++| ...+++.
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            34455555555555555555 4444433

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.98  E-value=1.5e-08  Score=69.13  Aligned_cols=121  Identities=8%  Similarity=0.055  Sum_probs=102.6

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...+..+...+...|++++|...+++..... +.+...+..+..++...|++++|...+++..+.. +.+...+..+.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~   87 (131)
T 2vyi_A           10 AEAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMG   87 (131)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHH
Confidence            456788889999999999999999999988754 4567888999999999999999999999999874 33577888899


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCh
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHT  138 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  138 (343)
                      ..+...|++++|.+.+++..+.... +...+..+..++...|++
T Consensus        88 ~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           88 LALSSLNKHVEAVAYYKKALELDPD-NETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHhcC
Confidence            9999999999999999999887543 667777888888777764

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.97  E-value=3e-07  Score=72.57  Aligned_cols=168  Identities=11%  Similarity=0.018  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH-----HHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV-----FTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      ..+...+..+...|++++|.+.+.+..+.......     ..+..+...+...|++++|...+++.......     ..+
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~-----~~~  150 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLT-----GID  150 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCC-----SSC
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc-----CCc
Confidence            34445566677777777777777776654322111     12334455566677777777777777776421     111


Q ss_pred             ----cchHHHHHHHHHhcCChHHHHHHHHHhhh---C-CCCC--ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCC--
Q 040261          163 ----AITYSTITDGLCKEGFVDKAKELFLKMKD---E-NINP--DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQ--  230 (343)
Q Consensus       163 ----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~-~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--  230 (343)
                          ..+++.+...|...|++++|...+++..+   . +..+  ...++..+..+|...|++++|...+++..+....  
T Consensus       151 ~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~  230 (293)
T 2qfc_A          151 VYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRIN  230 (293)
T ss_dssp             TTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcC
Confidence                23566777777777777777777777652   1 1111  1146667777777777777777777777654200  


Q ss_pred             --C-CHHHHHHHHHHHHhCCChhHH-HHHHHHHH
Q 040261          231 --P-NVVTFNVIMNELCKNGKMDEA-SRLLELMI  260 (343)
Q Consensus       231 --~-~~~~~~~l~~~~~~~~~~~~a-~~~~~~~~  260 (343)
                        . -..+|..+..++.+.|++++| ...+++..
T Consensus       231 ~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          231 SMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             BCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence              0 145666677777777777777 55565553

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.97  E-value=6.9e-09  Score=81.34  Aligned_cols=194  Identities=10%  Similarity=-0.039  Sum_probs=121.3

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      +...+..+...+...|++++|...|++.++... .+...|..+..++.+.|++++|++.+++..+.... +...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            456777788888888999999999988887642 36778888888888889999999999888877433 6677888888


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY  210 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (343)
                      ++...|++++|...+++.....+       .+...+...+....+.   ..+... ........+.+......+.. + .
T Consensus        81 ~~~~~g~~~~A~~~~~~al~l~p-------~~~~~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~i~~~l~~-l-~  147 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAYSLAK-------EQRLNFGDDIPSALRI---AKKKRW-NSIEERRIHQESELHSYLTR-L-I  147 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHH-------HTTCCCCSHHHHHHHH---HHHHHH-HHHHHTCCCCCCHHHHHHHH-H-H
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCc-------cchhhHHHHHHHHHHH---HHHHHH-HHHHHHHHhhhHHHHHHHHH-H-H
Confidence            88889999999988888776541       1111111122211111   111111 11222223334433333322 2 2


Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhC-CChhHHHHHHHHHHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPNV-VTFNVIMNELCKN-GKMDEASRLLELMIQ  261 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~-~~~~~a~~~~~~~~~  261 (343)
                      .|++++|.+.++...+.  .|+. .....+...+.+. +.+++|..+|..+.+
T Consensus       148 ~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          148 AAERERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHHHHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            57888888887776654  4443 3333333334333 567778888877654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.97  E-value=2.9e-08  Score=67.41  Aligned_cols=102  Identities=12%  Similarity=0.034  Sum_probs=90.3

Q ss_pred             CCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           49 FPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        49 ~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      .|+ ...+......+.+.|++++|++.|++.++.. +.+...|..+..++.+.|++++|+..+++..+.+.. +...|..
T Consensus         9 nP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~   86 (126)
T 4gco_A            9 NPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-FIKGYIR   86 (126)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-hhHHHHH
Confidence            343 3578888999999999999999999999875 337889999999999999999999999999988544 6888999


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccC
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      +..++...|++++|.+.|++..+..
T Consensus        87 lg~~~~~~~~~~~A~~~~~~al~l~  111 (126)
T 4gco_A           87 KAACLVAMREWSKAQRAYEDALQVD  111 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            9999999999999999999999865

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.96  E-value=1.4e-08  Score=78.05  Aligned_cols=203  Identities=9%  Similarity=-0.071  Sum_probs=141.0

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHH-------HHHHHhcCChHHHHHHHHHHHccCCCC-C-----------ccc
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTL-------INGLCRTGHTIVALNLFEEMANGNGEF-G-----------VVC  159 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~~~~-~-----------~~~  159 (343)
                      ..++...|.+.|.+.....+. ....|..+       ...+.+.++..+++..+.......... .           ...
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~-~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDES-ACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCEE
T ss_pred             cCCCHHHHHHHHHHHHHhChh-hhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCccccccc
Confidence            578889999999998887544 56677776       455555555666666555554422100 0           000


Q ss_pred             c--CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCC--HHH
Q 040261          160 K--PDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPN--VVT  235 (343)
Q Consensus       160 ~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~  235 (343)
                      +  ........+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  ...
T Consensus        97 ~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a  173 (282)
T 4f3v_A           97 PVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAA  173 (282)
T ss_dssp             ECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHH
T ss_pred             ccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHH
Confidence            0  011234556778889999999999999887754  443355666668889999999999998554431 121  236


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHH
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQIGVRPD--ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYG  307 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  307 (343)
                      +..+..++...|++++|+..|++.......|.  .........++.+.|+.++|...|+++...  .|+...+.
T Consensus       174 ~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~~~~  245 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPKVAA  245 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHHH
Confidence            77788999999999999999999985443243  346667777889999999999999999986  35543333

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.94  E-value=2.5e-08  Score=69.90  Aligned_cols=98  Identities=18%  Similarity=0.025  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...+..+...+.+.|++++|++.|++.....+. +...|..+..+|...|++++|...|++.....       |.++..+
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-------P~~~~~~  107 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-------KNDYTPV  107 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-------SSCCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-------CCCcHHH
Confidence            445566666667777777777777777766433 56666777777777777777777777777654       3455666


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhC
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                      ..+..+|.+.|++++|...|++..+.
T Consensus       108 ~~lg~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          108 FHTGQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            77777777777777777777776664

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.93  E-value=7.2e-06  Score=64.92  Aligned_cols=177  Identities=11%  Similarity=-0.006  Sum_probs=123.4

Q ss_pred             hhhHHHHHHHH---HhcCChh-HHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC----------cchHHHHHHHHHHcC
Q 040261           17 VCSFNILFGCL---AKNKHYD-TVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR----------VSPGFVVLGRILRSC   82 (343)
Q Consensus        17 ~~~~~~l~~~~---~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~   82 (343)
                      ...|..+...+   .+.|.+. +|+.+++.+...+ |-+..+|+.--.++...+.          +++++.+++.+....
T Consensus        26 i~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~n-P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~  104 (331)
T 3dss_A           26 LKLYQSATQAVFQKRQAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN  104 (331)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC
Confidence            34455554444   3456655 8999999999865 3345566665544444443          678899999998876


Q ss_pred             CCccHHHHHHHHHHHhhcC--cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC-hHHHHHHHHHHHccCCCCCccc
Q 040261           83 FTPDAVTFTSLIKGLCAES--RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGH-TIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                      ++ +..+|+.-.-.+.+.+  .+++++.+++++.+..+. +..+|+.-.-++...|. ++++++.++.+.+.+       
T Consensus       105 PK-ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dpr-Ny~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-------  175 (331)
T 3dss_A          105 PK-SYGTWHHRCWLLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-------  175 (331)
T ss_dssp             TT-CHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-------
T ss_pred             CC-CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-------
Confidence            44 7888888777777777  489999999999998755 88888888888888888 589999999999876       


Q ss_pred             cCCcchHHHHHHHHHhc--------------CChHHHHHHHHHhhhCCCCCChhhHHHH
Q 040261          160 KPDAITYSTITDGLCKE--------------GFVDKAKELFLKMKDENINPDVVTYTSL  204 (343)
Q Consensus       160 ~~~~~~~~~l~~~~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l  204 (343)
                      +.|..+|+.....+.+.              +.++++++.+....... |-|...|+.+
T Consensus       176 p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~  233 (331)
T 3dss_A          176 FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYH  233 (331)
T ss_dssp             SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence            56777787776665554              23555666665555433 2244444433

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.93  E-value=4.5e-08  Score=66.73  Aligned_cols=118  Identities=13%  Similarity=0.015  Sum_probs=67.5

Q ss_pred             hhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          198 VVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDG  277 (343)
Q Consensus       198 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  277 (343)
                      ...+..+...+...|++++|...++...+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+...
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            3444555555555666666666666655542 2345555556666666666666666666666553 3345566666666


Q ss_pred             HhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          278 FCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       278 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                      +...|++++|...+++..+.. +.+...+..+..++...|+
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhc
Confidence            666666666666666665542 2244555555555555554

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.93  E-value=1e-07  Score=64.26  Aligned_cols=96  Identities=17%  Similarity=0.272  Sum_probs=48.5

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      .+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|..+++++.+.. +.+..++..+...+.
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~   88 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHH
Confidence            34444444555555555555555554432 2234444455555555555555555555555443 334445555555555


Q ss_pred             cCCchHHHHHHHHHHHhC
Q 040261          280 LTGRVNRAKELFVSMESN  297 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~~  297 (343)
                      ..|++++|...++++.+.
T Consensus        89 ~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHh
Confidence            555555555555555443

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.93  E-value=1.6e-08  Score=73.28  Aligned_cols=123  Identities=12%  Similarity=0.129  Sum_probs=99.6

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH-HhhcCcH--
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG-LCAESRI--  103 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--  103 (343)
                      +...|++++|...++...+.. +.+...+..+..++...|++++|...|++..+... .+...+..+..+ +...|++  
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTCCC
T ss_pred             hhhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCCcch
Confidence            346788999999999887755 45778899999999999999999999999988653 367777788888 7788998  


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ++|...+++..+.... +...+..+..++...|++++|...++++....
T Consensus        98 ~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           98 AQTRAMIDKALALDSN-EITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            9999999999887543 57788889999999999999999999998865

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.92  E-value=7.1e-08  Score=66.02  Aligned_cols=120  Identities=8%  Similarity=-0.070  Sum_probs=100.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 040261           49 FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTL  128 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  128 (343)
                      +.+...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|.+.+++..+.... +...+..+
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l   90 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT-FIKGYTRK   90 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-chHHHHHH
Confidence            3456688889999999999999999999998864 336788899999999999999999999999987543 67888999


Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      ..++...|++++|.+.+++.....       +.+...+..+..++.+.|
T Consensus        91 a~~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           91 AAALEAMKDYTKAMDVYQKALDLD-------SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-------GGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhC-------CCchHHHHHHHHHHHHhc
Confidence            999999999999999999998864       344566666666666554

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.92  E-value=2.2e-08  Score=70.22  Aligned_cols=110  Identities=11%  Similarity=0.011  Sum_probs=88.5

Q ss_pred             HHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261            4 FDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus         4 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      |+.+....|  .+...+..+...+.+.|++++|...|+...... +.+...|..+..++...|++++|...|++.....+
T Consensus        10 ~~~al~~~p--~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p   86 (148)
T 2vgx_A           10 IAMLNEISS--DTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDI   86 (148)
T ss_dssp             HHHHTTCCH--HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHcCCH--hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            444444333  467788888899999999999999999988765 45777888888899999999999999999888753


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                       .+...+..+..++...|++++|.+.|++..+..
T Consensus        87 -~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  119 (148)
T 2vgx_A           87 -XEPRFPFHAAECLLQXGELAEAESGLFLAQELI  119 (148)
T ss_dssp             -TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             -CCchHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence             367778888889999999999999999887753

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.92  E-value=2.7e-08  Score=73.81  Aligned_cols=157  Identities=11%  Similarity=-0.001  Sum_probs=112.2

Q ss_pred             HhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhCCC
Q 040261          174 CKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQ----GVQP-NVVTFNVIMNELCKNGK  248 (343)
Q Consensus       174 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~  248 (343)
                      ...|++++|.+.++.+... .......+..+...+...|++++|...+++..+.    +..+ ....+..+...+...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            4578999999955555432 2235677888888999999999999999888762    2122 24567778888999999


Q ss_pred             hhHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCc-cHHHHHHHHHHHHhcC
Q 040261          249 MDEASRLLELMIQI----GVRP--DASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMR-DVFSYGILINGYCKNK  317 (343)
Q Consensus       249 ~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~  317 (343)
                      +++|...+++..+.    +-.+  ....+..+...+...|++++|...+++..+.    +... ...++..+...+...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            99999999887764    2111  2456777888899999999999999877642    1111 1234577788899999


Q ss_pred             ChHHHHHHHHHHHh
Q 040261          318 EIEGALSLYSEMLS  331 (343)
Q Consensus       318 ~~~~a~~~~~~~~~  331 (343)
                      ++++|.+.+++...
T Consensus       162 ~~~~A~~~~~~al~  175 (203)
T 3gw4_A          162 NLLEAQQHWLRARD  175 (203)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999888764

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.91  E-value=4.5e-08  Score=70.95  Aligned_cols=122  Identities=9%  Similarity=0.076  Sum_probs=95.1

Q ss_pred             HhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH-HHhcCCh--H
Q 040261           63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING-LCRTGHT--I  139 (343)
Q Consensus        63 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~  139 (343)
                      ...|++++|...+++..+.. +.+...+..+...+...|++++|...|++..+.... +...+..+..+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE-NAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCCcchH
Confidence            45688889999998888764 336778888889999999999999999998876533 66777777877 7788888  9


Q ss_pred             HHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          140 VALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       140 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                      +|...++++....       +.+...+..+..++...|++++|...++++.+..
T Consensus        99 ~A~~~~~~al~~~-------p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           99 QTRAMIDKALALD-------SNEITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhC-------CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            9999999988865       3456778888888999999999999999887764

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.90  E-value=2.2e-08  Score=80.62  Aligned_cols=132  Identities=16%  Similarity=0.058  Sum_probs=111.5

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC--------------HHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD--------------LYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ....+..+...+.+.|++++|+..|++..+......              ...|..+..++.+.|++++|...+++.++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            567889999999999999999999999987542211              478999999999999999999999999987


Q ss_pred             CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHH-HHHHHHHH
Q 040261           82 CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVA-LNLFEEMA  149 (343)
Q Consensus        82 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a-~~~~~~~~  149 (343)
                      .. .+...+..+..++...|++++|+..|++..+..+. +...+..+..++.+.|+.+++ ...++.+.
T Consensus       226 ~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 DS-NNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            53 37888999999999999999999999999988544 677888899999999999888 44555553

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.90  E-value=4.4e-08  Score=66.56  Aligned_cols=101  Identities=6%  Similarity=-0.046  Sum_probs=88.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...|..+...+.+.|++++|+..|++..+.. +.+...|..+..++.+.|++++|...+++.++... .+...|..+.
T Consensus         2 ~~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg   79 (126)
T 3upv_A            2 MKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKA   79 (126)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHH
Confidence            356678889999999999999999999988765 45778899999999999999999999999998753 3677888899


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcC
Q 040261           95 KGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      .++...|++++|.+.|++..+..
T Consensus        80 ~~~~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           80 TAQIAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCHHHHHHHHHHHHHhC
Confidence            99999999999999999988763

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.90  E-value=2e-07  Score=71.63  Aligned_cols=187  Identities=7%  Similarity=-0.070  Sum_probs=107.9

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHH-------HHHHHhcCCcchHHHHHHHHHHcCCCcc---------------
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNIL-------INCFCKMGRVSPGFVVLGRILRSCFTPD---------------   86 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------   86 (343)
                      ..++...|.+.|.++.+.. +-....|..+       ...+...++..+++..+......  .|+               
T Consensus        18 ~~~d~~~A~~~F~~a~~~d-P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l--~p~~l~a~~~~~g~y~~~   94 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQI--SMSTLNARIAIGGLYGDI   94 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTC--CGGGGCCEEECCTTTCCC
T ss_pred             cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcC--ChhhhhhhhccCCccccc
Confidence            5778888888888887754 3345667666       44555555555555555444331  111               


Q ss_pred             -------HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccc
Q 040261           87 -------AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVC  159 (343)
Q Consensus        87 -------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  159 (343)
                             ......+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+......       
T Consensus        95 ~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-------  165 (282)
T 4f3v_A           95 TYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-------  165 (282)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-------
T ss_pred             ccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-------
Confidence                   1223345556666777777777777666543  332244455556677777777777776443321       


Q ss_pred             cC--CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCC--hhhHHHHHHHHhccCcHHHHHHHHHHHHHc
Q 040261          160 KP--DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPD--VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ  227 (343)
Q Consensus       160 ~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  227 (343)
                      .|  ....+..+..++...|++++|+..|++.......|.  .........++.+.|+.++|..+|+++...
T Consensus       166 d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          166 DKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            11  123555666667777777777777776654322132  234445555666677777777777777665

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.89  E-value=7.4e-08  Score=77.56  Aligned_cols=87  Identities=6%  Similarity=-0.113  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      ..|..+..++.+.|++++|+..++++++.. +.+...+..+..+|...|++++|...|++..+.. +.+...+..+..++
T Consensus       197 ~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~  274 (336)
T 1p5q_A          197 ASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQ  274 (336)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHH
Confidence            444445555555555555555555555543 3344455555555555555555555555554432 22344444455555


Q ss_pred             HhcCChHHH
Q 040261          314 CKNKEIEGA  322 (343)
Q Consensus       314 ~~~~~~~~a  322 (343)
                      ...|++++|
T Consensus       275 ~~~~~~~~a  283 (336)
T 1p5q_A          275 QRIRRQLAR  283 (336)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.89  E-value=3e-08  Score=73.55  Aligned_cols=161  Identities=11%  Similarity=-0.046  Sum_probs=88.8

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      ..|++++|.+.++.+... .......+..+...+...|++++|...+++........+. .+....++..+...+...|+
T Consensus         4 ~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGD-HTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ---CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC-HHHHHHHHHHHHHHHHHTTC
T ss_pred             ccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCC-cHHHHHHHHHHHHHHHHcCC
Confidence            456777777744444332 2224556666777777777777777777766552110000 12234556666777777777


Q ss_pred             hHHHHHHHHHhhhC----CCCC--ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC---CCCC--HHHHHHHHHHHHhCC
Q 040261          179 VDKAKELFLKMKDE----NINP--DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG---VQPN--VVTFNVIMNELCKNG  247 (343)
Q Consensus       179 ~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~--~~~~~~l~~~~~~~~  247 (343)
                      +++|...+++....    +..+  ....+..+...+...|++++|...+++..+..   -.+.  ..++..+..++...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            77777777665432    1011  13345556666667777777777776655321   0111  223455566666677


Q ss_pred             ChhHHHHHHHHHHH
Q 040261          248 KMDEASRLLELMIQ  261 (343)
Q Consensus       248 ~~~~a~~~~~~~~~  261 (343)
                      ++++|...+++..+
T Consensus       162 ~~~~A~~~~~~al~  175 (203)
T 3gw4_A          162 NLLEAQQHWLRARD  175 (203)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            77777666666544

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.87  E-value=1.5e-08  Score=71.01  Aligned_cols=111  Identities=9%  Similarity=0.002  Sum_probs=87.2

Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcC
Q 040261          184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIG  263 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  263 (343)
                      ..++++.... +.+...+..+...+...|++++|...|+.+.+.. +.+...|..+..++...|++++|...|+++.+..
T Consensus         8 ~~~~~al~~~-p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~   85 (148)
T 2vgx_A            8 GTIAMLNEIS-SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD   85 (148)
T ss_dssp             CSHHHHTTCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             hhHHHHHcCC-HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            3455555432 2245667777888888999999999999888874 4467788888888999999999999999988875


Q ss_pred             CCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          264 VRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       264 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                       +.+...+..+..+|...|++++|...|++..+.
T Consensus        86 -p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           86 -IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             -TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             456778888888999999999999999888764

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.86  E-value=5e-09  Score=77.62  Aligned_cols=153  Identities=11%  Similarity=-0.061  Sum_probs=73.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc---------------
Q 040261           22 ILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD---------------   86 (343)
Q Consensus        22 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------   86 (343)
                      ..+......|+++++.+.|+.-.... ......+..+...+...|++++|...|++..+......               
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~   87 (198)
T 2fbn_A            9 HHSSGRENLYFQGAKKSIYDYTDEEK-VQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIE   87 (198)
T ss_dssp             -------------CCCSGGGCCHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHH
T ss_pred             chhhhhhhhhhccccCchhhCCHHHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHH
Confidence            33444445556666666554322211 11334566666677777777777777777776422111               


Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...+..+..++...|++++|+..+++..+.... +...+..+..++...|++++|...|++.....       +.+..++
T Consensus        88 ~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~  159 (198)
T 2fbn_A           88 ISCNLNLATCYNKNKDYPKAIDHASKVLKIDKN-NVKALYKLGVANMYFGFLEEAKENLYKAASLN-------PNNLDIR  159 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-------TTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-------CCcHHHH
Confidence            145555555555666666666666665554322 44555555556666666666666666655543       2233444


Q ss_pred             HHHHHHHHhcCChHHHH
Q 040261          167 STITDGLCKEGFVDKAK  183 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~  183 (343)
                      ..+..++...++..++.
T Consensus       160 ~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          160 NSYELCVNKLKEARKKD  176 (198)
T ss_dssp             HHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444444444333

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.85  E-value=7.5e-08  Score=63.59  Aligned_cols=103  Identities=7%  Similarity=0.015  Sum_probs=81.8

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCc--cHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTP--DAVTFT   91 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~   91 (343)
                      |.+...+..+...+.+.|++++|...+++..+.. +.+...+..+..++...|++++|...+++..+.. +.  +...+.
T Consensus         3 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~   80 (112)
T 2kck_A            3 DQNPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWA   80 (112)
T ss_dssp             CSSTTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHH
Confidence            3567788888888889999999999998887754 4466778888888888888888888888888763 23  467777


Q ss_pred             HHHHHHhhc-CcHHHHHHHHHHHHhcCC
Q 040261           92 SLIKGLCAE-SRIMEAAALFTKLRAFGC  118 (343)
Q Consensus        92 ~l~~~~~~~-~~~~~a~~~~~~~~~~~~  118 (343)
                      .+..++... |++++|.+.+++......
T Consensus        81 ~l~~~~~~~~~~~~~A~~~~~~~~~~~p  108 (112)
T 2kck_A           81 AKADALRYIEGKEVEAEIAEARAKLEHH  108 (112)
T ss_dssp             HHHHHHTTCSSCSHHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHhhccc
Confidence            888888888 888888888888887643

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.82  E-value=2.1e-05  Score=62.26  Aligned_cols=224  Identities=8%  Similarity=-0.040  Sum_probs=155.1

Q ss_pred             HHHhcCCcc-hHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc----------HHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           61 CFCKMGRVS-PGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR----------IMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        61 ~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      ...+.|.+. +|+++++.++..++. +..+|+.--..+...+.          +++++.+++.+....++ +..+|+.-.
T Consensus        38 ~~~~~~e~s~eaL~~t~~~L~~nP~-~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PK-ny~aW~hR~  115 (331)
T 3dss_A           38 QKRQAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRC  115 (331)
T ss_dssp             HHHHTTCCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            344567766 789999999987533 55667665444444333          67889999999887655 788888877


Q ss_pred             HHHHhcCC--hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC-hHHHHHHHHHhhhCCCCCChhhHHHHHH
Q 040261          130 NGLCRTGH--TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF-VDKAKELFLKMKDENINPDVVTYTSLIR  206 (343)
Q Consensus       130 ~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~  206 (343)
                      .++.+.++  +++++.+++++.+.+       +.+..+|+.-..++...|. ++++++.++.+.+.++ -|...|+....
T Consensus       116 wlL~~l~~~~~~~EL~~~~k~l~~d-------prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~~R~~  187 (331)
T 3dss_A          116 WLLSRLPEPNWARELELCARFLEAD-------ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSC  187 (331)
T ss_dssp             HHHHHCSSCCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHHHHHH
T ss_pred             HHHhccCcccHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHHHHHH
Confidence            77777774  789999999999876       5677888888778888888 5899999999888753 46777776655


Q ss_pred             HHhcc--------------CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-----------CChhHHHHHHHHHHH
Q 040261          207 GFCYA--------------NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN-----------GKMDEASRLLELMIQ  261 (343)
Q Consensus       207 ~~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~  261 (343)
                      .+.+.              +.++++++.+....... +-|...|+.+-..+.+.           +.++++++.++++.+
T Consensus       188 ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle  266 (331)
T 3dss_A          188 LLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQE  266 (331)
T ss_dssp             HHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHh
Confidence            55443              45788888888888764 45677776555555544           346677788888877


Q ss_pred             cCCCCCH-HHHHHHH---HHHhcCCchHHHHHHHHHHHhC
Q 040261          262 IGVRPDA-SVYNTLM---DGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       262 ~~~~~~~-~~~~~l~---~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ..  |+. -.+..++   ......+..+++...+.++.+.
T Consensus       267 ~~--pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          267 LE--PENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HC--TTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             hC--cccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            63  332 2222211   1222456667777777777764

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.82  E-value=1.3e-07  Score=64.30  Aligned_cols=107  Identities=9%  Similarity=0.034  Sum_probs=85.2

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--cc----HHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PD----AVTF   90 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~   90 (343)
                      ..++..++..+.+.|++++|++.|++.++.. |.+...|..+..++.+.|++++|++.+++.++....  ++    ..+|
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            4568889999999999999999999988865 456778999999999999999999999998864311  11    2367


Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHH
Q 040261           91 TSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYT  126 (343)
Q Consensus        91 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  126 (343)
                      ..+..++...|++++|++.|++....  .|++....
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHH
Confidence            77788888899999999999998875  45555443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.82  E-value=3.6e-08  Score=68.61  Aligned_cols=100  Identities=12%  Similarity=-0.014  Sum_probs=80.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...+..+...+.+.|++++|...|++..... +.+...|..+..++...|++++|...|++.....+ .+...+..+.
T Consensus        16 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg   93 (142)
T 2xcb_A           16 DTLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDI-NEPRFPFHAA   93 (142)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHH
Confidence            356677778888888899999999998887755 45677888888888888999999999988888753 3567777788


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhc
Q 040261           95 KGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .++...|++++|.+.|++..+.
T Consensus        94 ~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           94 ECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh
Confidence            8888889999999888888765

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.81  E-value=3.1e-07  Score=61.14  Aligned_cols=111  Identities=10%  Similarity=-0.027  Sum_probs=89.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      .+..+..+...+...|++++|...|+...... +.+...+..+..++...|++++|...+++..+... .+...+..+..
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~   80 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAA   80 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHHH
Confidence            45678888999999999999999999988754 44677888888999999999999999999988743 36778888889


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      ++...|++++|.+.+++..+.+.. +...+..+.
T Consensus        81 ~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~  113 (118)
T 1elw_A           81 ALEFLNRFEEAKRTYEEGLKHEAN-NPQLKEGLQ  113 (118)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHH
Confidence            999999999999999998877433 444444433

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.79  E-value=1.5e-05  Score=67.46  Aligned_cols=125  Identities=10%  Similarity=0.104  Sum_probs=89.9

Q ss_pred             chHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccC-cHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          164 ITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAN-DWNEAKCLFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       164 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      ..|...+....+.++.+.|..+|++. ... ..+...|......-...+ +.+.|..+|+...+.. +-+...+...+..
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~-~~~~~~~~~yid~  363 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH-PDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            45666666666788899999999999 321 224444443332222233 6999999999998863 2234455667777


Q ss_pred             HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          243 LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       243 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      ....|+.+.|..+|+++.     .....|...+..=...|+.+.+..++++..+
T Consensus       364 e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          364 LLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            788899999999999972     3577888888777788999999998887763

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.79  E-value=6.9e-08  Score=67.15  Aligned_cols=100  Identities=11%  Similarity=-0.127  Sum_probs=87.1

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      +...+..+...+.+.|++++|...|+++....+ .+...|..+..++.+.|++++|+..|++.....+. +...+..+..
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~   94 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLDH-YDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-EPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHHHHH
Confidence            445677788889999999999999999998753 37888889999999999999999999999988644 6677888999


Q ss_pred             HHHhcCChHHHHHHHHHHHccC
Q 040261          131 GLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ++...|++++|...|++.....
T Consensus        95 ~~~~~g~~~~A~~~~~~al~~~  116 (142)
T 2xcb_A           95 CHLQLGDLDGAESGFYSARALA  116 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999998754

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.78  E-value=2e-07  Score=61.48  Aligned_cols=97  Identities=9%  Similarity=-0.043  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCc--cHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMR--DVFSYGILIN  311 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~  311 (343)
                      ..+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...+++..+.. +.  +...+..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~   84 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKAD   84 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHH
Confidence            344445555555555555555555555543 3344555555555666666666666666555542 22  3455555556


Q ss_pred             HHHhc-CChHHHHHHHHHHHhC
Q 040261          312 GYCKN-KEIEGALSLYSEMLSK  332 (343)
Q Consensus       312 ~~~~~-~~~~~a~~~~~~~~~~  332 (343)
                      .+... |++++|.+.+++....
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           85 ALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHhCCHHHHHHHHHHHhhc
Confidence            66666 6666666666666544

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=6.3e-07  Score=62.49  Aligned_cols=113  Identities=12%  Similarity=0.035  Sum_probs=92.3

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD----LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      |.+...+..+...+.+.|++++|...|++..+..  |+    ...+..+..++...|++++|...+++..+... .+...
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~  101 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDG-GDVKA  101 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTS-CCHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCc-cCHHH
Confidence            3567889999999999999999999999998754  55    67888888999999999999999999988743 36778


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      +..+..++...|++++|.+.|++..+.... +...+..+..
T Consensus       102 ~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~  141 (148)
T 2dba_A          102 LYRRSQALEKLGRLDQAVLDLQRCVSLEPK-NKVFQEALRN  141 (148)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCSS-CHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHH
Confidence            888999999999999999999999887432 4444444433

>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=98.76  E-value=8.9e-08  Score=65.24  Aligned_cols=113  Identities=12%  Similarity=0.069  Sum_probs=91.4

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--cc----HHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PD----AVT   89 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~   89 (343)
                      ....+..+...+...|++++|...|++..... +.+...+..+..++...|++++|...+++.......  ++    ..+
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~   81 (131)
T 1elr_A            3 QALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKA   81 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHH
Confidence            45678889999999999999999999988765 456778888999999999999999999998875321  11    667


Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING  131 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  131 (343)
                      +..+..++...|++++|.+.+++..+..  |+......+..+
T Consensus        82 ~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~  121 (131)
T 1elr_A           82 YARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQA  121 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHHH
Confidence            8888899999999999999999998864  455555544443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.76  E-value=4.8e-07  Score=61.29  Aligned_cols=95  Identities=14%  Similarity=0.072  Sum_probs=55.8

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      .+......+.+.|++++|...+++..+.. +.+...+..+..++.+.|++++|...+++.++.. +.+...+..+..++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            34445555556666666666666665542 3345555566666666666666666666666554 334555666666666


Q ss_pred             cCCchHHHHHHHHHHHh
Q 040261          280 LTGRVNRAKELFVSMES  296 (343)
Q Consensus       280 ~~~~~~~a~~~~~~~~~  296 (343)
                      ..|++++|...+++..+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            66666666666665554

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.76  E-value=7.7e-07  Score=59.17  Aligned_cols=97  Identities=11%  Similarity=0.033  Sum_probs=54.0

Q ss_pred             hhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040261          199 VTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGF  278 (343)
Q Consensus       199 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  278 (343)
                      ..+..+...+...|++++|...++...+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+..++
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            334445555555566666666665555542 2244555555555556666666666666655543 33455555555666


Q ss_pred             hcCCchHHHHHHHHHHHhC
Q 040261          279 CLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...|++++|...+++..+.
T Consensus        83 ~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHHhhHHHHHHHHHHHHHc
Confidence            6666666666666665554

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.75  E-value=3.2e-07  Score=63.19  Aligned_cols=100  Identities=14%  Similarity=0.026  Sum_probs=69.7

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...+..+...+.+.|++++|...|+...... +.+...+..+..++...|++++|...+++..+... .+...+..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHHH
Confidence            566777777777777777777777777776654 34566677777777777777777777777776542 2556666677


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhc
Q 040261           95 KGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .++...|++++|...|++..+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            7777777777777777766654

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.73  E-value=5.9e-07  Score=61.81  Aligned_cols=100  Identities=9%  Similarity=-0.050  Sum_probs=80.0

Q ss_pred             CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          196 PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM  275 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  275 (343)
                      .+...+..+...+...|++++|...++...+.. +.+...+..+..++...|++++|...++++.+.. +.+...+..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            356777888888888888888888888888764 4456778888888888888888888888888875 45677888888


Q ss_pred             HHHhcCCchHHHHHHHHHHHhC
Q 040261          276 DGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       276 ~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .++...|++++|...|++..+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            8888888888888888887764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.73  E-value=2.7e-07  Score=65.86  Aligned_cols=101  Identities=10%  Similarity=-0.031  Sum_probs=87.8

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      .+...+..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|+..+++.++... .+...|..+.
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg   86 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDP-KYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHH
Confidence            456788899999999999999999999988765 44778899999999999999999999999998753 3678888899


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcC
Q 040261           95 KGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      .++...|++++|.+.|++..+..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC
Confidence            99999999999999999988764

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.72  E-value=4.2e-07  Score=67.13  Aligned_cols=98  Identities=16%  Similarity=0.031  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      ..+..+..++...|++++|...++++.+.. +.+...+..+..+|...|++++|...|++..+.. +.+...+..+..++
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            566667777778888888888888877764 4566777777778888888888888888777653 23556666677777


Q ss_pred             HhcCChHHHH-HHHHHHHhCC
Q 040261          314 CKNKEIEGAL-SLYSEMLSKG  333 (343)
Q Consensus       314 ~~~~~~~~a~-~~~~~~~~~~  333 (343)
                      ...++.+++. ..+..|...+
T Consensus       167 ~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          167 NKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHHHC-------------
T ss_pred             HHHHHHHHHHHHHHHHHhccc
Confidence            7777766666 5555555443

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.71  E-value=2.2e-07  Score=63.15  Aligned_cols=113  Identities=13%  Similarity=0.040  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchH
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITY  166 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  166 (343)
                      ...+..+...+.+.|++++|++.|++..+..+. +...|..+..+|...|++++|++.+++..+..+........-..+|
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            445677888888999999999999998887544 6778888999999999999999999988775311000000002356


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHH
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENINPDVVTYT  202 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  202 (343)
                      ..+..++...|++++|++.|++....  .|+.....
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHH
Confidence            66777788888888888888887664  34554433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.70  E-value=3.5e-06  Score=70.39  Aligned_cols=203  Identities=8%  Similarity=-0.003  Sum_probs=141.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHccCCCCCccccC----------CcchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCC
Q 040261          129 INGLCRTGHTIVALNLFEEMANGNGEFGVVCKP----------DAITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPD  197 (343)
Q Consensus       129 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~  197 (343)
                      ...+...|++++|.+.+..+.+..+........          ...++..+...|...|++++|.+.+..+...- ..++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            455677888888888888887765321100000          01236778999999999999999998875421 1111


Q ss_pred             h----hhHHHHHHHHhccCcHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHc--CC--
Q 040261          198 V----VTYTSLIRGFCYANDWNEAKCLFIEMMDQ----GVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQI--GV--  264 (343)
Q Consensus       198 ~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~--  264 (343)
                      .    ...+.+-..+...|+++.+..+++.....    +..+. ..++..+...+...|++++|..+++.+...  +.  
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~  170 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD  170 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhccc
Confidence            1    23344445566778999999998887643    32333 457788999999999999999999988653  11  


Q ss_pred             -CCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCcc--HHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          265 -RPDASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMRD--VFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       265 -~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                       +....++..++..|...|++++|...+++....    +.++.  ...+..+...+...|++++|...|.+...
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          171 KPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             STHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence             122467888999999999999999999877542    21111  24566667778889999999988877754

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.69  E-value=4.2e-07  Score=64.87  Aligned_cols=101  Identities=11%  Similarity=-0.028  Sum_probs=89.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      .+...+..+...+.+.|++++|...|++.++... .+...|..+..++.+.|++++|+..+++..+.... +...+..+.
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg   86 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIAP-ANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHH
Confidence            3556788889999999999999999999998753 37888999999999999999999999999988544 688899999


Q ss_pred             HHHHhcCChHHHHHHHHHHHccC
Q 040261          130 NGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       130 ~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      .++...|++++|...|++..+..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC
Confidence            99999999999999999998864

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.69  E-value=4.4e-07  Score=61.04  Aligned_cols=93  Identities=13%  Similarity=-0.013  Sum_probs=58.7

Q ss_pred             HHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhc
Q 040261          237 NVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKN  316 (343)
Q Consensus       237 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  316 (343)
                      ..+...+.+.|++++|...++++++.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+..++...
T Consensus        21 ~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           21 MEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc
Confidence            344555666666666766666666654 4456666666666666677777777776666543 22455666666666667


Q ss_pred             CChHHHHHHHHHHHh
Q 040261          317 KEIEGALSLYSEMLS  331 (343)
Q Consensus       317 ~~~~~a~~~~~~~~~  331 (343)
                      |++++|+..+++.++
T Consensus        99 g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           99 HNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHH
Confidence            777777777766664

>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=98.67  E-value=4.7e-07  Score=61.53  Aligned_cols=108  Identities=14%  Similarity=0.140  Sum_probs=59.2

Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCC--CCC----HHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGV--RPD----ASVYNT  273 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~----~~~~~~  273 (343)
                      .+..+...+...|++++|...++...+.. +.+...+..+...+...|++++|...++++.+...  .++    ..++..
T Consensus         6 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHH
Confidence            34445555555666666666666655542 33445555556666666666666666666555421  111    455566


Q ss_pred             HHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHH
Q 040261          274 LMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILI  310 (343)
Q Consensus       274 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  310 (343)
                      +...+...|++++|...+++..+.  .|+......+.
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~  119 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKCQ  119 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHHH
Confidence            666666666666666666666654  24444443333

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.67  E-value=3.5e-07  Score=61.54  Aligned_cols=96  Identities=9%  Similarity=-0.125  Sum_probs=75.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      .+..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|+..+++.++..+. +...+..+..++.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~la~~~~   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHT   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH
Confidence            45667778888888888888888887754 446777888888888888888888888888876533 5667777888888


Q ss_pred             hcCcHHHHHHHHHHHHhc
Q 040261           99 AESRIMEAAALFTKLRAF  116 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~  116 (343)
                      ..|++++|+..+++..+.
T Consensus        97 ~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            888888888888887765

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.66  E-value=1.8e-06  Score=72.16  Aligned_cols=22  Identities=9%  Similarity=-0.011  Sum_probs=13.7

Q ss_pred             HHHHhcCCcchHHHHHHHHHHc
Q 040261           60 NCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      +.+.+.|++++|.+.|..+.+.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~   33 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDK   33 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHS
T ss_pred             HHHHHCCCHHHHHHHHHHHHhh
Confidence            3455666666666666666654

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.63  E-value=1.9e-06  Score=59.93  Aligned_cols=100  Identities=13%  Similarity=-0.050  Sum_probs=87.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc----HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHH
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD----AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTY  125 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  125 (343)
                      .+...+..+...+...|++++|.+.|++..+..  |+    ...+..+..++...|++++|++.+++..+.... +...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~  102 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-DVKAL  102 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-CHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-CHHHH
Confidence            466788889999999999999999999998864  44    678888899999999999999999999887433 67788


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261          126 TTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       126 ~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      ..+..++...|++++|...+++.....
T Consensus       103 ~~~a~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A          103 YRRSQALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            899999999999999999999998864

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.62  E-value=9.5e-08  Score=80.71  Aligned_cols=126  Identities=8%  Similarity=-0.043  Sum_probs=100.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGL   97 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~   97 (343)
                      ..+..+...+.+.|++++|++.|++..+.. +.+...|..+..++.+.|++++|.+.+++..+... .+...+..+..++
T Consensus         7 ~~~~~lg~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~~   84 (477)
T 1wao_1            7 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASN   84 (477)
T ss_dssp             TTSSSSSSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHH
Confidence            345556667788999999999999998864 44688999999999999999999999999998753 3678899999999


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH--HHhcCChHHHHHHHH
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLING--LCRTGHTIVALNLFE  146 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  146 (343)
                      ...|++++|++.+++..+.... +...+..+..+  +.+.|++++|.+.++
T Consensus        85 ~~~g~~~eA~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           85 MALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHTCHHHHHHHHHHHHHHSTT-CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999887433 34455555555  888899999999988

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.57  E-value=3.6e-06  Score=57.05  Aligned_cols=97  Identities=13%  Similarity=0.010  Sum_probs=79.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCH---HHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc---HHHHHH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDL---YTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD---AVTFTS   92 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~   92 (343)
                      .+..+...+.+.|++++|...|+.+.+.. +.+.   ..+..+..++...|++++|...++++.+..+. +   ...+..
T Consensus         4 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~   81 (129)
T 2xev_A            4 TAYNVAFDALKNGKYDDASQLFLSFLELY-PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLK   81 (129)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHH
Confidence            45667788889999999999999988754 2233   47778888999999999999999999886433 3   566778


Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      +..++...|++++|...|+++.+..
T Consensus        82 la~~~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           82 LGLSQYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            8889999999999999999998874

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.54  E-value=1e-06  Score=62.30  Aligned_cols=132  Identities=12%  Similarity=0.100  Sum_probs=76.5

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcC----CCC-CHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQ-PN----VVTFNVIMNELCKNGKMDEASRLLELMIQIG----VRP-DASV  270 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~~~  270 (343)
                      +..+...+...|++++|...+++..+.... ++    ..++..+...+...|++++|...+++..+..    .++ ....
T Consensus        12 ~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~   91 (164)
T 3ro3_A           12 FGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQS   91 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHH
Confidence            444444555555555555555554432100 01    1345556666667777777777776655431    001 1345


Q ss_pred             HHHHHHHHhcCCchHHHHHHHHHHHhC----CCC-ccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          271 YNTLMDGFCLTGRVNRAKELFVSMESN----GCM-RDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       271 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      +..+...+...|++++|...+++..+.    +.. .....+..+...+...|++++|.+.+++..+.
T Consensus        92 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  158 (164)
T 3ro3_A           92 CYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  158 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            666677777778888887777766532    111 12345667777888888888888888877643

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.53  E-value=9.3e-07  Score=74.32  Aligned_cols=130  Identities=9%  Similarity=0.002  Sum_probs=103.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC---------------HHHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD---------------LYTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      ....|..+...+.+.|++++|+..|++..+.. +.+               ...|..+..++.+.|++++|+..+++.++
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~-p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  345 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL-EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG  345 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh-cccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            45678888999999999999999999988743 222               57888899999999999999999999998


Q ss_pred             cCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHH-HHHHH
Q 040261           81 SCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALN-LFEEM  148 (343)
Q Consensus        81 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~-~~~~~  148 (343)
                      ... .+...|..+..++...|++++|...|++..+.... +...+..+..++.+.++.+++.+ .+..|
T Consensus       346 ~~p-~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          346 LDS-ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQ-NKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             HST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCC-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            753 36788888999999999999999999999887433 55677888888888888776653 34443

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.53  E-value=6.3e-07  Score=75.71  Aligned_cols=119  Identities=12%  Similarity=0.049  Sum_probs=69.9

Q ss_pred             HHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchH
Q 040261          206 RGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVN  285 (343)
Q Consensus       206 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  285 (343)
                      ..+.+.|++++|...+++..+.. +.+...+..+..++.+.|++++|...++++.+.. +.+...+..+..+|...|+++
T Consensus        14 ~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           14 NDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             SSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence            34455666677776666666652 3345666666666777777777777777766654 345566666666777777777


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHHH--HHhcCChHHHHHHHH
Q 040261          286 RAKELFVSMESNGCMRDVFSYGILING--YCKNKEIEGALSLYS  327 (343)
Q Consensus       286 ~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  327 (343)
                      +|.+.+++..+.. +.+...+..+..+  +.+.|++++|++.++
T Consensus        92 eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           92 AALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            7777777666542 1233344444444  666677777777666

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.52  E-value=2.8e-06  Score=71.41  Aligned_cols=150  Identities=10%  Similarity=-0.004  Sum_probs=109.0

Q ss_pred             ChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc--------------HHHHHHHHHHH
Q 040261           32 HYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPD--------------AVTFTSLIKGL   97 (343)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~   97 (343)
                      ++++|...|+...... +.....+..+...+.+.|+++.|...|++.++......              ...|..+..++
T Consensus       249 ~~~~A~~~~~~~~~~~-~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~  327 (457)
T 1kt0_A          249 SFEKAKESWEMDTKEK-LEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCY  327 (457)
T ss_dssp             EEECCCCGGGSCHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccCcchhhcCHHHH-HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555554333211 12345677888889999999999999999887543221              57788888899


Q ss_pred             hhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261           98 CAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus        98 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      .+.|++++|+..+++..+.... +...+..+..+|...|++++|...|+++.+..       +.+..++..+..++.+.+
T Consensus       328 ~~~g~~~~A~~~~~~al~~~p~-~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-------P~~~~a~~~l~~~~~~~~  399 (457)
T 1kt0_A          328 LKLREYTKAVECCDKALGLDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-------PQNKAARLQISMCQKKAK  399 (457)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----------CHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHH
Confidence            9999999999999998887544 67788888999999999999999999998875       455678888888888888


Q ss_pred             ChHHHHH-HHHHhh
Q 040261          178 FVDKAKE-LFLKMK  190 (343)
Q Consensus       178 ~~~~a~~-~~~~~~  190 (343)
                      +.+++.+ .+..|.
T Consensus       400 ~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          400 EHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHH
Confidence            8877664 344443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.49  E-value=1.2e-06  Score=61.99  Aligned_cols=135  Identities=15%  Similarity=0.006  Sum_probs=103.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCC-CC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC---C-c-c
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLF-PD----LYTYNILINCFCKMGRVSPGFVVLGRILRSCF---T-P-D   86 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~-~-~   86 (343)
                      ..++..+...+...|++++|...+++..+.... ++    ..++..+...+...|++++|.+.+++..+...   . + .
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            457888999999999999999999987653211 11    13678888999999999999999999875321   1 1 1


Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhc----CCC-CCHHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAF----GCK-PDVFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      ...+..+...+...|++++|.+.+++..+.    +.. .....+..+...+...|++++|.+.+++..+.
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  158 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  158 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            456777888899999999999999887653    111 12346777888999999999999999987754

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.49  E-value=2.5e-06  Score=60.63  Aligned_cols=100  Identities=13%  Similarity=0.113  Sum_probs=76.6

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhC--------C---------CCCCHHHHHHHHHHHHhcCCcchHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSI--------G---------LFPDLYTYNILINCFCKMGRVSPGFVVLGRI   78 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------~---------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~   78 (343)
                      ....+......+.+.|++++|+..|++....        .         -+.+...|..+..++.+.|++++|+..+++.
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~a   89 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEV   89 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3567888999999999999999999998764        1         0122356777777888888888888888888


Q ss_pred             HHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        79 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      ++.. +.+...|..+..++...|++++|...|++..+.
T Consensus        90 l~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           90 LKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            7764 335677777888888888888888888887776

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.49  E-value=1.8e-06  Score=70.28  Aligned_cols=124  Identities=10%  Similarity=-0.030  Sum_probs=98.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhC---------------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSI---------------GLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      ..+..+...+.+.|++++|+..|++..+.               --+.+...|..+..++.+.|++++|++.+++.++..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            45788889999999999999999988761               112345678889999999999999999999999865


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALN  143 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  143 (343)
                      . .+...+..+..++...|++++|++.|++..+.... +...+..+..++...++.+++.+
T Consensus       304 p-~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~-~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 P-SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             T-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             c-hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHH
Confidence            3 36788888999999999999999999999887433 56667777777777666665543

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.49  E-value=8.6e-06  Score=55.15  Aligned_cols=92  Identities=10%  Similarity=0.062  Sum_probs=48.6

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC---HHHHHHHHHH
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGVQPNV---VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD---ASVYNTLMDG  277 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~  277 (343)
                      +...+...|++++|...++.+.+.. +.+.   ..+..+..++...|++++|...++++.+.. +.+   ...+..+..+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELY-PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-PTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTSTTHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHH
Confidence            3444455555555555555555542 1112   344455555556666666666666655543 222   3445555555


Q ss_pred             HhcCCchHHHHHHHHHHHhC
Q 040261          278 FCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       278 ~~~~~~~~~a~~~~~~~~~~  297 (343)
                      +...|++++|...|+++.+.
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHH
Confidence            66666666666666665553

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.48  E-value=5.7e-07  Score=60.08  Aligned_cols=85  Identities=14%  Similarity=0.021  Sum_probs=36.1

Q ss_pred             cCChhHHHHHHHHhHhCC--CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHH
Q 040261           30 NKHYDTVLSLFKRLNSIG--LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAA  107 (343)
Q Consensus        30 ~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  107 (343)
                      .|++++|+..|++..+.+  -+.+...+..+..++...|++++|...+++.++..+. +...+..+..++...|++++|+
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHHH
Confidence            344455555555544432  0112234444444444445555555555544443321 3344444444444444444444


Q ss_pred             HHHHHHHh
Q 040261          108 ALFTKLRA  115 (343)
Q Consensus       108 ~~~~~~~~  115 (343)
                      ..+++...
T Consensus        82 ~~~~~al~   89 (117)
T 3k9i_A           82 ELLLKIIA   89 (117)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44444443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.47  E-value=8.2e-07  Score=59.28  Aligned_cols=106  Identities=9%  Similarity=-0.059  Sum_probs=77.2

Q ss_pred             hcCCcchHHHHHHHHHHcC--CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHH
Q 040261           64 KMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVA  141 (343)
Q Consensus        64 ~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  141 (343)
                      ..|++++|+..|++.++.+  -+.+...+..+..++...|++++|++.+++..+..+. +...+..+..++...|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHH
Confidence            4578888999998888763  1234667788888888899999999999998887544 577788888889999999999


Q ss_pred             HHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261          142 LNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      ...+++.....+     ..+....|...+..+..
T Consensus        81 ~~~~~~al~~~p-----~~~~~~~~~~ai~~~~~  109 (117)
T 3k9i_A           81 VELLLKIIAETS-----DDETIQSYKQAILFYAD  109 (117)
T ss_dssp             HHHHHHHHHHHC-----CCHHHHHTHHHHHHHTT
T ss_pred             HHHHHHHHHhCC-----CcHHHHHHHHHHHHHHH
Confidence            998888776654     34556666666666554

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.45  E-value=3.9e-05  Score=66.15  Aligned_cols=172  Identities=9%  Similarity=-0.071  Sum_probs=120.4

Q ss_pred             chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc----------HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC--
Q 040261           69 SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR----------IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG--  136 (343)
Q Consensus        69 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--  136 (343)
                      ++|++.+++++..++. +..+|+.--.++...|+          ++++++.++++.+..++ +..+|..-..++.+.+  
T Consensus        46 eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l~~l~~~  123 (567)
T 1dce_A           46 ESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPEP  123 (567)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCSSC
T ss_pred             HHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccc
Confidence            4567777777776433 45566665555555555          77888888888777655 6777777777777777  


Q ss_pred             ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC-ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc-----
Q 040261          137 HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG-FVDKAKELFLKMKDENINPDVVTYTSLIRGFCY-----  210 (343)
Q Consensus       137 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----  210 (343)
                      +++++++.++++.+.+       +.+..+|+.-..++.+.| .++++++.++++.+.++ -+...|+.....+.+     
T Consensus       124 ~~~~el~~~~k~l~~d-------~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p-~n~saW~~r~~ll~~l~~~~  195 (567)
T 1dce_A          124 NWARELELCARFLEAD-------ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQP  195 (567)
T ss_dssp             CHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCC
T ss_pred             cHHHHHHHHHHHHhhc-------cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCC-CCccHHHHHHHHHHhhcccc
Confidence            5588888888888775       456677777777777777 77888888877777643 356666665555444     


Q ss_pred             ---------cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhH
Q 040261          211 ---------ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDE  251 (343)
Q Consensus       211 ---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  251 (343)
                               .+.++++.+.+....... +-+...|..+...+.+.++.++
T Consensus       196 ~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          196 DSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCCCSC
T ss_pred             cccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCCccc
Confidence                     256889999999888874 4467788888777777766443

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.43  E-value=1.6e-06  Score=69.74  Aligned_cols=146  Identities=12%  Similarity=0.020  Sum_probs=76.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                      +..+...+.+.|++++|...|++.....  |+..       .+...++..++...+.          ...|..+..++.+
T Consensus       182 ~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~-------~~~~~~~~~~~~~~l~----------~~~~~nla~~~~~  242 (338)
T 2if4_A          182 RKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDF-------MFQLYGKYQDMALAVK----------NPCHLNIAACLIK  242 (338)
T ss_dssp             HHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHH-------HHTCCHHHHHHHHHHH----------THHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccch-------hhhhcccHHHHHHHHH----------HHHHHHHHHHHHH
Confidence            4444555556666666666666655432  2221       1122333333322211          1367888899999


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHH-HHhcCChHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILING-YCKNKEIEGALS  324 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~  324 (343)
                      .|++++|+..+++.++.. +.+...+..+..+|...|++++|...|++..+.. +.+...+..+... ....+..+.+.+
T Consensus       243 ~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~~~~~~~a~~  320 (338)
T 2if4_A          243 LKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQEKALYQKQKE  320 (338)
T ss_dssp             TTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-----------------------------
T ss_pred             cCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999875 5578899999999999999999999999987753 2234455555544 334567788888


Q ss_pred             HHHHHHhC
Q 040261          325 LYSEMLSK  332 (343)
Q Consensus       325 ~~~~~~~~  332 (343)
                      .|++|...
T Consensus       321 ~~~~~l~~  328 (338)
T 2if4_A          321 MYKGIFKG  328 (338)
T ss_dssp             --------
T ss_pred             HHHHhhCC
Confidence            99988854

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.43  E-value=3.4e-05  Score=66.50  Aligned_cols=174  Identities=11%  Similarity=-0.024  Sum_probs=139.1

Q ss_pred             CChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC----------cchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc
Q 040261           31 KHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR----------VSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE  100 (343)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  100 (343)
                      ...++|++.++.+...+ +-+..+|+.--.++...|+          ++++++.++.+.+..++ +..+|+.-.-.+.+.
T Consensus        43 ~~~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l~~l  120 (567)
T 1dce_A           43 ELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRL  120 (567)
T ss_dssp             CCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHc
Confidence            34568899999999865 3456678877777777777          89999999999988644 788898888888888


Q ss_pred             C--cHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC-ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc-
Q 040261          101 S--RIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG-HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE-  176 (343)
Q Consensus       101 ~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  176 (343)
                      +  +++++++.++++.+.... +..+|+.....+.+.| .++++++.++++.+.+       +.+..+|+....++.+. 
T Consensus       121 ~~~~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-------p~n~saW~~r~~ll~~l~  192 (567)
T 1dce_A          121 PEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-------FSNYSSWHYRSCLLPQLH  192 (567)
T ss_dssp             SSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-------CCCHHHHHHHHHHHHHHS
T ss_pred             ccccHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-------CCCccHHHHHHHHHHhhc
Confidence            9  779999999999998765 8889988888888888 8999999999998875       56777888777776653 


Q ss_pred             -------------CChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHH
Q 040261          177 -------------GFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWN  215 (343)
Q Consensus       177 -------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  215 (343)
                                   +.++++++.+++..... +-+...|...-..+.+.++.+
T Consensus       193 ~~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~~~  243 (567)
T 1dce_A          193 PQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEPHD  243 (567)
T ss_dssp             CCCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCCCS
T ss_pred             ccccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCCcc
Confidence                         55789999998887754 346778888777777766633

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.41  E-value=4e-06  Score=68.27  Aligned_cols=124  Identities=10%  Similarity=-0.089  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHc---------------CCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           53 YTYNILINCFCKMGRVSPGFVVLGRILRS---------------CFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        53 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      ..+..+...+.+.|++++|...|++.++.               .-+.+..+|..+..++.+.|++++|++.+++..+..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            35777888899999999999999998861               112246788889999999999999999999999875


Q ss_pred             CCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHH
Q 040261          118 CKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKE  184 (343)
Q Consensus       118 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  184 (343)
                      .. +...+..+..+|...|++++|...++++.+..       +.+...+..+..++...++.+++.+
T Consensus       304 p~-~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-------P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 PS-NTKALYRRAQGWQGLKEYDQALADLKKAQEIA-------PEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ch-hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            43 67888999999999999999999999998865       3456667777777777776666543

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.40  E-value=2.3e-05  Score=53.86  Aligned_cols=111  Identities=10%  Similarity=-0.079  Sum_probs=59.5

Q ss_pred             CChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHH
Q 040261          177 GFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEA  252 (343)
Q Consensus       177 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a  252 (343)
                      +++++|+++|++..+.+. |+.  .  +...|...+..++|...+++..+.|   +...+..+...|..    .+++++|
T Consensus         9 ~d~~~A~~~~~~aa~~g~-~~a--~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNE-MFG--C--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTC-TTH--H--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHcCCC-Hhh--h--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHH
Confidence            345566666666655541 122  2  4455555555555666666655543   34445555555555    5566666


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchHHHHHHHHHHHhCC
Q 040261          253 SRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVNRAKELFVSMESNG  298 (343)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  298 (343)
                      ..+|++..+.|   +...+..|...|..    .+++++|...|++..+.|
T Consensus        81 ~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           81 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            66666665544   34444555555555    555666666665555544

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.38  E-value=8.6e-06  Score=57.79  Aligned_cols=64  Identities=9%  Similarity=0.067  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          233 VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       233 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...|..+..++.+.|++++|...++++++.. +.+...|..+..+|...|++++|...|++..+.
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            3456666777777777777777777777764 445667777777777777777777777777664

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.38  E-value=6.6e-06  Score=57.19  Aligned_cols=61  Identities=10%  Similarity=0.001  Sum_probs=34.6

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC--------H-----HHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD--------L-----YTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      ..+......+.+.|++++|+..|++.++..  |+        .     ..|..+..++.+.|++++|+..+++.++
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~--p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~   85 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEIS--HTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   85 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--TTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345666677777778888888877776633  22        1     1444444444444555554444444444

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.37  E-value=1.9e-06  Score=69.39  Aligned_cols=133  Identities=11%  Similarity=0.043  Sum_probs=81.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHH------------------HHHHHHHHHHhcCCcchHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLY------------------TYNILINCFCKMGRVSPGFVVLGR   77 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~   77 (343)
                      ....+..+...+.+.|++++|+..|++.....  |+..                  .|..+..++.+.|++++|...+++
T Consensus       178 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~  255 (338)
T 2if4_A          178 AADRRKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNI  255 (338)
T ss_dssp             HHHHHHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34567788888999999999999999987643  4433                  788888899999999999999999


Q ss_pred             HHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH-HHhcCChHHHHHHHHHHHccC
Q 040261           78 ILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING-LCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        78 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      .++.. +.+...|..+..++...|++++|...|++..+.... +...+..+... ....+..+.+...|..+....
T Consensus       256 al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~-~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~~  329 (338)
T 2if4_A          256 VLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPD-DKAIRRELRALAEQEKALYQKQKEMYKGIFKGK  329 (338)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------------------
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            98875 336788888999999999999999999998876322 34444444444 233456677777888776654

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.31  E-value=5.8e-05  Score=51.82  Aligned_cols=113  Identities=11%  Similarity=0.009  Sum_probs=95.9

Q ss_pred             cCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchHH
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVNR  286 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~  286 (343)
                      .+++++|...+++..+.| .|...    +...|...+..++|..+|++..+.|   +...+..|...|..    .+++++
T Consensus         8 ~~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~   79 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRK   79 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHH
T ss_pred             ccCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHH
Confidence            357899999999999987 34433    7777777888999999999999976   56778888888887    789999


Q ss_pred             HHHHHHHHHhCCCCccHHHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 040261          287 AKELFVSMESNGCMRDVFSYGILINGYCK----NKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       287 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~  334 (343)
                      |...|++..+.|   ++..+..|...|..    .+++++|.++|++..+.|.
T Consensus        80 A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           80 AAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            999999999875   67788888999988    8999999999999998874

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.29  E-value=2e-05  Score=54.83  Aligned_cols=93  Identities=11%  Similarity=-0.053  Sum_probs=51.5

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCC------C-----HHHHHHHHHHHhcCCchHHHHHHHHHHHhC-----CCCc-
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVRP------D-----ASVYNTLMDGFCLTGRVNRAKELFVSMESN-----GCMR-  301 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~~------~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~-  301 (343)
                      ....+.+.|++++|+..|++.++.....      +     ...|..+..++.+.|++++|+..+++..+.     .+.| 
T Consensus        17 ~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd   96 (159)
T 2hr2_A           17 DAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQD   96 (159)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTST
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCc
Confidence            3344444555555555555554432110      1     225666666666666666666666666553     0023 


Q ss_pred             cHHHH----HHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          302 DVFSY----GILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       302 ~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      +...|    .....++...|++++|+..|++.++
T Consensus        97 ~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           97 EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            34455    6666777777777777777776654

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.27  E-value=7.9e-06  Score=68.76  Aligned_cols=126  Identities=10%  Similarity=-0.004  Sum_probs=95.8

Q ss_pred             HHhccCcHHHHHHHHHHHHHcC---C---CC-CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc-----CC-CCC-HHHHH
Q 040261          207 GFCYANDWNEAKCLFIEMMDQG---V---QP-NVVTFNVIMNELCKNGKMDEASRLLELMIQI-----GV-RPD-ASVYN  272 (343)
Q Consensus       207 ~~~~~~~~~~a~~~~~~~~~~~---~---~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~-~~~~~  272 (343)
                      .+...|++++|..++++.++..   +   .| ...+++.|..+|...|++++|..++++..+.     |. .|+ ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3567899999999998887541   1   12 2467889999999999999999999988653     21 233 45788


Q ss_pred             HHHHHHhcCCchHHHHHHHHHHHh-----CCCC-c-cHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          273 TLMDGFCLTGRVNRAKELFVSMES-----NGCM-R-DVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       273 ~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .|...|..+|++++|..++++..+     .|.. | ...+...+..++...+.+++|..+|+++.+.
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999987754     2311 2 2345566777888999999999999998763

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.21  E-value=2.3e-06  Score=56.31  Aligned_cols=93  Identities=12%  Similarity=-0.032  Sum_probs=63.6

Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc-------HH
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD-------VF  304 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-------~~  304 (343)
                      +...+..+...+...|++++|...+++..+.. +.+...+..+..++...|++++|...+++..+..  |+       ..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~   79 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT--STAEHVAIRSK   79 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC--SSTTSHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCccHHHHHHH
Confidence            34556667777777888888888888777764 4466777777778888888888888888777653  33       44


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHH
Q 040261          305 SYGILINGYCKNKEIEGALSLYS  327 (343)
Q Consensus       305 ~~~~l~~~~~~~~~~~~a~~~~~  327 (343)
                      .+..+..++...|+++.|...++
T Consensus        80 ~~~~~~~~~~~~~~~~~a~~~~~  102 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPVVEVD  102 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCSSSSS
T ss_pred             HHHHHHHHHHHHHhHhhhHhHHH
Confidence            55556666666666666555443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.17  E-value=1.3e-05  Score=67.55  Aligned_cols=131  Identities=10%  Similarity=-0.078  Sum_probs=82.9

Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccC-CcchHHHHHHHHHhcCChHHHHHHHHHhhhC-----C--CCCChhhHH
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKP-DAITYSTITDGLCKEGFVDKAKELFLKMKDE-----N--INPDVVTYT  202 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~  202 (343)
                      .+...|++++|..++++..+.....-....| ...+++.+..+|...|++++|..++++..+.     |  .+....+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3567899999999998876543221111122 2457788888888899998888888775431     1  122245677


Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHc-----CC-CCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          203 SLIRGFCYANDWNEAKCLFIEMMDQ-----GV-QPN-VVTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       203 ~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                      .|...|...|++++|..++++..+.     |. .|+ ..+.+.+..++...+.+++|+.++.++.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777777788888887777766532     21 122 23344455566666667777777766654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=98.13  E-value=2.6e-05  Score=48.94  Aligned_cols=80  Identities=14%  Similarity=0.109  Sum_probs=45.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      +...+..+...+.+.|++++|...|++..+.. +.+...+..+..++...|++++|...+++..+..+ .+...+..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCHHHHHHHHH
Confidence            34556666666666667777766666665543 23455566666666666666666666666665432 13444444444


Q ss_pred             HH
Q 040261           96 GL   97 (343)
Q Consensus        96 ~~   97 (343)
                      ++
T Consensus        86 ~~   87 (91)
T 1na3_A           86 AK   87 (91)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.11  E-value=3.6e-05  Score=50.92  Aligned_cols=80  Identities=14%  Similarity=0.099  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHH
Q 040261          216 EAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       216 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      ++...++...+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+..++...|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4677788887763 4467788889999999999999999999999875 5567888899999999999999999999887


Q ss_pred             hC
Q 040261          296 SN  297 (343)
Q Consensus       296 ~~  297 (343)
                      +.
T Consensus        81 ~~   82 (115)
T 2kat_A           81 AA   82 (115)
T ss_dssp             HH
T ss_pred             Hh
Confidence            64

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.11  E-value=3.1e-05  Score=51.23  Aligned_cols=79  Identities=13%  Similarity=0.041  Sum_probs=37.8

Q ss_pred             HHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHH
Q 040261           35 TVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLR  114 (343)
Q Consensus        35 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  114 (343)
                      +|+..|++..+.. +.+...+..+..++...|++++|...+++..+... .+...|..+..++...|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDP-TYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444455444432 23344455555555555555555555555554431 134444445555555555555555555444


Q ss_pred             h
Q 040261          115 A  115 (343)
Q Consensus       115 ~  115 (343)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.10  E-value=3.7e-06  Score=55.22  Aligned_cols=64  Identities=13%  Similarity=0.062  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           87 AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        87 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      ...+..+...+...|++++|++.|++..+.... +...+..+..++...|++++|...+++....
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQ-NPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            334444555555555555555555555554322 4445555555555555555555555555554

>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=98.10  E-value=2e-05  Score=54.60  Aligned_cols=100  Identities=7%  Similarity=-0.006  Sum_probs=78.6

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcc----------hHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVS----------PGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~----------~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      ..+.+.+++|+..++...+.. +.+...|..+..++...++++          +|+..|++.++..+. +..+|..+..+
T Consensus        12 ~~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~a   89 (158)
T 1zu2_A           12 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNA   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHH
Confidence            345677899999999988866 557888988888888887764          999999999987533 67788889999


Q ss_pred             HhhcC-----------cHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           97 LCAES-----------RIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        97 ~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      |...|           ++++|++.|++..+.  .|+...|...+.
T Consensus        90 y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~  132 (158)
T 1zu2_A           90 YTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            88764           899999999999987  556555544443

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=98.05  E-value=9.1e-05  Score=46.32  Aligned_cols=79  Identities=16%  Similarity=0.169  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      ..+..+...+...|++++|...+++..+.. +.+...+..+..++...|++++|...+++..+.. +.+...+..+..++
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~   87 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAK   87 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            445555556666666666666666666553 3345556666666666666666666666665542 22344444444444


Q ss_pred             H
Q 040261          314 C  314 (343)
Q Consensus       314 ~  314 (343)
                      .
T Consensus        88 ~   88 (91)
T 1na3_A           88 Q   88 (91)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.98  E-value=3.8e-05  Score=49.39  Aligned_cols=66  Identities=17%  Similarity=0.131  Sum_probs=47.6

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261           14 PPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus        14 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      |.++.++..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|.+.+++.++
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3567777777777778888888888887777654 33456777777777777777777777777664

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.92  E-value=6.4e-05  Score=52.15  Aligned_cols=96  Identities=9%  Similarity=0.017  Sum_probs=53.9

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC----------hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK----------MDEASRLLELMIQIGVRPDASVYNTLMDGFCLT  281 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  281 (343)
                      +.+++|...++...+.. +.+...|..+..++...++          +++|+..|++.++.+ +.+...|..+..+|...
T Consensus        16 ~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld-P~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           16 LLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHh
Confidence            44555555555555542 3344455545555554443          346666666666654 33455666666666655


Q ss_pred             -----------CchHHHHHHHHHHHhCCCCccHHHHHHHHH
Q 040261          282 -----------GRVNRAKELFVSMESNGCMRDVFSYGILIN  311 (343)
Q Consensus       282 -----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  311 (343)
                                 |++++|.+.|++..+.  .|+...|...+.
T Consensus        94 g~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~  132 (158)
T 1zu2_A           94 AFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLE  132 (158)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             cccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence                       3677777777777764  465555544333

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.80  E-value=9.8e-05  Score=47.39  Aligned_cols=63  Identities=16%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHH
Q 040261           51 DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLR  114 (343)
Q Consensus        51 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  114 (343)
                      +...+..+..++...|++++|...|++.++..+. +...|..+..++...|++++|.+.+++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3445555555555555555555555555554322 34455555555555555555555555544

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.73  E-value=0.002  Score=51.47  Aligned_cols=134  Identities=7%  Similarity=-0.023  Sum_probs=92.6

Q ss_pred             CChhhHHHHHHHHHh--cC---ChhHHHHHHHHhHhCCCCCC-HHHHHHHHHHHHh---cCCcc--hH---HHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAK--NK---HYDTVLSLFKRLNSIGLFPD-LYTYNILINCFCK---MGRVS--PG---FVVLGRILR   80 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~--~~---~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~---~~~~~--~a---~~~~~~~~~   80 (343)
                      .+..+|...+.+...  .+   +..+|+.+|++..+..  |+ ...|..+..++..   .+...  ..   ...+.....
T Consensus       192 ~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lD--P~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a  269 (372)
T 3ly7_A          192 HRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSS--PEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVT  269 (372)
T ss_dssp             SSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHh
Confidence            688888888766543  33   3578999999998854  54 4455544444321   11111  11   111221111


Q ss_pred             -cCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           81 -SCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        81 -~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                       ...+.+..+|..+...+...|++++|...+++....+  |+...|..+...+.-.|++++|.+.+++....+
T Consensus       270 ~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~  340 (372)
T 3ly7_A          270 LPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLR  340 (372)
T ss_dssp             CGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             cccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence             1124567788887777777899999999999999985  788888888999999999999999999998854

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.63  E-value=0.0023  Score=51.07  Aligned_cols=65  Identities=9%  Similarity=-0.016  Sum_probs=37.0

Q ss_pred             CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          196 PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      .+...|..+...+...|++++|...++++...+  |+...|..+...+.-.|++++|...++++.+.
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL  339 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL  339 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            345555555544455566666666666666553  45555555555555666666666666666554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.47  E-value=0.00029  Score=44.89  Aligned_cols=59  Identities=10%  Similarity=0.094  Sum_probs=43.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLY-TYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      ....+.+.|++++|+..|++..+.. +.+.. .+..+..++...|++++|.+.|++..+..
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            4556677788888888888877654 33556 77777777888888888888888877764

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.44  E-value=0.00033  Score=44.63  Aligned_cols=57  Identities=19%  Similarity=0.263  Sum_probs=32.0

Q ss_pred             HHHHHhCCChhHHHHHHHHHHHcCCCCCHH-HHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          240 MNELCKNGKMDEASRLLELMIQIGVRPDAS-VYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       240 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      ...+...|++++|...++++.+.. +.+.. .+..+..+|...|++++|...|++..+.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            334455566666666666655543 33444 5555555666666666666666665554

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.42  E-value=0.00061  Score=56.41  Aligned_cols=87  Identities=8%  Similarity=-0.124  Sum_probs=55.8

Q ss_pred             hCCChhHHHHHHHHHHHc-----C-CCCC-HHHHHHHHHHHhcCCchHHHHHHHHHHHhC-----CC-Cc-cHHHHHHHH
Q 040261          245 KNGKMDEASRLLELMIQI-----G-VRPD-ASVYNTLMDGFCLTGRVNRAKELFVSMESN-----GC-MR-DVFSYGILI  310 (343)
Q Consensus       245 ~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~-~~~~~~~l~  310 (343)
                      ..|++++|+.++++..+.     | -.|+ ..+++.|..+|...|++++|..++++..+.     |. .| ...+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            346777777777776553     1 0122 356777777788888888887777766531     21 12 234577777


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 040261          311 NGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       311 ~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ..|...|++++|..++++.++
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            778888888888777777653

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.37  E-value=0.00074  Score=55.92  Aligned_cols=88  Identities=8%  Similarity=-0.096  Sum_probs=69.5

Q ss_pred             hccCcHHHHHHHHHHHHHc---CCCC---C-HHHHHHHHHHHHhCCChhHHHHHHHHHHHc-----C-CCCC-HHHHHHH
Q 040261          209 CYANDWNEAKCLFIEMMDQ---GVQP---N-VVTFNVIMNELCKNGKMDEASRLLELMIQI-----G-VRPD-ASVYNTL  274 (343)
Q Consensus       209 ~~~~~~~~a~~~~~~~~~~---~~~~---~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~-~~~~~~l  274 (343)
                      ...|++++|..++++.++.   -+.|   + ..+++.|..+|...|++++|+.++++..+.     | -.|+ ..+++.|
T Consensus       309 ~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nL  388 (433)
T 3qww_A          309 KHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKL  388 (433)
T ss_dssp             TTTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHH
Confidence            3467899999999987753   1122   2 467889999999999999999999988753     2 1233 4578899


Q ss_pred             HHHHhcCCchHHHHHHHHHHHh
Q 040261          275 MDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       275 ~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      ...|..+|++++|..++++..+
T Consensus       389 a~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          389 GRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhccCHHHHHHHHHHHHH
Confidence            9999999999999999988764

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.36  E-value=0.002  Score=44.25  Aligned_cols=84  Identities=14%  Similarity=0.041  Sum_probs=55.5

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC---ChhHHHHHHHHHHHcCCCC--CHHHHHHHHHHHhcCCchHH
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNG---KMDEASRLLELMIQIGVRP--DASVYNTLMDGFCLTGRVNR  286 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~  286 (343)
                      .....+.+.|.+..+.+ .++..+.-.+..++++.+   +.++++.+++...+.+ .|  +...+-.+.-+|.+.|++++
T Consensus        12 ~~l~~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~   89 (152)
T 1pc2_A           12 EDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEK   89 (152)
T ss_dssp             HHHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHH
Confidence            34555666666666655 356666666777777777   5557888887777764 23  24445555567778888888


Q ss_pred             HHHHHHHHHhC
Q 040261          287 AKELFVSMESN  297 (343)
Q Consensus       287 a~~~~~~~~~~  297 (343)
                      |.+.++.+.+.
T Consensus        90 A~~y~~~lL~i  100 (152)
T 1pc2_A           90 ALKYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            88888887774

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.34  E-value=0.0029  Score=39.66  Aligned_cols=68  Identities=18%  Similarity=0.192  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHHHHHHhCCC---hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCC
Q 040261          230 QPNVVTFNVIMNELCKNGK---MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNG  298 (343)
Q Consensus       230 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  298 (343)
                      +.+...+..+..++...++   .++|..++++..+.. +-+......+...+.+.|++++|...|+++.+..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            3455666666666654444   577777777777765 5556667777777777777777777777777653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.33  E-value=0.0018  Score=40.67  Aligned_cols=66  Identities=12%  Similarity=-0.034  Sum_probs=37.3

Q ss_pred             CChhhHHHHHHHHHhcCC---hhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           15 PPVCSFNILFGCLAKNKH---YDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      .++..+..+..++...++   .++|..++++..+.. +.+......+...+.+.|++++|...|+++.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            455556666655543333   456666666665543 334455555555666666666666666666554

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.29  E-value=0.0018  Score=53.75  Aligned_cols=89  Identities=11%  Similarity=-0.034  Sum_probs=47.2

Q ss_pred             HHHhCCChhHHHHHHHHHHHcC---CCC----CHHHHHHHHHHHhcCCchHHHHHHHHHHHhC-----C-CCc-cHHHHH
Q 040261          242 ELCKNGKMDEASRLLELMIQIG---VRP----DASVYNTLMDGFCLTGRVNRAKELFVSMESN-----G-CMR-DVFSYG  307 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~---~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~-~~~~~~  307 (343)
                      .+.+.|++++|+.++++..+..   +.|    ...+++.+..+|...|++++|..++++..+.     | ..| ...+++
T Consensus       296 ~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~  375 (429)
T 3qwp_A          296 ELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVM  375 (429)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHH
Confidence            3445566666666666665431   011    1345556666666666666666666654421     1 011 223455


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHH
Q 040261          308 ILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       308 ~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      .|...|...|++++|..++++.+
T Consensus       376 nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          376 KVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHH
Confidence            56666666666666666666554

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.29  E-value=0.0038  Score=56.58  Aligned_cols=154  Identities=10%  Similarity=0.057  Sum_probs=87.3

Q ss_pred             HHHHhcCChhHHHH-HHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcH
Q 040261           25 GCLAKNKHYDTVLS-LFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRI  103 (343)
Q Consensus        25 ~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  103 (343)
                      ......+++++|.+ ++..+      ++......++..+.+.|..+.|.++.+.       |.     .-.......|++
T Consensus       607 ~~~~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~~-------~~-----~~f~~~l~~~~~  668 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISPD-------QD-----QKFELALKVGQL  668 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCCC-------HH-----HHHHHHHHHTCH
T ss_pred             hHHHHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCCC-------cc-----hheehhhhcCCH
Confidence            34455677777766 44211      1122336666777777777777655421       11     112334556888


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHH
Q 040261          104 MEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  183 (343)
                      ++|.++.+.+      .+...|..+...+.+.++++.|.+.|.++..               |..+...+...|+.+...
T Consensus       669 ~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------------~~~l~~l~~~~~~~~~~~  727 (814)
T 3mkq_A          669 TLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------------LESLFLLHSSFNNKEGLV  727 (814)
T ss_dssp             HHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------------HHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------------hhhhHHHHHHcCCHHHHH
Confidence            8888775443      2667788888888888888888888877543               334455555566666555


Q ss_pred             HHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHH
Q 040261          184 ELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIE  223 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  223 (343)
                      ++-+.....|      -++....++.+.|++++|.+++.+
T Consensus       728 ~~~~~a~~~~------~~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          728 TLAKDAETTG------KFNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHcC------chHHHHHHHHHcCCHHHHHHHHHH
Confidence            5544444332      123333344445555555555443

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.26  E-value=0.0029  Score=52.50  Aligned_cols=99  Identities=11%  Similarity=-0.056  Sum_probs=66.9

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccCCCC-CccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC-----C--CCCChh
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGNGEF-GVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE-----N--INPDVV  199 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~  199 (343)
                      .+.-+.+.|++++|+.++++........ +..-+....+++.+..+|...|++++|+.++++...-     |  .+....
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            3455667899999999999988654322 1111122357788888888899999998888776431     1  112245


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMD  226 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  226 (343)
                      +++.+...|...|++++|..++++..+
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            577777777788888888777776653

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=97.19  E-value=0.015  Score=44.61  Aligned_cols=83  Identities=17%  Similarity=0.182  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhC-----CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC-Cch
Q 040261          214 WNEAKCLFIEMMDQGVQPN---VVTFNVIMNELCKN-----GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT-GRV  284 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~  284 (343)
                      ...|...+++.++.  .|+   ...|..+...|...     |+.++|.+.|++.++.+..-+..++......++.. |+.
T Consensus       179 l~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            34555555555554  333   34555666666653     66666666666666653211245555555555553 666


Q ss_pred             HHHHHHHHHHHhCC
Q 040261          285 NRAKELFVSMESNG  298 (343)
Q Consensus       285 ~~a~~~~~~~~~~~  298 (343)
                      +++.+.+++.....
T Consensus       257 ~~a~~~L~kAL~a~  270 (301)
T 3u64_A          257 AGFDEALDRALAID  270 (301)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHcCC
Confidence            66666666666653

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.99  E-value=0.012  Score=40.46  Aligned_cols=82  Identities=15%  Similarity=0.062  Sum_probs=58.5

Q ss_pred             hhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcC---CcchHHHHHHHHHHcCCCc--cHHHHHHHHHHHhhcCcHHHHH
Q 040261           33 YDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMG---RVSPGFVVLGRILRSCFTP--DAVTFTSLIKGLCAESRIMEAA  107 (343)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~  107 (343)
                      ...+.+-|.+....| +++..+...+..++++++   +.+++..+++.+.+.. .|  +...+..+.-++.+.|++++|.
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 LLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            345555666655555 367777777777888877   5668888888888764 23  3455556777778888888888


Q ss_pred             HHHHHHHhc
Q 040261          108 ALFTKLRAF  116 (343)
Q Consensus       108 ~~~~~~~~~  116 (343)
                      +.++.+.+.
T Consensus        92 ~y~~~lL~i  100 (152)
T 1pc2_A           92 KYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            888888876

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.98  E-value=0.023  Score=51.52  Aligned_cols=134  Identities=14%  Similarity=0.126  Sum_probs=91.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKG   96 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~   96 (343)
                      ......++..+.+.|..++|+++.+.       |.     .-+......|+++.|.++.+.+      .+...|..+...
T Consensus       629 ~~~~~~~~~~l~~~~~~~~a~~~~~~-------~~-----~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~  690 (814)
T 3mkq_A          629 KDSLTKIARFLEGQEYYEEALNISPD-------QD-----QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDA  690 (814)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHCCC-------HH-----HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhCCChHHheecCCC-------cc-----hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHH
Confidence            33447777788888888888876531       11     1133456789999998886443      367899999999


Q ss_pred             HhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhc
Q 040261           97 LCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKE  176 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  176 (343)
                      +.+.++++.|.+.|.++.+         +..+...+...++.+...++.+.....+            -++....+|.+.
T Consensus       691 al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~------------~~~~A~~~~~~~  749 (814)
T 3mkq_A          691 SLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTG------------KFNLAFNAYWIA  749 (814)
T ss_dssp             HHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTT------------CHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcC------------chHHHHHHHHHc
Confidence            9999999999999998763         3455556666777777666655555443            234444455666


Q ss_pred             CChHHHHHHHHHh
Q 040261          177 GFVDKAKELFLKM  189 (343)
Q Consensus       177 ~~~~~a~~~~~~~  189 (343)
                      |++++|++++.++
T Consensus       750 g~~~~a~~~~~~~  762 (814)
T 3mkq_A          750 GDIQGAKDLLIKS  762 (814)
T ss_dssp             TCHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHc
Confidence            7777777666554

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.95  E-value=0.052  Score=38.27  Aligned_cols=99  Identities=11%  Similarity=0.158  Sum_probs=50.0

Q ss_pred             HhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHH
Q 040261           63 CKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVAL  142 (343)
Q Consensus        63 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  142 (343)
                      .+.|+++.|.++.+.+      .+...|..+.......|+++-|.+.|.+..+         +..+.-.|...|+.+...
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHH
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHH
Confidence            4455666655555443      1455566666666666666666666655442         233333444555555554


Q ss_pred             HHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHH
Q 040261          143 NLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLK  188 (343)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  188 (343)
                      ++-+.....+            -++.....+.-.|+++++.++|.+
T Consensus        81 kla~iA~~~g------------~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           81 KMQNIAQTRE------------DFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHHHHHTT------------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHCc------------cHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4444443332            233333444455666666655543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.93  E-value=0.011  Score=37.93  Aligned_cols=67  Identities=7%  Similarity=-0.004  Sum_probs=43.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCC------CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIG------LFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      .+...+..+...+.+.|++..|...|+...+.-      -.+...++..+..++.+.|+++.|...++++.+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            355566677777777888888877777765421      1234456666667777777777777777776654

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.89  E-value=0.036  Score=42.58  Aligned_cols=93  Identities=14%  Similarity=0.144  Sum_probs=69.4

Q ss_pred             hHHHHHHHHHhhhCCCCCC---hhhHHHHHHHHhcc-----CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC-CCh
Q 040261          179 VDKAKELFLKMKDENINPD---VVTYTSLIRGFCYA-----NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN-GKM  249 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~  249 (343)
                      ...|...+++..+..  |+   ...|..+...|.+.     |+.++|...|++.++.+..-+..++......++.. |+.
T Consensus       179 l~~A~a~lerAleLD--P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDLW--PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHHC--TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHhC--CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            557777777777753  55   56788888888884     99999999999999874222366677778888774 999


Q ss_pred             hHHHHHHHHHHHcCCC--CCHHHHHH
Q 040261          250 DEASRLLELMIQIGVR--PDASVYNT  273 (343)
Q Consensus       250 ~~a~~~~~~~~~~~~~--~~~~~~~~  273 (343)
                      +.+.+.+++..+....  |+....+.
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~  282 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVI  282 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHH
Confidence            9999999999987655  55444443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.85  E-value=0.02  Score=36.67  Aligned_cols=68  Identities=12%  Similarity=-0.031  Sum_probs=54.8

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC------CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           50 PDLYTYNILINCFCKMGRVSPGFVVLGRILRSC------FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      .+...+..+...+.+.|++..|..+|+...+..      ..+...++..+..++.+.|+++.|...+++..+..
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~   76 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            355667778888899999999999999887641      12356778888999999999999999999988763

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=96.82  E-value=0.02  Score=37.81  Aligned_cols=65  Identities=18%  Similarity=0.042  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHHHhcCCchHH---HHHHHHHHHhCCCCc--cHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          266 PDASVYNTLMDGFCLTGRVNR---AKELFVSMESNGCMR--DVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       266 ~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ++..+-..+..++++..+...   +..+++.+...+ .|  .......|.-++.+.|++++|.+.++.+++
T Consensus        33 ~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           33 VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            444444444444444443332   444444444432 11  222233344445555555555555555543

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.81  E-value=0.052  Score=36.09  Aligned_cols=139  Identities=13%  Similarity=0.079  Sum_probs=81.1

Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      -.|..++..++..+....   .+..-++-++--....-+-+-..++++..-...         |          ...+|+
T Consensus        19 ldG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiF---------D----------is~C~N   76 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYF---------D----------LDKCQN   76 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGS---------C----------GGGCSC
T ss_pred             HhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhc---------C----------cHhhhc
Confidence            346666667776666654   244445555544455555555555555544332         1          123445


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHH
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLEL  258 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  258 (343)
                      .......+-.+-.     +.......+......|.-++..+++..+... .+|++...-.+..+|.+.|+..++.+++.+
T Consensus        77 lKrVi~C~~~~n~-----~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~  150 (172)
T 1wy6_A           77 LKSVVECGVINNT-----LNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIE  150 (172)
T ss_dssp             THHHHHHHHHTTC-----CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcc-----hHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            5555444443322     4455566666677777777777777775443 366677777777777777777777777777


Q ss_pred             HHHcCCC
Q 040261          259 MIQIGVR  265 (343)
Q Consensus       259 ~~~~~~~  265 (343)
                      +.+.|++
T Consensus       151 AC~kG~k  157 (172)
T 1wy6_A          151 ACKKGEK  157 (172)
T ss_dssp             HHHTTCH
T ss_pred             HHHhhhH
Confidence            7777643

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.81  E-value=0.055  Score=36.77  Aligned_cols=114  Identities=13%  Similarity=0.071  Sum_probs=82.6

Q ss_pred             CCCChhhHHHHHHHHHhcCCh------hHHHHHHHHhHhCCCCCCHH-HHHHHHH------HHHhcCCcchHHHHHHHHH
Q 040261           13 SPPPVCSFNILFGCLAKNKHY------DTVLSLFKRLNSIGLFPDLY-TYNILIN------CFCKMGRVSPGFVVLGRIL   79 (343)
Q Consensus        13 ~~~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~~-~~~~l~~------~~~~~~~~~~a~~~~~~~~   79 (343)
                      .|.|.++|-..+..+-+.|+.      ++.+++|++.... ++|+.. .|...+.      .+...++.++|.++|+.++
T Consensus         9 ~p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~   87 (161)
T 4h7y_A            9 MANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMAR   87 (161)
T ss_dssp             -CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            357899999999999999999      8999999988763 466432 1111111      1234489999999999998


Q ss_pred             HcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 040261           80 RSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLI  129 (343)
Q Consensus        80 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  129 (343)
                      +.+-.- ...|......-.+.|+...|.+++.+.+..+.+|. ..+...+
T Consensus        88 ~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~-~~le~a~  135 (161)
T 4h7y_A           88 ANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPL-EMLEIAL  135 (161)
T ss_dssp             HHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCH-HHHHHHH
T ss_pred             HHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcH-HHHHHHH
Confidence            753332 77777788888899999999999999999877643 3333333

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.59  E-value=0.025  Score=38.38  Aligned_cols=112  Identities=14%  Similarity=0.112  Sum_probs=70.8

Q ss_pred             CChhhHHHHHHHHhccCcH------HHHHHHHHHHHHcCCCCCH----HHHHHHHHHH---HhCCChhHHHHHHHHHHHc
Q 040261          196 PDVVTYTSLIRGFCYANDW------NEAKCLFIEMMDQGVQPNV----VTFNVIMNEL---CKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~  262 (343)
                      -|..+|-..+...-+.|++      +...++|++.... ++|+.    ..|-.+---|   ...+|.++|.++|+.++..
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            3566677777766666777      7777888877775 45542    1222222211   2356788888888888665


Q ss_pred             CCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHH
Q 040261          263 GVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILI  310 (343)
Q Consensus       263 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  310 (343)
                      +-+. ...|....+.-.++|++..|.+++.+....+.. +.......+
T Consensus        90 hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k-~~~~le~a~  135 (161)
T 4h7y_A           90 CKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAV-PLEMLEIAL  135 (161)
T ss_dssp             CTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCB-CHHHHHHHH
T ss_pred             hHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCC-cHHHHHHHH
Confidence            3233 677777777777888888888888888876533 333333333

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.32  E-value=9.3e-07  Score=71.91  Aligned_cols=209  Identities=11%  Similarity=0.027  Sum_probs=113.7

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      .+.+|..|..+..+.++..+|++-|-   +.   .|+..|..++.+..+.|.+++-..++....+..-.  +..=+.|+-
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyI---kA---~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke--~~IDteLi~  124 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYI---KA---DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARE--SYVETELIF  124 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSC---CC---SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCS--TTTTHHHHH
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHH---hC---CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcc--cccHHHHHH
Confidence            45678888888888888887777652   21   24556777888888888888888888766654323  333356788


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCc--------------cccC
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGV--------------VCKP  161 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--------------~~~~  161 (343)
                      +|++.++..+-.+++.       .|+..-...+.+-|...|.++.|.-+|..+.....--..              ....
T Consensus       125 ayAk~~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAn  197 (624)
T 3lvg_A          125 ALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKAN  197 (624)
T ss_dssp             HHHTSCSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCC
T ss_pred             HHHhhCcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            8888887655433321       245555666777777777777776555544322110000              0122


Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      ++.+|..+..+|...+++.-|...--.+.-.     ..-...++..|-..|.+++.+.+++.-.... ......|+.|.-
T Consensus       198 s~ktWKeV~~ACvd~~EfrLAqicGLniIvh-----adeL~elv~~YE~~G~f~ELIsLlEaglglE-rAHmGmFTELaI  271 (624)
T 3lvg_A          198 STRTWKEVCFACVDGKEFRLAQMCGLHIVVH-----ADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAI  271 (624)
T ss_dssp             SSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC-----SSCCSGGGSSSSTTCCCTTSTTTHHHHTTST-TCCHHHHHHHHH
T ss_pred             ChhHHHHHHHHHhCchHHHHHHHhcchhccc-----HHHHHHHHHHHHhCCCHHHHHHHHHHHhCCC-chhHHHHHHHHH
Confidence            3445555555555555554443332222211     1112223444555555555555555444221 234445555555


Q ss_pred             HHHh
Q 040261          242 ELCK  245 (343)
Q Consensus       242 ~~~~  245 (343)
                      .|++
T Consensus       272 LYsK  275 (624)
T 3lvg_A          272 LYSK  275 (624)
T ss_dssp             HHHS
T ss_pred             HHHh
Confidence            5543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.98  E-value=0.25  Score=34.86  Aligned_cols=131  Identities=14%  Similarity=0.076  Sum_probs=93.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      -.....+.|+++.|.++.+.+      .+...|..+.......|+++-|.+.|.+...         +..+.-.|.-.|+
T Consensus        11 rF~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~   75 (177)
T 3mkq_B           11 RFDLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGD   75 (177)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTC
T ss_pred             HHHHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCC
Confidence            455667899999999998766      3678999999999999999999999987642         3345555566788


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKA  182 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  182 (343)
                      .+...++-+.....|      -++.....+...|+++++.+++.+...               +..-.......|..+.|
T Consensus        76 ~e~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~~r---------------~~eA~~~A~t~g~~~~a  134 (177)
T 3mkq_B           76 VNKLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEGGS---------------LPLAYAVAKANGDEAAA  134 (177)
T ss_dssp             HHHHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTC---------------HHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHCCC---------------hHHHHHHHHHcCcHHHH
Confidence            777666655555443      245556667789999999999866432               11122223345677788


Q ss_pred             HHHHHHh
Q 040261          183 KELFLKM  189 (343)
Q Consensus       183 ~~~~~~~  189 (343)
                      .++.+.+
T Consensus       135 ~~~~~~~  141 (177)
T 3mkq_B          135 SAFLEQA  141 (177)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            8887765

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.93  E-value=0.063  Score=35.42  Aligned_cols=84  Identities=14%  Similarity=0.025  Sum_probs=46.4

Q ss_pred             ChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcch---HHHHHHHHHHcCCC-ccHHHHHHHHHHHhhcCcHHHHH
Q 040261           32 HYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSP---GFVVLGRILRSCFT-PDAVTFTSLIKGLCAESRIMEAA  107 (343)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~  107 (343)
                      ....+.+-|......| .++..+-..+..+++++.+...   ++.+++.+.+.+.+ -.......+.-++.+.|++++|.
T Consensus        16 ~l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~   94 (126)
T 1nzn_A           16 DLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKAL   94 (126)
T ss_dssp             HHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHH
Confidence            3444455555444434 2555555556666666655444   66666666654311 12333344555666677777777


Q ss_pred             HHHHHHHhc
Q 040261          108 ALFTKLRAF  116 (343)
Q Consensus       108 ~~~~~~~~~  116 (343)
                      +.++.+.+.
T Consensus        95 ~~~~~lL~~  103 (126)
T 1nzn_A           95 KYVRGLLQT  103 (126)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            777776665

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=95.53  E-value=0.3  Score=32.45  Aligned_cols=66  Identities=11%  Similarity=-0.022  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHHHHHhcCCc---hHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261          265 RPDASVYNTLMDGFCLTGR---VNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       265 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      .|+..+-..+..++++..+   ..+++.+++.+.+.+..-....+-.+.-++.+.|++++|.+..+.++
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL  105 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLF  105 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            3444444444444444432   23444444444443211122333344444555555555555555554

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=95.50  E-value=0.18  Score=44.71  Aligned_cols=126  Identities=14%  Similarity=0.089  Sum_probs=80.7

Q ss_pred             HHHHHHHHhcCC-hhHHHHHHHHhHhCCCCCCHHHH--HHHHHHHHhcCC-cchHHHHHHHHHHc------CCCc-c---
Q 040261           21 NILFGCLAKNKH-YDTVLSLFKRLNSIGLFPDLYTY--NILINCFCKMGR-VSPGFVVLGRILRS------CFTP-D---   86 (343)
Q Consensus        21 ~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~-~~~a~~~~~~~~~~------~~~~-~---   86 (343)
                      ..++..+.-.++ .+.|+.+|+++....  |...++  ..++..+...++ --+|.+++.+.++.      ...+ +   
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            344555555666 578999999988754  433332  233333333332 22355555554421      1111 1   


Q ss_pred             -------HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 040261           87 -------AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMA  149 (343)
Q Consensus        87 -------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  149 (343)
                             ....+.-.+.+...|+++-|+++.++.....+. +-.+|..|..+|...|+++.|+-.++.+.
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPs-eF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALD-SFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCch-hhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                   112333345677789999999999999887332 57799999999999999999999998874

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.33  E-value=0.36  Score=32.20  Aligned_cols=140  Identities=12%  Similarity=0.053  Sum_probs=88.6

Q ss_pred             HhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccC
Q 040261          133 CRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYAN  212 (343)
Q Consensus       133 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  212 (343)
                      .-.|..++..++..+.....         +..-||.++--....-+-+-..++++.+-+.   .|.          ...|
T Consensus        18 ildG~v~qGveii~k~~~ss---------ni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FDi----------s~C~   75 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKSS---------TKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQ   75 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS---------CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCS
T ss_pred             HHhhhHHHHHHHHHHHcCCC---------CccccceeeeecchhhchhHHHHHHHHHhhh---cCc----------Hhhh
Confidence            34677777777777766532         4445555555555555555566666655442   121          1233


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHH
Q 040261          213 DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFV  292 (343)
Q Consensus       213 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  292 (343)
                      +.......+-.+     ..+.......+......|..++..+++..+... .+|++...-.+..+|.+.|+..+|.+++.
T Consensus        76 NlKrVi~C~~~~-----n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~  149 (172)
T 1wy6_A           76 NLKSVVECGVIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLI  149 (172)
T ss_dssp             CTHHHHHHHHHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHh-----cchHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHH
Confidence            444433333322     234555666777888888888888888886443 37778888888888888888888888888


Q ss_pred             HHHhCCCC
Q 040261          293 SMESNGCM  300 (343)
Q Consensus       293 ~~~~~~~~  300 (343)
                      +..+.|++
T Consensus       150 ~AC~kG~k  157 (172)
T 1wy6_A          150 EACKKGEK  157 (172)
T ss_dssp             HHHHTTCH
T ss_pred             HHHHhhhH
Confidence            88888753

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.27  E-value=1.7  Score=39.66  Aligned_cols=258  Identities=11%  Similarity=0.045  Sum_probs=132.3

Q ss_pred             HHhcCChhHHHHHHHHhHhCCCCCCHH--HHHHHHHHHHhcCCcchHHHHHHHHHHcCC-------CccHHHHHHHHHHH
Q 040261           27 LAKNKHYDTVLSLFKRLNSIGLFPDLY--TYNILINCFCKMGRVSPGFVVLGRILRSCF-------TPDAVTFTSLIKGL   97 (343)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~~~~~l~~~~   97 (343)
                      ....|+.++++.++......+...+..  .=..+.-.....|..+++..++...+...-       .+....-..+.-++
T Consensus       384 lIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLGl  463 (963)
T 4ady_A          384 VIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGL  463 (963)
T ss_dssp             HHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             hhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHHH
Confidence            345677777777776654321012222  222222334455555567776666554321       01111122222223


Q ss_pred             hhcCc-HHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           98 CAESR-IMEAAALFTKLRAFGCKPDVF--TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        98 ~~~~~-~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      +-.|. -+++.+.+..+.... .+...  +-.++...+.-.|+.+....++..+.+..       ..+..-...+.-++.
T Consensus       464 a~~GS~~eev~e~L~~~L~dd-~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~-------~e~vrR~aalgLGll  535 (963)
T 4ady_A          464 AAMGSANIEVYEALKEVLYND-SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQ-------HGNITRGLAVGLALI  535 (963)
T ss_dssp             HSTTCCCHHHHHHHHHHHHTC-CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCS-------CHHHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccC-------cHHHHHHHHHHHHhh
Confidence            22232 245555555555431 11111  11223334556677777777777666532       112222233333444


Q ss_pred             hcCChHHHHHHHHHhhhCCCCCChhhHH---HHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhH
Q 040261          175 KEGFVDKAKELFLKMKDENINPDVVTYT---SLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDE  251 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  251 (343)
                      -.|+.+.+..+++.+.... .| ..-|.   .+.-+|+..|+......++..+.... ..+......+.-++...|+.+.
T Consensus       536 ~~g~~e~~~~li~~L~~~~-dp-~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~  612 (963)
T 4ady_A          536 NYGRQELADDLITKMLASD-ES-LLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTT  612 (963)
T ss_dssp             TTTCGGGGHHHHHHHHHCS-CH-HHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSS
T ss_pred             hCCChHHHHHHHHHHHhCC-CH-HHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHH
Confidence            6788888888887776542 12 22232   33456778888877777888887642 2334433444445556777777


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCch-HHHHHHHHHHHh
Q 040261          252 ASRLLELMIQIGVRPDASVYNTLMDGFCLTGRV-NRAKELFVSMES  296 (343)
Q Consensus       252 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~  296 (343)
                      +.++++.+.+.+ .|....-..+.-+....|.. .++..++..+..
T Consensus       613 v~rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~~  657 (963)
T 4ady_A          613 VPRIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK  657 (963)
T ss_dssp             HHHHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc
Confidence            777777666654 45544444444455555543 567778887765

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.21  E-value=1.8  Score=39.54  Aligned_cols=260  Identities=11%  Similarity=0.065  Sum_probs=133.3

Q ss_pred             HHhcCCcchHHHHHHHHHHcC--CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCC-------CCCHHHHHHHHHHH
Q 040261           62 FCKMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGC-------KPDVFTYTTLINGL  132 (343)
Q Consensus        62 ~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~~~~~l~~~~  132 (343)
                      ....|+.++++.++......+  -.+....-..+.-+....|...++..++.......-       .+....-..+.-++
T Consensus       384 lIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLGl  463 (963)
T 4ady_A          384 VIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGL  463 (963)
T ss_dssp             HHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             hhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHHH
Confidence            445667777776666554321  111222223333445555655567776666554311       01111122222233


Q ss_pred             HhcCC-hHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          133 CRTGH-TIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       133 ~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                      .-.|. -+++.+.+..+.....     ......+-.++...+.-.|+.+....++..+.+.. .-+..-...+.-++...
T Consensus       464 a~~GS~~eev~e~L~~~L~dd~-----~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~-~e~vrR~aalgLGll~~  537 (963)
T 4ady_A          464 AAMGSANIEVYEALKEVLYNDS-----ATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQ-HGNITRGLAVGLALINY  537 (963)
T ss_dssp             HSTTCCCHHHHHHHHHHHHTCC-----HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTT
T ss_pred             HhcCCCCHHHHHHHHHHHhcCC-----HHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccC-cHHHHHHHHHHHHhhhC
Confidence            33332 2355555555554331     00001122233444556777777777777766532 11222223333344467


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHH
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFN--VIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKE  289 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  289 (343)
                      |+.+.+..+++.+.... .|....-.  .+.-+|+..|+.....+++..+.... ..+..-...+.-++...|+.+.+.+
T Consensus       538 g~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~r  615 (963)
T 4ady_A          538 GRQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVPR  615 (963)
T ss_dssp             TCGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHHH
T ss_pred             CChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHHH
Confidence            78888888888777642 33322222  33456677888877777888887642 2233333333345556677777777


Q ss_pred             HHHHHHhCCCCccHHHHHHHHHHHHhcCCh-HHHHHHHHHHH
Q 040261          290 LFVSMESNGCMRDVFSYGILINGYCKNKEI-EGALSLYSEML  330 (343)
Q Consensus       290 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~  330 (343)
                      +++.+.+.+ .|..+.-..+.-+....|.. .+++.++..+.
T Consensus       616 lv~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~L~~L~  656 (963)
T 4ady_A          616 IVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDVLDPLT  656 (963)
T ss_dssp             HTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHHHHHHc
Confidence            777666543 45555544555555555544 46677777765

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.20  E-value=1.2  Score=37.22  Aligned_cols=164  Identities=12%  Similarity=0.170  Sum_probs=99.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhC--CCCCC---hhhHHHHHHHHhccCcHHHHHHHHHHHHHc----CCCCC--HH
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDE--NINPD---VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ----GVQPN--VV  234 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~  234 (343)
                      ...|...+...|++.+|..++..+...  +....   ...+...++.|...+++..|..++..+...    ...|+  ..
T Consensus       140 ~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~  219 (445)
T 4b4t_P          140 TKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLE  219 (445)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHH
Confidence            456788899999999999999997542  22111   345667788899999999999999887532    22222  24


Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHc-CCCCCHHHHH----HHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMIQI-GVRPDASVYN----TLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGIL  309 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  309 (343)
                      .+...+..+...+++.+|-+.|.++.+. ....+...+.    .++.+..-.+....-.+++.........++...+..+
T Consensus       220 ~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L  299 (445)
T 4b4t_P          220 YYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESL  299 (445)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhcccccccHHHHHH
Confidence            5566777888899999999888877653 1111222221    1111212222222222333333322223567788888


Q ss_pred             HHHHHhc--CChHHHHHHHHHH
Q 040261          310 INGYCKN--KEIEGALSLYSEM  329 (343)
Q Consensus       310 ~~~~~~~--~~~~~a~~~~~~~  329 (343)
                      +.+|...  .+++.+.+.|+..
T Consensus       300 ~k~f~~~~L~~~~~~~~~~~~~  321 (445)
T 4b4t_P          300 VKLFTTNELMRWPIVQKTYEPV  321 (445)
T ss_dssp             HHHHHHCCSSSHHHHHHHTCSS
T ss_pred             HHHHHhchHhhhHHHHHHHHHH
Confidence            8888764  3566666655443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=95.13  E-value=0.64  Score=37.93  Aligned_cols=67  Identities=12%  Similarity=0.100  Sum_probs=37.7

Q ss_pred             HHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh-----CCCCccHHH
Q 040261          238 VIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES-----NGCMRDVFS  305 (343)
Q Consensus       238 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~  305 (343)
                      .++..+...|+++++...+..+.... +.+...+..++.++.+.|+..+|.+.|+++.+     .|+.|+..+
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            34455555666666666665555543 44555666666666666666666666655432     355555544

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.10  E-value=3.2e-05  Score=63.21  Aligned_cols=190  Identities=9%  Similarity=0.048  Sum_probs=130.5

Q ss_pred             CCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHH
Q 040261           12 PSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFT   91 (343)
Q Consensus        12 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   91 (343)
                      ....++..|..++....+.|++++-+..+.-..+.  ..+...=+.|+.+|++.++..+-.+++.       .||..-..
T Consensus        78 IkA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~--~ke~~IDteLi~ayAk~~rL~elEefl~-------~~N~A~iq  148 (624)
T 3lvg_A           78 IKADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQ  148 (624)
T ss_dssp             CCCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT--CCSTTTTHHHHHHHHTSCSSSTTTSTTS-------CCSSSCTH
T ss_pred             HhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccHHHHHHHHHhhCcHHHHHHHHc-------CCCcccHH
Confidence            33467778999999999999999999998765553  2344556789999999998776433321       34555555


Q ss_pred             HHHHHHhhcCcHHHHHHHHHHHHhcC--------------------CCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261           92 SLIKGLCAESRIMEAAALFTKLRAFG--------------------CKPDVFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus        92 ~l~~~~~~~~~~~~a~~~~~~~~~~~--------------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                      .+.+-|...|.++.|.-+|..+....                    -.-++.||..+-.+|...+++.-|.-.--.+.-.
T Consensus       149 ~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh  228 (624)
T 3lvg_A          149 QVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH  228 (624)
T ss_dssp             HHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC
T ss_pred             HHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhccc
Confidence            66666667776666666555432110                    1236678999999999999998876655554433


Q ss_pred             CCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHH
Q 040261          152 NGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIE  223 (343)
Q Consensus       152 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  223 (343)
                      .           .-...++..|-..|.+++.+.+++.-.... ......|+-|.-.|++- ++++..+.++.
T Consensus       229 a-----------deL~elv~~YE~~G~f~ELIsLlEaglglE-rAHmGmFTELaILYsKY-~PeKlmEHlkl  287 (624)
T 3lvg_A          229 A-----------DELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF-KPQKMREHLEL  287 (624)
T ss_dssp             S-----------SCCSGGGSSSSTTCCCTTSTTTHHHHTTST-TCCHHHHHHHHHHHHSS-CTTHHHHHHTT
T ss_pred             H-----------HHHHHHHHHHHhCCCHHHHHHHHHHHhCCC-chhHHHHHHHHHHHHhc-CHHHHHHHHHH
Confidence            2           223446778899999999999999876432 34577788888887775 44555444443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=95.03  E-value=1.3  Score=42.05  Aligned_cols=190  Identities=14%  Similarity=0.107  Sum_probs=115.6

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCCC-------
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NINP-------  196 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-------  196 (343)
                      ++..+...+..+.+.++..-           ++.++...-.+..++...|++++|.+.|.+....    ....       
T Consensus       818 l~~~l~~~~~~~~~~~l~~~-----------~~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~  886 (1139)
T 4fhn_B          818 LVEKLFLFKQYNACMQLIGW-----------LNSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQ  886 (1139)
T ss_dssp             HHHHHHHHSCTTHHHHHHHH-----------SCCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHhhh-----------ccCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccc
Confidence            44455666666666554432           2334444455678899999999999999875321    0000       


Q ss_pred             -----------ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhCCChhHHHHHHHHHHH
Q 040261          197 -----------DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV----VTFNVIMNELCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       197 -----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~  261 (343)
                                 -..-|..++..+.+.+.++.+.++-....+....-+.    ..|..+...+...|++++|...+-.+..
T Consensus       887 ~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd  966 (1139)
T 4fhn_B          887 EIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLST  966 (1139)
T ss_dssp             HHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHH
T ss_pred             cccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCC
Confidence                       1123667777888888888888888777665322221    2577888999999999999998887766


Q ss_pred             cCCCCCHHHHHHHHHHHhcCCch------------HHHHHHHHHHHhC--CCCccHHHHHHHHHHHHhcCChHHHH-HHH
Q 040261          262 IGVRPDASVYNTLMDGFCLTGRV------------NRAKELFVSMESN--GCMRDVFSYGILINGYCKNKEIEGAL-SLY  326 (343)
Q Consensus       262 ~~~~~~~~~~~~l~~~~~~~~~~------------~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~  326 (343)
                      ...+  ...+..|+...+..|..            ++..+++....+.  .....+.-|..|-.-+..+|++.+|- -+|
T Consensus       967 ~~~r--~~cLr~LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmY 1044 (1139)
T 4fhn_B          967 TPLK--KSCLLDFVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIY 1044 (1139)
T ss_dssp             SSSC--HHHHHHHHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHH
T ss_pred             HHHH--HHHHHHHHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHH
Confidence            5433  45666666666655543            4444444332211  01112234566666667778777654 444


Q ss_pred             HHHH
Q 040261          327 SEML  330 (343)
Q Consensus       327 ~~~~  330 (343)
                      +.+.
T Consensus      1045 e~~~ 1048 (1139)
T 4fhn_B         1045 EKLS 1048 (1139)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.98  E-value=0.64  Score=41.37  Aligned_cols=125  Identities=14%  Similarity=0.055  Sum_probs=72.0

Q ss_pred             HHHHHHHhccCc-HHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhCCC-hhHHHHHHHHHHHc------CCCC-C---
Q 040261          202 TSLIRGFCYAND-WNEAKCLFIEMMDQGVQPNVVTFN--VIMNELCKNGK-MDEASRLLELMIQI------GVRP-D---  267 (343)
Q Consensus       202 ~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~-~~~a~~~~~~~~~~------~~~~-~---  267 (343)
                      ..++..+...++ .+.|..+++.+.+..  |...++.  .++..+...++ --+|.+++.+..+.      ..++ +   
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            334444444555 577888888877763  3322222  22222222222 22344444444321      1111 1   


Q ss_pred             -------HHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          268 -------ASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       268 -------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                             ......-.+.+...|+++-|+.+.++....- +.+-.+|..|..+|...|+++.|+-.++.+
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence                   1122333445667788888888888887752 345788888899999999999988888777

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=94.77  E-value=2.9  Score=39.69  Aligned_cols=134  Identities=13%  Similarity=0.115  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHH
Q 040261          124 TYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTS  203 (343)
Q Consensus       124 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  203 (343)
                      -|..++..+.+.+.++.+.++-....+......  .......|..+.+.+...|++++|...+-.+.....  -...+..
T Consensus       901 YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~--~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~--r~~cLr~  976 (1139)
T 4fhn_B          901 YYLHLSKKLFEESAYIDALEFSLLADASKETDD--EDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL--KKSCLLD  976 (1139)
T ss_dssp             HHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCC--HHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS--CHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCC--hhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH--HHHHHHH
Confidence            345555666666666666655555544321000  000112455556666666666666666655544322  2334444


Q ss_pred             HHHHHhccCc------------HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhCCChhHHH-HHHHHHHH
Q 040261          204 LIRGFCYAND------------WNEAKCLFIEMMDQ--GVQPNVVTFNVIMNELCKNGKMDEAS-RLLELMIQ  261 (343)
Q Consensus       204 l~~~~~~~~~------------~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~  261 (343)
                      ++...+..|.            .++..+++..-.+.  .+...+.-|..|-.-+...|++.+|- -+|+.+.+
T Consensus       977 LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmYe~~~R 1049 (1139)
T 4fhn_B          977 FVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIYEKLSR 1049 (1139)
T ss_dssp             HHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHHHHHHH
Confidence            4444444333            34444444332221  11112233555555566677776654 44455544

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.28  E-value=1.3  Score=36.21  Aligned_cols=72  Identities=6%  Similarity=0.015  Sum_probs=53.7

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHH-----cCCCCCHHHHHH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQ-----IGVRPDASVYNT  273 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~  273 (343)
                      ...++.++...|++.++...+..+.... +.+...+..++.++.+.|+..+|.+.|+.+.+     .|+.|+..+-..
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            4445667777888888888888877663 55777888888888888888888888877654     477887665433

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.22  E-value=2.1  Score=35.69  Aligned_cols=96  Identities=13%  Similarity=0.038  Sum_probs=70.2

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHc--CCCCC---HHHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCC--HH
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQ--GVQPN---VVTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPD--AS  269 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~  269 (343)
                      ...+...+...|++.+|..++..+...  +....   ...+...++.|...+++.+|..++.++...    ..+|+  ..
T Consensus       140 ~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~  219 (445)
T 4b4t_P          140 TKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLE  219 (445)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHH
Confidence            356778889999999999999998754  22111   346667788999999999999999887532    21222  23


Q ss_pred             HHHHHHHHHhcCCchHHHHHHHHHHHh
Q 040261          270 VYNTLMDGFCLTGRVNRAKELFVSMES  296 (343)
Q Consensus       270 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  296 (343)
                      .+...+..+...+++.+|.+.|.++..
T Consensus       220 ~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          220 YYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            556677778888999998888877654

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=94.21  E-value=0.56  Score=31.58  Aligned_cols=68  Identities=13%  Similarity=0.003  Sum_probs=46.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCc---chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           49 FPDLYTYNILINCFCKMGRV---SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .|+..+-..+..+++++.+.   .+++.+++.+.+.+....-.....+.-++.+.|++++|.++.+.+.+.
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~  106 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  106 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            46666666666666666543   467778888777643334445555667788888888888888888876

>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=94.17  E-value=0.59  Score=29.21  Aligned_cols=63  Identities=11%  Similarity=0.150  Sum_probs=41.2

Q ss_pred             ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          178 FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      |.=+..+-+..+....+.|++....+.+++|.+.+++..|.++++-+..+- .+...+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHH
Confidence            344556666666666777777777777777777777777777777776552 333445555544

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=93.93  E-value=0.3  Score=32.45  Aligned_cols=68  Identities=13%  Similarity=0.003  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCc---chHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           49 FPDLYTYNILINCFCKMGRV---SPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        49 ~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .|+..+--.+..+++++.+.   .+++.+++.+.+.+..-....+-.+.-++.+.|++++|.+..+.+.+.
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~  107 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  107 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Confidence            46666655566666666543   457777777777653223455556667777888888888888888776

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=93.81  E-value=3.1  Score=36.27  Aligned_cols=279  Identities=10%  Similarity=-0.047  Sum_probs=132.0

Q ss_pred             ChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHH
Q 040261           32 HYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFT  111 (343)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  111 (343)
                      ...+....+++-..  .+.....-...+..+.+.+++...+.++..     .+.+...-.....+....|+..+|.....
T Consensus        54 ~~~ev~~Fl~~~~~--~p~~~~Lr~~~l~~l~~~~~w~~~l~~~~~-----~p~~~~~~c~~~~A~~~~G~~~~a~~~~~  126 (618)
T 1qsa_A           54 PAVTVTNFVRANPT--LPPARTLQSRFVNELARREDWRGLLAFSPE-----KPGTTEAQCNYYYAKWNTGQSEEAWQGAK  126 (618)
T ss_dssp             CHHHHHHHHHHCTT--CHHHHHHHHHHHHHHHHTTCHHHHHHHCCS-----CCSSHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHCCC--ChhHHHHHHHHHHHHHhCCCHHHHHHhccC-----CCCCHHHHHHHHHHHHHcCChhHHHHHHH
Confidence            44555555444322  122223334556666677776655553332     12344444445666667787777777666


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhcCChHH--HHHHHHHHHccCCCC-----CccccCCcc-hHHHHHHHHHhcCChHHHH
Q 040261          112 KLRAFGCKPDVFTYTTLINGLCRTGHTIV--ALNLFEEMANGNGEF-----GVVCKPDAI-TYSTITDGLCKEGFVDKAK  183 (343)
Q Consensus       112 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~--a~~~~~~~~~~~~~~-----~~~~~~~~~-~~~~l~~~~~~~~~~~~a~  183 (343)
                      .+-..|.. .+..+..++..+.+.|....  ...-++.+...+...     ...++++.. ....++....   ++..+.
T Consensus       127 ~lW~~~~~-~p~~c~~l~~~~~~~g~lt~~~~~~R~~~al~~~~~~~a~~l~~~l~~~~~~~a~~~~al~~---~p~~~~  202 (618)
T 1qsa_A          127 ELWLTGKS-QPNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLAN---NPNTVL  202 (618)
T ss_dssp             HHHSCSSC-CCTHHHHHHHHHHHTTCSCHHHHHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHH---CGGGHH
T ss_pred             HHHhCCCC-CcHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHhCCHHHHHHHHHHHHHHh---ChHhHH
Confidence            66655432 34456666666665554433  222222222222000     000001110 0111111111   111111


Q ss_pred             HHHHHhhhCCCCCChh---hHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH----HHHHHHhCCChhHHHHHH
Q 040261          184 ELFLKMKDENINPDVV---TYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV----IMNELCKNGKMDEASRLL  256 (343)
Q Consensus       184 ~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~a~~~~  256 (343)
                      .....     ..++..   .+...+.-.. ..+.+.|...+....+.. ..+......    +.......+...++...+
T Consensus       203 ~~~~~-----~~~~~~~~~~~~~~~~rla-r~d~~~A~~~~~~~~~~~-~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~  275 (618)
T 1qsa_A          203 TFART-----TGATDFTRQMAAVAFASVA-RQDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWR  275 (618)
T ss_dssp             HHHHH-----SCCCHHHHHHHHHHHHHHH-HHCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHH
T ss_pred             HHHhc-----cCCChhhHHHHHHHHHHHH-hcCHHHHHHHHHhhhhcc-CCCHHHHHHHHHHHHHHHHHcCCChHHHHHH
Confidence            11111     011211   1111222222 336788888887776543 223322222    222233344345566666


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          257 ELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       257 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ......  ..+.....-.+....+.|+++.|...|+.|.... .........+.+++...|+.++|..+|+++..
T Consensus       276 ~~~~~~--~~~~~~~e~~~r~Alr~~d~~~a~~~~~~l~~~~-~~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          276 DDAIMR--SQSTSLIERRVRMALGTGDRRGLNTWLARLPMEA-KEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHT--CCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTG-GGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             Hhcccc--CCChHHHHHHHHHHHHCCCHHHHHHHHHHccccc-cccHhHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            654433  2344344444455556788888888888876532 12344455667778888888888888887753

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=93.72  E-value=0.74  Score=28.78  Aligned_cols=63  Identities=8%  Similarity=0.112  Sum_probs=46.4

Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHH
Q 040261          248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILIN  311 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  311 (343)
                      |.-+..+-++.+....+.|++.+..+.+++|.+.+++..|.++++.++.+- .+....|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHH
Confidence            455677777777777888888888888899988899999999888887642 233445655553

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.68  E-value=1  Score=30.32  Aligned_cols=72  Identities=13%  Similarity=0.022  Sum_probs=44.6

Q ss_pred             CCCHHHHHHHHHHHHhCCC---hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccH
Q 040261          230 QPNVVTFNVIMNELCKNGK---MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDV  303 (343)
Q Consensus       230 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  303 (343)
                      .|+..+--.+..++.+..+   ..+++.+++.+.+.+..-.....-.|.-++.+.|++++|++..+.+.+.  .|+.
T Consensus        36 ~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~--eP~n  110 (144)
T 1y8m_A           36 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH--ERNN  110 (144)
T ss_dssp             TSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT--CCCC
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhc--CCCc
Confidence            4555555556666666654   3457777777776542122334444555778888888888888888775  4543

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=92.88  E-value=1.3  Score=29.35  Aligned_cols=60  Identities=12%  Similarity=0.208  Sum_probs=41.8

Q ss_pred             HHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          181 KAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       181 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      +..+-+..+...++.|++....+.+++|.+.+++..|.++++-+..+ ..+...+|..+++
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~lq  130 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHHH
Confidence            45556666667777788888888888888888888888888777665 2334555665554

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=92.56  E-value=1.5  Score=29.12  Aligned_cols=61  Identities=8%  Similarity=0.109  Sum_probs=38.0

Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHH
Q 040261          249 MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILI  310 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  310 (343)
                      .-+..+-++.+...++.|++.+..+.+++|.+.+|+..|.++|+.++.+- .+....|..++
T Consensus        69 ~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~l  129 (152)
T 2y69_E           69 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHH
Confidence            33455555566666667777777777777777777777777777766542 23333455444

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=92.47  E-value=1.2  Score=30.92  Aligned_cols=65  Identities=11%  Similarity=-0.060  Sum_probs=45.2

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCC-CCCCH-------HHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIG-LFPDL-------YTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      +..++..-+..+...|.++.|+-+.+.+.... ..|+.       .++..+..++...+++..|...|++.++
T Consensus        19 ~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq   91 (167)
T 3ffl_A           19 SHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQ   91 (167)
T ss_dssp             --CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            34556666788888899999888887755421 12331       2566677888889999999999988754

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.73  E-value=5.3  Score=33.07  Aligned_cols=61  Identities=8%  Similarity=0.053  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHcC--CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHH
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRSC--FTPDAVTFTSLIKGLCAESRIMEAAALFTKLR  114 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  114 (343)
                      +...+...+.+.|+++.|.+.+.++....  ...-...+-..++.+...+++..+...+.+..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~  195 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVN  195 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            44555556666666666666666655421  22234455555566666666666666555543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=89.17  E-value=6.8  Score=30.68  Aligned_cols=149  Identities=15%  Similarity=0.046  Sum_probs=75.7

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHH----HHHHHHHcCCCCCHHHHHHHHHH
Q 040261          167 STITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKC----LFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       167 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~----~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      .++..-|.+.+++++|++++..-..               .+.+.|+...|-+    +++-+.+.+++++......++..
T Consensus        37 Rtl~~Ry~~~~~~~eAidlL~~ga~---------------~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l  101 (312)
T 2wpv_A           37 RTIANRYVRSKSYEHAIELISQGAL---------------SFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRL  101 (312)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHH---------------HHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            3344445666677777666544221               2233344444333    33444455666676666666666


Q ss_pred             HHhCCChh-HHHHHHHHHHH----cC--CCCCHHHHHHHHHHHhcCCchHHHHHHHH----------------HHHhC--
Q 040261          243 LCKNGKMD-EASRLLELMIQ----IG--VRPDASVYNTLMDGFCLTGRVNRAKELFV----------------SMESN--  297 (343)
Q Consensus       243 ~~~~~~~~-~a~~~~~~~~~----~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----------------~~~~~--  297 (343)
                      +.....-+ .-.++++++++    .|  ..-++.....+...|.+.|++.+|+..|-                ...+.  
T Consensus       102 ~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~~~~s~~~~a~~l~~w~~~~~~  181 (312)
T 2wpv_A          102 IAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDD  181 (312)
T ss_dssp             HTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhCCCccHHHHHHHHHHHHHhcCC
Confidence            55432211 12333444432    11  12356667777777777777777766442                11111  


Q ss_pred             CCCccHHHH-HHHHHHHHhcCChHHHHHHHHHHH
Q 040261          298 GCMRDVFSY-GILINGYCKNKEIEGALSLYSEML  330 (343)
Q Consensus       298 ~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~  330 (343)
                      |.+-+...| ...+--|.-.|+...|..+++...
T Consensus       182 ~~~~e~dlf~~RaVL~yL~l~n~~~A~~~~~~f~  215 (312)
T 2wpv_A          182 IEDSTVAEFFSRLVFNYLFISNISFAHESKDIFL  215 (312)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            221122222 222334667788888888887665

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=88.50  E-value=7.9  Score=30.61  Aligned_cols=21  Identities=19%  Similarity=0.145  Sum_probs=13.9

Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 040261          311 NGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       311 ~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      --|...++...|..+++...+
T Consensus       195 L~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          195 LPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHH
Confidence            346667788888777666553

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=88.14  E-value=5  Score=27.89  Aligned_cols=24  Identities=8%  Similarity=0.147  Sum_probs=14.2

Q ss_pred             HHHHHHHhcCCchHHHHHHHHHHH
Q 040261          272 NTLMDGFCLTGRVNRAKELFVSME  295 (343)
Q Consensus       272 ~~l~~~~~~~~~~~~a~~~~~~~~  295 (343)
                      -.+..+|.+.+++++|+.+++.+.
T Consensus       126 ykia~C~~~l~~~~~Ai~~Le~Ip  149 (167)
T 3ffl_A          126 YKLAECYTVLKQDKDAIAILDGIP  149 (167)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHCCHHHHHHHHhcCC
Confidence            335556666666666666665543

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=87.32  E-value=1.7  Score=29.73  Aligned_cols=56  Identities=16%  Similarity=0.153  Sum_probs=45.4

Q ss_pred             hhHHHHHHHHhHhCCCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHH
Q 040261           33 YDTVLSLFKRLNSIGLFP-DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAV   88 (343)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~   88 (343)
                      .+++.++|..|...|+-. -+..|......+...|++.+|.++|..-++.+..|-..
T Consensus        81 ~~dp~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~~r  137 (152)
T 4a1g_A           81 NSDLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQNQAEPREF  137 (152)
T ss_dssp             BSCHHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHHH
T ss_pred             cCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHHH
Confidence            345899999998887654 34578888888999999999999999999987777543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=87.19  E-value=9.3  Score=29.93  Aligned_cols=25  Identities=24%  Similarity=0.227  Sum_probs=16.7

Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHH
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLL  256 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~  256 (343)
                      ++.....+...|.+.+++.+|...|
T Consensus       133 dp~LH~~~a~~~~~e~~~~~A~~H~  157 (312)
T 2wpv_A          133 DPYLHNTIGSKLLEGDFVYEAERYF  157 (312)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhcCCHHHHHHHH
Confidence            4556666677777777777766655

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=86.90  E-value=5.5  Score=30.28  Aligned_cols=117  Identities=12%  Similarity=0.025  Sum_probs=71.3

Q ss_pred             HHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC--ccHHHHHHHHHHHhhcCc
Q 040261           25 GCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT--PDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  102 (343)
                      ..+.+.|++++|++....-++.. |-|...-..++..+|-.|++++|.+-++...+....  |-...|..+|++      
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~a------   77 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKA------   77 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH------
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHH------
Confidence            45667888999988888877765 567777788888899999999998888887765321  122233333332      


Q ss_pred             HHHHHHHHHHHHhcCCCC-----CHHHHHHHHHHH--HhcCChHHHHHHHHHHHccC
Q 040261          103 IMEAAALFTKLRAFGCKP-----DVFTYTTLINGL--CRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~  152 (343)
                          +..=.+...-+-.|     ...-...++.+.  ...|+.++|..+-.++.+..
T Consensus        78 ----E~~R~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~a  130 (273)
T 1zbp_A           78 ----AQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  130 (273)
T ss_dssp             ----HHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             ----HHHHHHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhcC
Confidence                22222222222111     222233444443  34688888888888876654

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.77  E-value=10  Score=31.37  Aligned_cols=62  Identities=8%  Similarity=-0.067  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHc
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFG--CKPDVFTYTTLINGLCRTGHTIVALNLFEEMAN  150 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  150 (343)
                      +...+...|.+.|+++.|.+.+.++....  ...-...+...+..+...+++..+...+.++..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~  196 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNS  196 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            45566777777777777777777776542  222344566667777777777777777766543

>2wvi_A Mitotic checkpoint serine/threonine-protein kinase BUB1 beta; tumor suppressor, TPR, apoptosis, cell division, cell cycle, kinetochore, transferase; 1.80A {Homo sapiens} PDB: 3si5_A

Probab=85.30  E-value=2.5  Score=29.34  Aligned_cols=56  Identities=9%  Similarity=0.045  Sum_probs=45.4

Q ss_pred             hHHHHHHHHhHhCCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHH
Q 040261           34 DTVLSLFKRLNSIGLFPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVT   89 (343)
Q Consensus        34 ~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   89 (343)
                      +.+.++|..|...|+-.. +..|......+-..|++.+|.++|..-++.+..|-...
T Consensus        77 ~~p~~if~~L~~~~IG~~~AlfY~~wA~~lE~~~~~~~A~~Iy~~Gi~~~A~P~~~L  133 (164)
T 2wvi_A           77 NEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLERL  133 (164)
T ss_dssp             SCHHHHHHHHHHTTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHHHH
T ss_pred             CCHHHHHHHHHHCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHH
Confidence            457889999988876543 45688888889999999999999999999887776543

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=85.20  E-value=8.7  Score=27.72  Aligned_cols=57  Identities=12%  Similarity=0.130  Sum_probs=43.5

Q ss_pred             CCcchHHHHHHHHHHcCCCcc-HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCH
Q 040261           66 GRVSPGFVVLGRILRSCFTPD-AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDV  122 (343)
Q Consensus        66 ~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  122 (343)
                      +....+.++|..|...|+... +..|......+-..|++.+|.++|+.-++.+..|-.
T Consensus        93 ~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P~~  150 (202)
T 3esl_A           93 NNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPYN  150 (202)
T ss_dssp             TCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHH
T ss_pred             cccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHH
Confidence            335688888888888765543 556777788888889999999999988888777643

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.27  E-value=5.6  Score=24.79  Aligned_cols=88  Identities=14%  Similarity=0.114  Sum_probs=55.7

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      -....++|..+-+.+...+.  ...+--+-+..+...|++++|..+.+..    ..||...|..+..  .+.|..+++..
T Consensus        18 G~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce--~rlGl~s~le~   89 (115)
T 2uwj_G           18 GQHCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGN----PWPALEPWFALCE--WHLGLGAALDR   89 (115)
T ss_dssp             TTTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTC----CCGGGHHHHHHHH--HHTTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHHH--HhcccHHHHHH
Confidence            34567888888888776542  2222233344567788888887766543    3678887766655  36677778877


Q ss_pred             HHHHHHhcCCCCCHHHH
Q 040261          109 LFTKLRAFGCKPDVFTY  125 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~  125 (343)
                      .+.++...| +|....|
T Consensus        90 rL~~la~sg-~p~~q~F  105 (115)
T 2uwj_G           90 RLAGLGGSS-DPALADF  105 (115)
T ss_dssp             HHHHHHTCS-SHHHHHH
T ss_pred             HHHHHHhCC-CHHHHHH
Confidence            777777665 3344333

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=83.78  E-value=6  Score=24.72  Aligned_cols=88  Identities=13%  Similarity=0.112  Sum_probs=56.6

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      -....++|..+-+.+...+.  ...+--+-+..+...|++++|..+.+..    ..||...|..+..  .+.|..+++..
T Consensus        19 G~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce--~rlGl~s~le~   90 (116)
T 2p58_C           19 GNHYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKL----AYPDLEPWLALCE--YRLGLGSALES   90 (116)
T ss_dssp             TTTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTS----CCGGGHHHHHHHH--HHHTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHHH--HhcccHHHHHH
Confidence            35567888888888776542  2222233345567888888888776554    3678888776655  36677777777


Q ss_pred             HHHHHHhcCCCCCHHHH
Q 040261          109 LFTKLRAFGCKPDVFTY  125 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~  125 (343)
                      .+.++...| .|....|
T Consensus        91 rL~~la~sg-~p~~q~F  106 (116)
T 2p58_C           91 RLNRLARSQ-DPRIQTF  106 (116)
T ss_dssp             HHHHHTTCC-CHHHHHH
T ss_pred             HHHHHHhCC-CHHHHHH
Confidence            777777665 3344443

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=82.57  E-value=18  Score=29.43  Aligned_cols=166  Identities=11%  Similarity=0.027  Sum_probs=93.9

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhc-CCCC---CHHHHHHHHHHHHhc-CChHHHHHHHHHHHccCCCCCccccCCc
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAF-GCKP---DVFTYTTLINGLCRT-GHTIVALNLFEEMANGNGEFGVVCKPDA  163 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~  163 (343)
                      ....+...|.+.|+.++..+++...+.. +.-+   .......++..+... +..+.-.++.....+..       ....
T Consensus        21 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a-------~~~~   93 (394)
T 3txn_A           21 GILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWA-------KQEK   93 (394)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHH-------HHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH-------HHHH
Confidence            3444556666666666666665554321 0001   122344455555443 22333333333333321       1122


Q ss_pred             chH------HHHHHHHHhcCChHHHHHHHHHhhhCCCCCC-----hhhHHHHHHHHhccCcHHHHHHHHHHHHHc--CCC
Q 040261          164 ITY------STITDGLCKEGFVDKAKELFLKMKDENINPD-----VVTYTSLIRGFCYANDWNEAKCLFIEMMDQ--GVQ  230 (343)
Q Consensus       164 ~~~------~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~  230 (343)
                      .+|      ..++..|...|++.+|..++..+.+.--..|     ...+..-++.|...+++.++...+......  .+.
T Consensus        94 r~flr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~  173 (394)
T 3txn_A           94 RTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIY  173 (394)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCC
Confidence            333      2578899999999999999988765311112     233555567788899999999988877643  233


Q ss_pred             CCHHHHHHH----HHHHH-hCCChhHHHHHHHHHHH
Q 040261          231 PNVVTFNVI----MNELC-KNGKMDEASRLLELMIQ  261 (343)
Q Consensus       231 ~~~~~~~~l----~~~~~-~~~~~~~a~~~~~~~~~  261 (343)
                      +++.....+    ...+. ..+++..|...|-+..+
T Consensus       174 ~~p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~  209 (394)
T 3txn_A          174 CPPKVQGALDLQSGILHAADERDFKTAFSYFYEAFE  209 (394)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhHHHHHhccCHHHHHHHHHHHHh
Confidence            444333222    23455 78999999888866643

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=82.47  E-value=12  Score=27.07  Aligned_cols=57  Identities=25%  Similarity=0.325  Sum_probs=36.8

Q ss_pred             cCcHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCC
Q 040261          211 ANDWNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPD  267 (343)
Q Consensus       211 ~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  267 (343)
                      .+...++..+|..|...|+--. ...|......+...|++.+|..+|+.-++.+-.|-
T Consensus        92 ~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~A~P~  149 (202)
T 3esl_A           92 SNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENNCRPY  149 (202)
T ss_dssp             TTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSH
T ss_pred             ccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccH
Confidence            3345567777777776655433 44555666666777777777777777777665553

>3eiq_C Programmed cell death protein 4; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Mus musculus}

Probab=80.89  E-value=20  Score=28.73  Aligned_cols=66  Identities=15%  Similarity=0.194  Sum_probs=31.7

Q ss_pred             HHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC--hhHHHHHHHHHHHcCCCCC
Q 040261          201 YTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK--MDEASRLLELMIQIGVRPD  267 (343)
Q Consensus       201 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~  267 (343)
                      ...++.-|...++.++|...++++..-... ...+...+..++.+.++  .+....++..+...|+-+.
T Consensus       220 i~~lL~EY~~s~D~~EA~~ci~EL~~p~fh-he~V~~av~~aLE~~~~~~re~~~~LL~~L~~~glls~  287 (358)
T 3eiq_C          220 IDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITI  287 (358)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHCCTTCH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCH
T ss_pred             HHHHHHHhccCCCHHHHHHHHHHccCCcch-HHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCCCH
Confidence            355566666667777777777666321100 12222333333333222  3345566666665554433

>4aez_C MAD3, mitotic spindle checkpoint component MAD3; cell cycle, KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}

Probab=80.75  E-value=3.7  Score=30.16  Aligned_cols=67  Identities=16%  Similarity=0.062  Sum_probs=50.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccH
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFP-DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDA   87 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~   87 (343)
                      -|-.+--.|+..  .+++.++|..|...|+-. -+..|......+...|++.+|.++|..-++.+..|-.
T Consensus       118 RyLklWl~Ya~~--~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~~  185 (223)
T 4aez_C          118 RYLRIWMQYVNY--IDEPVELFSFLAHHHIGQESSIFYEEYANYFESRGLFQKADEVYQKGKRMKAKPFL  185 (223)
T ss_dssp             HHHHHHHHHHTT--CSCHHHHHHHHHHTTCSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCBSHH
T ss_pred             HHHHHHHHHHHc--cCCHHHHHHHHHHCCcchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHH
Confidence            344444444443  467889999998887654 3457888888899999999999999999988777654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	343
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.93
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.9
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.78
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.76
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.53
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.52
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.47
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.47
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.45
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.44
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.42
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.36
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.35
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.33
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	99.02
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	99.0
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.97
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.94
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.94
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.91
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.9
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.87
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.85
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.82
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.81
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.8
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.7
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.69
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.68
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.59
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.55
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.48
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.46
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.42
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.39
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.36
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.35
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.3
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.27
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.24
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.24
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.24
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.23
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.15
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.14
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.12
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.1
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.03
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.95
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.7
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.63
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.55
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.5
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	97.44
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	97.34
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.55
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.39
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	96.12
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	95.93
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.73
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	93.28
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.18
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	88.74
d1bpoa1	157	Clathrin heavy-chain linker domain {Rat (Rattus no	87.03

>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=99.93  E-value=6.8e-22  Score=161.23  Aligned_cols=319  Identities=15%  Similarity=0.074  Sum_probs=250.7

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRS   81 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   81 (343)
                      ++|+.+.+..|.  ++.++..+..++.+.|++++|...|++..+.. +.+..++..+..++.+.|++++|...+......
T Consensus        20 ~~~~~~l~~~p~--~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~   96 (388)
T d1w3ba_          20 RHCMQLWRQEPD--NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRL   96 (388)
T ss_dssp             HHHHHHHHHCTT--CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccccccccccccc
Confidence            456777776654  77888888888888888888888888887754 445678888888888888888888888887765


Q ss_pred             CCCccHHHHH----------------------------------HHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261           82 CFTPDAVTFT----------------------------------SLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus        82 ~~~~~~~~~~----------------------------------~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      ... +.....                                  .........+....+...+......... +...+..
T Consensus        97 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  174 (388)
T d1w3ba_          97 KPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPN-FAVAWSN  174 (388)
T ss_dssp             CTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             ccc-cccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcc-hhHHHHh
Confidence            422 111111                                  1222222333444455555554444322 5667778


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHH
Q 040261          128 LINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRG  207 (343)
Q Consensus       128 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  207 (343)
                      +...+...|++++|...+++..+..       +.+..++..+...+...|++++|...+++....+ +.+...+..+...
T Consensus       175 l~~~~~~~~~~~~A~~~~~~al~~~-------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  246 (388)
T d1w3ba_         175 LGCVFNAQGEIWLAIHHFEKAVTLD-------PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACV  246 (388)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hcccccccCcHHHHHHHHHHHHHhC-------cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHH
Confidence            8888999999999999999998865       4456788899999999999999999999987764 3467778888999


Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      +.+.|++++|...+++..+.. +-+..++..+...+...|++++|...++...... +.+...+..+...+...|++++|
T Consensus       247 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A  324 (388)
T d1w3ba_         247 YYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEA  324 (388)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHH
Confidence            999999999999999998863 4457788899999999999999999999998875 67788899999999999999999


Q ss_pred             HHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          288 KELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      ...+++..+.. +.+..++..+..+|...|++++|.+.|++.++.  .|+.
T Consensus       325 ~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~  372 (388)
T d1w3ba_         325 VRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTF  372 (388)
T ss_dssp             HHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCC
Confidence            99999998763 345778889999999999999999999999854  5654

>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=99.90  E-value=9.4e-20  Score=148.39  Aligned_cols=300  Identities=14%  Similarity=0.061  Sum_probs=243.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCc
Q 040261           23 LFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESR  102 (343)
Q Consensus        23 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  102 (343)
                      +...+.+.|++++|.+.++++.+.. |-+...+..+..++.+.|++++|...++++++..+ -+..++..+..++.+.|+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNP-LLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHhhhhcc
Confidence            5567789999999999999998764 44678899999999999999999999999998753 367889999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHH----------------------------------HHHhcCChHHHHHHHHHH
Q 040261          103 IMEAAALFTKLRAFGCKPDVFTYTTLIN----------------------------------GLCRTGHTIVALNLFEEM  148 (343)
Q Consensus       103 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~----------------------------------~~~~~~~~~~a~~~~~~~  148 (343)
                      +++|++.+......... +.........                                  .....+....+...+...
T Consensus        83 ~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (388)
T d1w3ba_          83 LQEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             ccccccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHh
Confidence            99999999998876433 2222222222                                  223344444555555555


Q ss_pred             HccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040261          149 ANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG  228 (343)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  228 (343)
                      ....       +.+...+..+...+...|++++|...+++..+.. +-+...+..+...+...|++++|...++.....+
T Consensus       162 ~~~~-------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  233 (388)
T d1w3ba_         162 IETQ-------PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS  233 (388)
T ss_dssp             HHHC-------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC
T ss_pred             hccC-------cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh
Confidence            5443       3345677888889999999999999999987754 3357788899999999999999999999998875


Q ss_pred             CCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHH
Q 040261          229 VQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGI  308 (343)
Q Consensus       229 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  308 (343)
                       +.+...+..+...+.+.|++++|...++++.+.. +-+..++..+...+...|++++|.+.++...... +.+...+..
T Consensus       234 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~  310 (388)
T d1w3ba_         234 -PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNN  310 (388)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             -hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhH
Confidence             5567778889999999999999999999999875 5567889999999999999999999999988763 567788889


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhCCCCCCc
Q 040261          309 LINGYCKNKEIEGALSLYSEMLSKGIRPTV  338 (343)
Q Consensus       309 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  338 (343)
                      +...+...|++++|++.|++.++.  .|+.
T Consensus       311 l~~~~~~~~~~~~A~~~~~~al~~--~p~~  338 (388)
T d1w3ba_         311 LANIKREQGNIEEAVRLYRKALEV--FPEF  338 (388)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHTTS--CTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh--CCCC
Confidence            999999999999999999998854  5654

>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=99.78  E-value=3.3e-16  Score=124.15  Aligned_cols=232  Identities=12%  Similarity=0.010  Sum_probs=138.6

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      ........+.+.|++++|+..|+++.+.. |.+..+|..+..++...|+++.|...+.+..+..+. +...+..+...+.
T Consensus        21 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~   98 (323)
T d1fcha_          21 QPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPD-NQTALMALAVSFT   98 (323)
T ss_dssp             SHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc-ccccccccccccc
Confidence            34456778889999999999999998865 446788999999999999999999999999887533 6778888899999


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHH----------------HHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCC
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTY----------------TTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPD  162 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~----------------~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  162 (343)
                      ..|++++|.+.+++......  +....                ...+..+...+...++...+.+.....+     ...+
T Consensus        99 ~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p-----~~~~  171 (323)
T d1fcha_          99 NESLQRQACEILRDWLRYTP--AYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDP-----TSID  171 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHTST--TTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHST-----TSCC
T ss_pred             ccccccccccchhhHHHhcc--chHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhh-----cccc
Confidence            99999999999999877532  21110                0111122223334444444444443321     1122


Q ss_pred             cchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040261          163 AITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNE  242 (343)
Q Consensus       163 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  242 (343)
                      ..++..+...+...|++++|+..+++..... +-+...|..+..++...|++++|...+++..+.. +-+..++..+..+
T Consensus       172 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~  249 (323)
T d1fcha_         172 PDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGIS  249 (323)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHH
Confidence            3334444444555555555555555544332 1234444444455555555555555555544432 1223344444455


Q ss_pred             HHhCCChhHHHHHHHHHHH
Q 040261          243 LCKNGKMDEASRLLELMIQ  261 (343)
Q Consensus       243 ~~~~~~~~~a~~~~~~~~~  261 (343)
                      |.+.|++++|+..|++.++
T Consensus       250 ~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         250 CINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            5555555555555544443

>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=99.76  E-value=2e-15  Score=119.56  Aligned_cols=263  Identities=11%  Similarity=0.029  Sum_probs=201.3

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 040261           57 ILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG  136 (343)
Q Consensus        57 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  136 (343)
                      .....+.+.|++++|...|+++++..+. +..+|..+..++...|++++|...+++..+..+. +...+..+..+|...|
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENEQELLAISALRRCLELKPD-NQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc-cccccccccccccccc
Confidence            4566788999999999999999987533 6888999999999999999999999999987544 6788889999999999


Q ss_pred             ChHHHHHHHHHHHccCCCCCccccC--------CcchHHHHHHHHHhcCChHHHHHHHHHhhhCC-CCCChhhHHHHHHH
Q 040261          137 HTIVALNLFEEMANGNGEFGVVCKP--------DAITYSTITDGLCKEGFVDKAKELFLKMKDEN-INPDVVTYTSLIRG  207 (343)
Q Consensus       137 ~~~~a~~~~~~~~~~~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~  207 (343)
                      ++++|.+.+++.....+........        +.......+..+...+...+|...+.+..... -.++...+..+...
T Consensus       102 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~  181 (323)
T d1fcha_         102 LQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL  181 (323)
T ss_dssp             CHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH
T ss_pred             cccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHH
Confidence            9999999999988765321110000        00011112233445567788888888876543 22356678888889


Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      +...|++++|...++...... +-+...|..+..++...|++++|...++++++.. +-+..++..+..+|.+.|++++|
T Consensus       182 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A  259 (323)
T d1fcha_         182 FNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREA  259 (323)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHHHHHCCCHHHH
Confidence            999999999999999998874 4457788899999999999999999999999875 45678899999999999999999


Q ss_pred             HHHHHHHHhCC----------CCccHHHHHHHHHHHHhcCChHHHH
Q 040261          288 KELFVSMESNG----------CMRDVFSYGILINGYCKNKEIEGAL  323 (343)
Q Consensus       288 ~~~~~~~~~~~----------~~~~~~~~~~l~~~~~~~~~~~~a~  323 (343)
                      ...|++..+..          .......|..+-.++...|+.+.+.
T Consensus       260 ~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~  305 (323)
T d1fcha_         260 VEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  305 (323)
T ss_dssp             HHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            99999887631          1112235666666777777766554

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=3.6e-12  Score=99.76  Aligned_cols=165  Identities=4%  Similarity=-0.004  Sum_probs=107.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC-cchHHHHHHHHHHcCCCccHHHHHHHHH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR-VSPGFVVLGRILRSCFTPDAVTFTSLIK   95 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~   95 (343)
                      ..+|+.+...+.+.+.+++|+++++++++.+ |-+..+|+....++...|+ +++|+..++..++..+. +..+|+.+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHHHhH
Confidence            4556666667777777777777777777754 3455566777766666553 67777777777766433 5667777777


Q ss_pred             HHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHh
Q 040261           96 GLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCK  175 (343)
Q Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  175 (343)
                      .+.+.|++++|+..++++.+..+. +...|..+...+...|++++|++.++++.+.+       +.+..+|+.+..++.+
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~dp~-n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-------p~n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-------VRNNSVWNQRYFVISN  192 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHhhhhhhhhc-chHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-------CccHHHHHHHHHHHHH
Confidence            777777777777777777766443 56677777777777777777777777777754       3445566655555444


Q ss_pred             cCC------hHHHHHHHHHhhh
Q 040261          176 EGF------VDKAKELFLKMKD  191 (343)
Q Consensus       176 ~~~------~~~a~~~~~~~~~  191 (343)
                      .+.      +++|+..+.+..+
T Consensus       193 ~~~~~~~~~~~~ai~~~~~al~  214 (315)
T d2h6fa1         193 TTGYNDRAVLEREVQYTLEMIK  214 (315)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHH
T ss_pred             ccccchhhhhHHhHHHHHHHHH
Confidence            433      3444444444444

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.7e-11  Score=95.86  Aligned_cols=233  Identities=10%  Similarity=0.043  Sum_probs=178.4

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcC-cHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 040261           52 LYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAES-RIMEAAALFTKLRAFGCKPDVFTYTTLIN  130 (343)
Q Consensus        52 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  130 (343)
                      ...++.+...+.+.+..++|++.++++++.++. +...|+....++...| ++++|+..+++..+..+. +..+|..+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~-~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCC-ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHHHhH
Confidence            346777777888999999999999999998643 6778888888888766 589999999999988655 7889999999


Q ss_pred             HHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc
Q 040261          131 GLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY  210 (343)
Q Consensus       131 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  210 (343)
                      .+.+.|++++|+..++++.+.+       +.+..+|..+..++.+.|++++|+..++++.+.+. .+...|+.+..++.+
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-------p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISN  192 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-------hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHH
Confidence            9999999999999999999976       56788999999999999999999999999988752 366777766655544


Q ss_pred             cC------cHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhcC--
Q 040261          211 AN------DWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVR-PDASVYNTLMDGFCLT--  281 (343)
Q Consensus       211 ~~------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~--  281 (343)
                      .+      .+++|+..+....+.. +.+...|..+...+.. ...+++...++...+.... .+...+..++..|...  
T Consensus       193 ~~~~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~~~~  270 (315)
T d2h6fa1         193 TTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLE  270 (315)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHH
T ss_pred             ccccchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHHHHh
Confidence            43      4788999998888874 4467777777666554 4467888888888775322 2345556666665432  


Q ss_pred             C-------chHHHHHHHHHHHh
Q 040261          282 G-------RVNRAKELFVSMES  296 (343)
Q Consensus       282 ~-------~~~~a~~~~~~~~~  296 (343)
                      +       .+++|..++..+..
T Consensus       271 ~~~~~~~~~~~ka~~l~~~l~~  292 (315)
T d2h6fa1         271 NQCDNKEDILNKALELCEILAK  292 (315)
T ss_dssp             TTCSSHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHHHHH
Confidence            2       24455555555443

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.47  E-value=4.3e-11  Score=95.41  Aligned_cols=306  Identities=9%  Similarity=-0.036  Sum_probs=212.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC-----ccH
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD----LYTYNILINCFCKMGRVSPGFVVLGRILRSCFT-----PDA   87 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~   87 (343)
                      .+........+...|++++|++++++..+.....+    ...+..+..++...|++++|...+++..+....     ...
T Consensus        12 ae~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   91 (366)
T d1hz4a_          12 AEFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYAL   91 (366)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHH
Confidence            34555567778899999999999999877431111    246777888999999999999999988753211     113


Q ss_pred             HHHHHHHHHHhhcCcHHHHHHHHHHHHhc----CCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcccc
Q 040261           88 VTFTSLIKGLCAESRIMEAAALFTKLRAF----GCKP---DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        88 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      ..+..+...+...|++..+...+.+....    +...   ....+..+...+...|+++.+...+...........  ..
T Consensus        92 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~  169 (366)
T d1hz4a_          92 WSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQ--PQ  169 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSC--GG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhh--hh
Confidence            35566677888899999999988876542    1111   123455677889999999999999998877653221  12


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCCC--ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCC---
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDE----NINP--DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQP---  231 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---  231 (343)
                      .....+......+...++...+...+......    +..+  ....+......+...|++++|...++...+.....   
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  249 (366)
T d1hz4a_         170 QQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHF  249 (366)
T ss_dssp             GGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGG
T ss_pred             hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchH
Confidence            22345566677788899999998888765432    1111  12345666777888999999999998876543222   


Q ss_pred             CHHHHHHHHHHHHhCCChhHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHhcCCchHHHHHHHHHHHhC----CCCc-
Q 040261          232 NVVTFNVIMNELCKNGKMDEASRLLELMIQI----GVRPD-ASVYNTLMDGFCLTGRVNRAKELFVSMESN----GCMR-  301 (343)
Q Consensus       232 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-  301 (343)
                      ....+..+..++...|++++|...++.+...    +..|+ ...+..+...|...|++++|.+.+++..+.    |... 
T Consensus       250 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~  329 (366)
T d1hz4a_         250 LQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISH  329 (366)
T ss_dssp             GHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHH
Confidence            2345566788999999999999999988643    33333 456788888999999999999999887542    2211 


Q ss_pred             ---cHHHHHHHHHHHHhcCChHHHHH
Q 040261          302 ---DVFSYGILINGYCKNKEIEGALS  324 (343)
Q Consensus       302 ---~~~~~~~l~~~~~~~~~~~~a~~  324 (343)
                         .......++..+...++.+++.+
T Consensus       330 ~~~~~~~~~~~~~~l~~~~~l~e~e~  355 (366)
T d1hz4a_         330 FVIEGEAMAQQLRQLIQLNTLPELEQ  355 (366)
T ss_dssp             HHTTHHHHHHHHHHHHHTTCSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCChHHHH
Confidence               12234455666667777666654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=6.1e-11  Score=92.57  Aligned_cols=189  Identities=10%  Similarity=0.054  Sum_probs=150.8

Q ss_pred             CChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHH
Q 040261          136 GHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWN  215 (343)
Q Consensus       136 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  215 (343)
                      +..++|..++++..+..      .+.+...|...+....+.|+.+.|..+|+++.+.........|...+..+.+.|+.+
T Consensus        78 ~~~~~a~~i~~ral~~~------~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~  151 (308)
T d2onda1          78 LFSDEAANIYERAISTL------LKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIK  151 (308)
T ss_dssp             HHHHHHHHHHHHHHTTT------TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHH
T ss_pred             cchHHHHHHHHHHHHHc------CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChH
Confidence            34578889999988754      344556788888999999999999999999987643333457889999999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHH
Q 040261          216 EAKCLFIEMMDQGVQPNVVTFNVIMNE-LCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSM  294 (343)
Q Consensus       216 ~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  294 (343)
                      .|..+|+.+.+.+ +.+...|...... +...|+.+.|..+|+.+.+.. +.+...|...+..+...|+++.|+.+|++.
T Consensus       152 ~ar~i~~~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~a  229 (308)
T d2onda1         152 SGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERV  229 (308)
T ss_dssp             HHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            9999999998874 3344455444433 345689999999999999873 667889999999999999999999999998


Q ss_pred             HhCC-CCcc--HHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          295 ESNG-CMRD--VFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       295 ~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      .... ..|+  ...|...+..-...|+.+.+.++++++.+.
T Consensus       230 i~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         230 LTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            8753 2332  457888888888899999999999988654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=4.2e-11  Score=93.49  Aligned_cols=188  Identities=10%  Similarity=0.059  Sum_probs=139.3

Q ss_pred             CcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHH
Q 040261           67 RVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFE  146 (343)
Q Consensus        67 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  146 (343)
                      ..++|..+|++.++...+.+...|...+....+.|+++.|..+|+++.+.........|...+..+.+.|+.+.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            45677888888876544445667777788888888888888888888876544345577888888888888888888888


Q ss_pred             HHHccCCCCCccccCCcchHHHHHHH-HHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHH
Q 040261          147 EMANGNGEFGVVCKPDAITYSTITDG-LCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMM  225 (343)
Q Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  225 (343)
                      ++....       +.+...|...... +...|+.+.|..+|+.+.... +.+...|...+..+.+.|+++.|..+|++..
T Consensus       159 ~al~~~-------~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai  230 (308)
T d2onda1         159 KAREDA-------RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVL  230 (308)
T ss_dssp             HHHTST-------TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHhC-------CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            888764       3444555544443 344678888888888887753 3457778888888888888999989998887


Q ss_pred             HcC-CCCC--HHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          226 DQG-VQPN--VVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       226 ~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      +.. ..|.  ...|...+..-...|+.+.+..+++++.+.
T Consensus       231 ~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         231 TSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            763 2332  346777777777788999988888888764

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.44  E-value=3.4e-11  Score=95.98  Aligned_cols=278  Identities=12%  Similarity=0.002  Sum_probs=196.2

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHcCCCcc----HHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCC-CC----HHH
Q 040261           54 TYNILINCFCKMGRVSPGFVVLGRILRSCFTPD----AVTFTSLIKGLCAESRIMEAAALFTKLRAFGCK-PD----VFT  124 (343)
Q Consensus        54 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~  124 (343)
                      ........+...|++++|.+++++.++.....+    ...+..+..++...|++++|.+.+++..+.... ++    ...
T Consensus        14 ~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~   93 (366)
T d1hz4a_          14 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   93 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHH
Confidence            344456677899999999999999987643211    245677788999999999999999987653211 11    234


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccC-CcchHHHHHHHHHhcCChHHHHHHHHHhhhC----CCCCChh
Q 040261          125 YTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKP-DAITYSTITDGLCKEGFVDKAKELFLKMKDE----NINPDVV  199 (343)
Q Consensus       125 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~  199 (343)
                      +..+...+...|++..+...+...............+ ....+..+...+...|+++.+...+......    +......
T Consensus        94 ~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  173 (366)
T d1hz4a_          94 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  173 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHH
Confidence            5667778899999999999988765432100000011 1235566778889999999999999887653    2222344


Q ss_pred             hHHHHHHHHhccCcHHHHHHHHHHHHHcC--CCCC----HHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCC---CCHHH
Q 040261          200 TYTSLIRGFCYANDWNEAKCLFIEMMDQG--VQPN----VVTFNVIMNELCKNGKMDEASRLLELMIQIGVR---PDASV  270 (343)
Q Consensus       200 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~  270 (343)
                      .+......+...+++..+...+.......  ....    ...+..+...+...|++++|...++...+....   .....
T Consensus       174 ~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  253 (366)
T d1hz4a_         174 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  253 (366)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHH
Confidence            55566677788899999888887765431  1111    234556677788999999999999887664322   22455


Q ss_pred             HHHHHHHHhcCCchHHHHHHHHHHHh----CCCCcc-HHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          271 YNTLMDGFCLTGRVNRAKELFVSMES----NGCMRD-VFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       271 ~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      +..+..++...|++++|...+++...    .+..|+ ...+..+...|...|++++|.+.+++.+.
T Consensus       254 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         254 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            66788899999999999999988763    233333 45777888999999999999999998764

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.42  E-value=1.7e-12  Score=102.89  Aligned_cols=275  Identities=9%  Similarity=-0.026  Sum_probs=184.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCC-HHHHHHHHHHH----------HhcCCcchHHHHHHHHHHcCCCccHH
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPD-LYTYNILINCF----------CKMGRVSPGFVVLGRILRSCFTPDAV   88 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~----------~~~~~~~~a~~~~~~~~~~~~~~~~~   88 (343)
                      ...++......+..++|++++++..+..  |+ ...|+..-..+          ...|++++|+..++.+.+..+. +..
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~~--P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk-~~~  108 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYG  108 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCC-cHH
Confidence            3334333334444589999999988754  44 34454433322          2334577888899988876533 666


Q ss_pred             HHHHHHHHHhhcC--cHHHHHHHHHHHHhcCCCCCHHHHH-HHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcch
Q 040261           89 TFTSLIKGLCAES--RIMEAAALFTKLRAFGCKPDVFTYT-TLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAIT  165 (343)
Q Consensus        89 ~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  165 (343)
                      .|..+..++...+  ++++|...+.+..+.... +...+. .....+...+.+++|+..++.+...+       +.+...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-------p~~~~a  180 (334)
T d1dcea1         109 TWHHRCWLLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-------FSNYSS  180 (334)
T ss_dssp             HHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-------CCCHHH
T ss_pred             HHHHhhHHHHHhccccHHHHHHHHHHHHhhCch-hhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-------CCCHHH
Confidence            7777766666654  478999999998887443 455544 44567777899999999999888875       456778


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 040261          166 YSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK  245 (343)
Q Consensus       166 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  245 (343)
                      |..+..++.+.|++++|...+.......  |..   ......+...+..+++...+....... +++...+..+...+..
T Consensus       181 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~---~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~  254 (334)
T d1dcea1         181 WHYRSCLLPQLHPQPDSGPQGRLPENVL--LKE---LELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTV  254 (334)
T ss_dssp             HHHHHHHHHHHSCCCCSSSCCSSCHHHH--HHH---HHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHhHHhH--HHH---HHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHH
Confidence            8888888999998887766655443321  111   112233344555666777777766653 4445556666777777


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCcc-HHHHHHHHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRD-VFSYGILINGYC  314 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~  314 (343)
                      .++.++|...+.+..... +.+..++..+...+...|+.++|.+.++++.+.  .|+ ...|..+...+.
T Consensus       255 ~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         255 LQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            888999999888887654 345677788888999999999999999999885  454 445555554444

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.36  E-value=3.8e-11  Score=91.33  Aligned_cols=96  Identities=13%  Similarity=-0.066  Sum_probs=56.7

Q ss_pred             HHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHH
Q 040261           89 TFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYST  168 (343)
Q Consensus        89 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (343)
                      ++..+..+|.+.|++++|++.|++..+..+. +..+|..+..++.+.|++++|...|+++.+..       +.+..++..
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-------p~~~~a~~~  110 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-------PTYNYAHLN  110 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCTHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-------hhhhhhHHH
Confidence            4445555566666666666666666655333 45556666666666666666666666666543       233445556


Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                      +..++...|++++|...|+...+.
T Consensus       111 lg~~~~~~g~~~~A~~~~~~al~~  134 (259)
T d1xnfa_         111 RGIALYYGGRDKLAQDDLLAFYQD  134 (259)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHhh
Confidence            666666666666666666665554

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.35  E-value=3.5e-11  Score=91.52  Aligned_cols=216  Identities=10%  Similarity=-0.031  Sum_probs=132.5

Q ss_pred             hhHHHHHHHHhHhCCC-CC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHH
Q 040261           33 YDTVLSLFKRLNSIGL-FP--DLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAAL  109 (343)
Q Consensus        33 ~~~a~~~~~~~~~~~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  109 (343)
                      .+.++.-+++...... .+  ...+|..+..+|.+.|++++|.+.|++.++..+ -+..+|..+..++.+.|++++|++.
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p-~~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRP-DMPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCC-CCHHHHhhhchHHHHHHHHHHhhhh
Confidence            4455555666554321 11  234677778888899999999999999988753 3678888899999999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHh
Q 040261          110 FTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKM  189 (343)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  189 (343)
                      |++..+..+. +..++..+..++...|++++|...++...+..       +.+......+...+.+.+..+.+..+....
T Consensus        94 ~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (259)
T d1xnfa_          94 FDSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-------PNDPFRSLWLYLAEQKLDEKQAKEVLKQHF  165 (259)
T ss_dssp             HHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             hhHHHHHHhh-hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-------cccHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence            9999887543 56678888888999999999999999988764       333444444444555555555555555554


Q ss_pred             hhCCCCCChhhHHHHHHHHhccCc----HHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          190 KDENINPDVVTYTSLIRGFCYAND----WNEAKCLFIEMMDQGVQPN-VVTFNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       190 ~~~~~~~~~~~~~~l~~~~~~~~~----~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      ....  +....+. ++..+.....    .+.+...+......  .|+ ..++..+...+...|++++|...|+..+..
T Consensus       166 ~~~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  238 (259)
T d1xnfa_         166 EKSD--KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSL--AEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  238 (259)
T ss_dssp             HHSC--CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHH--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hccc--hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhc--CcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            4432  1222222 2222222111    22222221111111  111 234455666666677777777777766654

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.33  E-value=6.8e-12  Score=99.40  Aligned_cols=259  Identities=9%  Similarity=-0.045  Sum_probs=187.3

Q ss_pred             hhHHHHHhcCCCCCChhhHHHHHHHHHh----------cCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC--cc
Q 040261            2 CIFDYMLRMHPSPPPVCSFNILFGCLAK----------NKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR--VS   69 (343)
Q Consensus         2 ~i~~~m~~~~~~~~~~~~~~~l~~~~~~----------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~   69 (343)
                      ++++......|.  +..+|+..-..+..          .|++++|+.+++...+.. +.+...|..+..++...++  ++
T Consensus        50 ~~~~~~l~~~P~--~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~  126 (334)
T d1dcea1          50 ELTSQILGANPD--FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWA  126 (334)
T ss_dssp             HHHHHHHHHCTT--CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHH
T ss_pred             HHHHHHHHHCCC--cHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHH
Confidence            467777776664  67777655444433          344788999999988765 4467778888777777665  67


Q ss_pred             hHHHHHHHHHHcCCCccHHHHH-HHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261           70 PGFVVLGRILRSCFTPDAVTFT-SLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEM  148 (343)
Q Consensus        70 ~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  148 (343)
                      +|...+.++.+.... +...+. .....+...+.+++|+..++++.+.++. +...|..+..++.+.|++++|...++..
T Consensus       127 ~a~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~-~~~a~~~l~~~~~~~~~~~~A~~~~~~~  204 (334)
T d1dcea1         127 RELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLP  204 (334)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCCSSC
T ss_pred             HHHHHHHHHHhhCch-hhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHh
Confidence            899999999887533 455544 4556777789999999999999988655 7888999999999999998776555443


Q ss_pred             HccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcC
Q 040261          149 ANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQG  228 (343)
Q Consensus       149 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  228 (343)
                      ....        |.   .......+...+..+++...+....... +++...+..+...+...+++.+|...+.+..+..
T Consensus       205 ~~~~--------~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  272 (334)
T d1dcea1         205 ENVL--------LK---ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQELEPEN  272 (334)
T ss_dssp             HHHH--------HH---HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHhH--------HH---HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC
Confidence            3321        11   1223344556677778888888776654 3456666677778888899999999998887653


Q ss_pred             CCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          229 VQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       229 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                       +.+...+..+..++...|++++|...++.+.+.. |.+...|..+...+.
T Consensus       273 -p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ld-P~~~~y~~~L~~~~~  321 (334)
T d1dcea1         273 -KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVD-PMRAAYLDDLRSKFL  321 (334)
T ss_dssp             -HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHH
T ss_pred             -chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-cccHHHHHHHHHHHh
Confidence             3346777888899999999999999999999874 334556666655554

>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=99.02  E-value=1.5e-08  Score=77.99  Aligned_cols=169  Identities=12%  Similarity=-0.010  Sum_probs=81.0

Q ss_pred             HHHHHhhcCcHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHH
Q 040261           93 LIKGLCAESRIMEAAALFTKLRAF----GCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYS  167 (343)
Q Consensus        93 l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (343)
                      ....|...+++++|.+.|.+..+.    +-.+ ...+|..+..+|.+.|++++|.+.+++........+. ......++.
T Consensus        43 aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~-~~~~~~~~~  121 (290)
T d1qqea_          43 AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQ-FRRGANFKF  121 (290)
T ss_dssp             HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhccc-chhHHHHHH
Confidence            344556666677777666665442    1111 1235566666666666666666666666664311000 000022333


Q ss_pred             HHHHHHH-hcCChHHHHHHHHHhhhC----CCCC-ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCH------HH
Q 040261          168 TITDGLC-KEGFVDKAKELFLKMKDE----NINP-DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNV------VT  235 (343)
Q Consensus       168 ~l~~~~~-~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~  235 (343)
                      .+...|. ..|++++|+..+++..+.    +.++ ...++..+...+...|++++|...++++.........      ..
T Consensus       122 ~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~  201 (290)
T d1qqea_         122 ELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDY  201 (290)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHH
T ss_pred             HHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHH
Confidence            4444443 246666666666554321    1111 1233455555566666666666666665543211110      11


Q ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHc
Q 040261          236 FNVIMNELCKNGKMDEASRLLELMIQI  262 (343)
Q Consensus       236 ~~~l~~~~~~~~~~~~a~~~~~~~~~~  262 (343)
                      +...+..+...|+++.|...+++..+.
T Consensus       202 ~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         202 FLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            222333444556666666666555443

>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=99.00  E-value=1.7e-06  Score=65.22  Aligned_cols=224  Identities=11%  Similarity=-0.033  Sum_probs=135.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHHcCCCccHHHHH
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCK----MGRVSPGFVVLGRILRSCFTPDAVTFT   91 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~   91 (343)
                      |+..+..|...+.+.+++++|++.|++..+.|   +...+..|...|..    ..+...|..++......+   +.....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhh
Confidence            46678888888889999999999999988765   55666667777665    456777888888877665   333333


Q ss_pred             HHHHHHhh----cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHHccCCCCCccccCCc
Q 040261           92 SLIKGLCA----ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCR----TGHTIVALNLFEEMANGNGEFGVVCKPDA  163 (343)
Q Consensus        92 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  163 (343)
                      .+...+..    ..+.+.|...++...+.|..   .....+...+..    ......+...+......+         +.
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~---~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~---------~~  142 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYA---EGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---------DG  142 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH---HHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---------CH
T ss_pred             ccccccccccccchhhHHHHHHHhhhhhhhhh---hHHHhhcccccCCCcccchhHHHHHHhhhhhccc---------cc
Confidence            34333332    45678888888887776532   222233333322    334556666666655432         45


Q ss_pred             chHHHHHHHHHh----cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhc----cCcHHHHHHHHHHHHHcCCCCCHHH
Q 040261          164 ITYSTITDGLCK----EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCY----ANDWNEAKCLFIEMMDQGVQPNVVT  235 (343)
Q Consensus       164 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  235 (343)
                      ..+..+...+..    ..+...+...++...+.|   +......+...+..    ..++++|...|....+.|   +...
T Consensus       143 ~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a  216 (265)
T d1ouva_         143 DGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGG  216 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             chhhhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHH
Confidence            556666666654    445566666666666554   34444444444433    446677777777766655   3344


Q ss_pred             HHHHHHHHHh----CCChhHHHHHHHHHHHcC
Q 040261          236 FNVIMNELCK----NGKMDEASRLLELMIQIG  263 (343)
Q Consensus       236 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  263 (343)
                      +..|...|..    ..+.++|..+|++..+.|
T Consensus       217 ~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         217 CFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             HHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCccCHHHHHHHHHHHHHCc
Confidence            4455555543    335666777777766665

>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=98.97  E-value=1.9e-08  Score=77.45  Aligned_cols=207  Identities=12%  Similarity=-0.039  Sum_probs=136.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhC----CCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC-----Ccc
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSI----GLFP-DLYTYNILINCFCKMGRVSPGFVVLGRILRSCF-----TPD   86 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~   86 (343)
                      ...|......|...|++++|.+.|.+..+.    +-++ -..+|..+..+|.+.|++++|.+.+++......     ...
T Consensus        37 a~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~  116 (290)
T d1qqea_          37 ADLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRG  116 (290)
T ss_dssp             HHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhH
Confidence            446888899999999999999999988652    2112 235788899999999999999999998765311     112


Q ss_pred             HHHHHHHHHHHh-hcCcHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCcccc
Q 040261           87 AVTFTSLIKGLC-AESRIMEAAALFTKLRAF----GCKP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCK  160 (343)
Q Consensus        87 ~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  160 (343)
                      ..++..+...+. ..|++++|++.+++..+.    +..+ ...++..+...+...|++++|...++++............
T Consensus       117 ~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~  196 (290)
T d1qqea_         117 ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (290)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhh
Confidence            345666666664 469999999999887642    1111 1345778899999999999999999998876532111000


Q ss_pred             CCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCC-CC---hhhHHHHHHHHhc--cCcHHHHHHHHHH
Q 040261          161 PDAITYSTITDGLCKEGFVDKAKELFLKMKDENIN-PD---VVTYTSLIRGFCY--ANDWNEAKCLFIE  223 (343)
Q Consensus       161 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~---~~~~~~l~~~~~~--~~~~~~a~~~~~~  223 (343)
                      .-...+...+..+...|+++.|...+++..+.... ++   ......++.++..  .+.+++|+..|+.
T Consensus       197 ~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~  265 (290)
T d1qqea_         197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDN  265 (290)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            00122344555677889999999999988765311 11   1233444444433  2335555555543

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=6.2e-08  Score=69.29  Aligned_cols=128  Identities=9%  Similarity=-0.094  Sum_probs=106.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      .|+. ...+...|+++.|++.|+++.    +|+..+|..+..++...|++++|++.|++.++.++. +...|..+..++.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~   81 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYY   81 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHH
Confidence            4543 677789999999999998753    577888999999999999999999999999997643 6889999999999


Q ss_pred             hcCcHHHHHHHHHHHHhcCC--------------CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHHccC
Q 040261           99 AESRIMEAAALFTKLRAFGC--------------KP-DVFTYTTLINGLCRTGHTIVALNLFEEMANGN  152 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~--------------~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  152 (343)
                      +.|++++|++.|++......              .+ ...++..+..++.+.|++++|.+.++......
T Consensus        82 ~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          82 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             hhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            99999999999999865311              11 13456677888999999999999999988764

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=4.1e-08  Score=64.01  Aligned_cols=105  Identities=9%  Similarity=-0.040  Sum_probs=86.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      +..-...+.+.|++++|+..|++.++.. +.+...|..+..++...|++++|+..+.+.++.++ .+...|..+..++..
T Consensus         6 l~~~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~~~~   83 (117)
T d1elwa_           6 LKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAALEF   83 (117)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHHHHH
Confidence            4556778889999999999999998765 56778899999999999999999999999998763 478889999999999


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHHHHHH
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVFTYTT  127 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~  127 (343)
                      .|++++|+..|++..+..+. +...+..
T Consensus        84 ~~~~~~A~~~~~~a~~~~p~-~~~~~~~  110 (117)
T d1elwa_          84 LNRFEEAKRTYEEGLKHEAN-NPQLKEG  110 (117)
T ss_dssp             TTCHHHHHHHHHHHHTTCTT-CHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCCC-CHHHHHH
Confidence            99999999999999987433 3444433

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=1.3e-07  Score=67.66  Aligned_cols=83  Identities=11%  Similarity=-0.036  Sum_probs=36.9

Q ss_pred             HHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHH
Q 040261           62 FCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVA  141 (343)
Q Consensus        62 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  141 (343)
                      +...|+++.|++.|.++    .+|+..+|..+..++...|++++|++.|++.++.+.. +...|..+..++.+.|++++|
T Consensus        15 ~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~~~g~~~~A   89 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYYQTEKYDLA   89 (192)
T ss_dssp             HHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHHhhccHHHH
Confidence            34444444444444432    1233444444444444444444444444444444322 334444444444444444444


Q ss_pred             HHHHHHHH
Q 040261          142 LNLFEEMA  149 (343)
Q Consensus       142 ~~~~~~~~  149 (343)
                      .+.|++..
T Consensus        90 ~~~~~kAl   97 (192)
T d1hh8a_          90 IKDLKEAL   97 (192)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            44444443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.90  E-value=4.2e-06  Score=63.00  Aligned_cols=111  Identities=9%  Similarity=-0.032  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchH
Q 040261          214 WNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVN  285 (343)
Q Consensus       214 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~  285 (343)
                      ...+...+......   .+...+..+...+..    ..+...+..+++...+.|   +......+...|..    ..+++
T Consensus       126 ~~~a~~~~~~~~~~---~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~  199 (265)
T d1ouva_         126 FKKAVEYFTKACDL---NDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFK  199 (265)
T ss_dssp             HHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHH
T ss_pred             hHHHHHHhhhhhcc---cccchhhhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchh
Confidence            44444444444332   233344444444443    234445555555555443   33333334333332    34566


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHHHHHh----cCChHHHHHHHHHHHhCC
Q 040261          286 RAKELFVSMESNGCMRDVFSYGILINGYCK----NKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       286 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  333 (343)
                      +|...|++..+.|   ++..+..|...|.+    .+++++|.++|++....|
T Consensus       200 ~A~~~~~~aa~~g---~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         200 EALARYSKACELE---NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             hhhhhHhhhhccc---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCc
Confidence            6666666666554   33444445555543    235566666666665554

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=7.9e-08  Score=66.54  Aligned_cols=107  Identities=7%  Similarity=-0.021  Sum_probs=90.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHh
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLC   98 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~   98 (343)
                      .+......+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|.+.|++.++... -+..+|..+..++.
T Consensus        12 ~l~~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p-~~~~a~~~~g~~~~   89 (159)
T d1a17a_          12 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNM   89 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcc-cchHHHHHHHHHHH
Confidence            45667788999999999999999999876 56788999999999999999999999999998753 36788999999999


Q ss_pred             hcCcHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 040261           99 AESRIMEAAALFTKLRAFGCKPDVFTYTTL  128 (343)
Q Consensus        99 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  128 (343)
                      ..|++++|...+++.....+. +...+..+
T Consensus        90 ~~g~~~eA~~~~~~a~~~~p~-~~~~~~~l  118 (159)
T d1a17a_          90 ALGKFRAALRDYETVVKVKPH-DKDAKMKY  118 (159)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTT-CHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHcCCC-CHHHHHHH
Confidence            999999999999999987533 44444443

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=1.3e-07  Score=61.53  Aligned_cols=94  Identities=11%  Similarity=-0.042  Sum_probs=84.7

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 040261           57 ILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG  136 (343)
Q Consensus        57 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  136 (343)
                      .-...+.+.|++++|+..|++.++.. +.+...|..+..++...|++++|+..+++..+.++. +...|..+..++...|
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~   85 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLN   85 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHcc
Confidence            35667889999999999999999876 337888999999999999999999999999988654 8889999999999999


Q ss_pred             ChHHHHHHHHHHHccC
Q 040261          137 HTIVALNLFEEMANGN  152 (343)
Q Consensus       137 ~~~~a~~~~~~~~~~~  152 (343)
                      ++++|+..+++..+..
T Consensus        86 ~~~~A~~~~~~a~~~~  101 (117)
T d1elwa_          86 RFEEAKRTYEEGLKHE  101 (117)
T ss_dssp             CHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHhC
Confidence            9999999999999865

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.82  E-value=2.2e-07  Score=64.24  Aligned_cols=119  Identities=12%  Similarity=0.049  Sum_probs=77.8

Q ss_pred             HHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCc
Q 040261          204 LIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGR  283 (343)
Q Consensus       204 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  283 (343)
                      ....|.+.|++++|...|++..+.. +-+...|..+..++...|++++|...|+++++.. +-+...|..+..++...|+
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCC
Confidence            3456667777777777777777764 4456677777777777788888888887777765 4556777777777778888


Q ss_pred             hHHHHHHHHHHHhCCCCccHHHHHHHHHH--HHhcCChHHHHHH
Q 040261          284 VNRAKELFVSMESNGCMRDVFSYGILING--YCKNKEIEGALSL  325 (343)
Q Consensus       284 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~  325 (343)
                      +++|...+++..... +-+...+..+..+  ....+.++++...
T Consensus        94 ~~eA~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          94 FRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             HHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            888888777777653 2233443333333  2333445555443

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.81  E-value=7.5e-08  Score=69.56  Aligned_cols=100  Identities=9%  Similarity=-0.050  Sum_probs=84.1

Q ss_pred             CChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          196 PDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLM  275 (343)
Q Consensus       196 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  275 (343)
                      |+...+......+.+.|++++|+..|...++.. +.+...|..+..+|.+.|++++|+..|+.+++.. +-+..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~-p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC-CCcHHHHHHHH
Confidence            667777788888999999999999999888874 5567888888999999999999999999988764 44677888899


Q ss_pred             HHHhcCCchHHHHHHHHHHHhC
Q 040261          276 DGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       276 ~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+|...|++++|...|++..+.
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh
Confidence            9999999999999999887653

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.80  E-value=5.2e-08  Score=70.41  Aligned_cols=99  Identities=14%  Similarity=0.021  Sum_probs=67.5

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      |+...+...+..+.+.|++++|+..|++.+... |.+...|..+..+|.+.|++++|+..|++.++..+. +..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~-~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCC-cHHHHHHHH
Confidence            566667777777777777777777777766654 445666777777777777777777777777664322 455666677


Q ss_pred             HHHhhcCcHHHHHHHHHHHHh
Q 040261           95 KGLCAESRIMEAAALFTKLRA  115 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~  115 (343)
                      .++...|++++|+..|++..+
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            777777777777777766654

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.70  E-value=1.1e-07  Score=61.38  Aligned_cols=91  Identities=10%  Similarity=-0.101  Sum_probs=60.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhc
Q 040261           21 NILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAE  100 (343)
Q Consensus        21 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  100 (343)
                      ..+...+.+.|++++|+..|++..... +-+...|..+..++.+.|++++|...+++.++..+ .+...+..+..+|...
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~la~~y~~~   97 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTNE   97 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhccccccccccc-ccccchHHHHHHHHHC
Confidence            345566667777777777777766644 33566677777777777777777777777766542 2566666677777777


Q ss_pred             CcHHHHHHHHHHH
Q 040261          101 SRIMEAAALFTKL  113 (343)
Q Consensus       101 ~~~~~a~~~~~~~  113 (343)
                      |++++|++.+++.
T Consensus        98 g~~~~A~~~l~~~  110 (112)
T d1hxia_          98 HNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            7777777776654

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.69  E-value=2e-07  Score=60.02  Aligned_cols=89  Identities=12%  Similarity=-0.006  Sum_probs=55.0

Q ss_pred             HHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCC
Q 040261          239 IMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKE  318 (343)
Q Consensus       239 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  318 (343)
                      +...+.+.|++++|...++++++.. +-+...|..+..++.+.|++++|...+++..+.. +.+...|..+...|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCC
Confidence            3445556666666666666666654 3355666666666666666666666666666543 2345566666666666666


Q ss_pred             hHHHHHHHHHH
Q 040261          319 IEGALSLYSEM  329 (343)
Q Consensus       319 ~~~a~~~~~~~  329 (343)
                      +++|++.+++.
T Consensus       100 ~~~A~~~l~~~  110 (112)
T d1hxia_         100 ANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            66666666654

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=7.2e-08  Score=63.03  Aligned_cols=94  Identities=13%  Similarity=0.059  Sum_probs=49.3

Q ss_pred             HHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC---hhHHHHHHHHHHHcCCCCC-HHHHHHHHHHH
Q 040261          203 SLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK---MDEASRLLELMIQIGVRPD-ASVYNTLMDGF  278 (343)
Q Consensus       203 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~  278 (343)
                      .++..+...+++++|.+.|+.....+ +.+..++..+..++.+.++   .++|+.+++++.+.+..|+ ..++..+..+|
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            34555555566666666666665553 3344555555555554333   3345555555554432222 12445555556


Q ss_pred             hcCCchHHHHHHHHHHHhC
Q 040261          279 CLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       279 ~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+.|++++|.+.|+++.+.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHh
Confidence            6666666666666665553

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=2.9e-07  Score=60.06  Aligned_cols=96  Identities=14%  Similarity=0.058  Sum_probs=66.5

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCC---cchHHHHHHHHHHcCCCcc-HHHHHHHHHH
Q 040261           21 NILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGR---VSPGFVVLGRILRSCFTPD-AVTFTSLIKG   96 (343)
Q Consensus        21 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~   96 (343)
                      ..++..+...+++++|.+.|++....+ +.+..++..+..++.+.++   +++|+.+++++...+..|+ ..++..+..+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            346667777778888888888877765 4566777777777766443   4457777777776543333 2356667777


Q ss_pred             HhhcCcHHHHHHHHHHHHhcC
Q 040261           97 LCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        97 ~~~~~~~~~a~~~~~~~~~~~  117 (343)
                      |.+.|++++|.+.|+++.+..
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~  102 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTE  102 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhhHHHHHHHHHHHHhC
Confidence            778888888888888877763

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.55  E-value=3.6e-08  Score=81.79  Aligned_cols=113  Identities=11%  Similarity=-0.065  Sum_probs=49.4

Q ss_pred             CcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040261          162 DAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMN  241 (343)
Q Consensus       162 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  241 (343)
                      +...+..+...+.+.|+.+.|...+.......   ...++..+...+...|++++|...+++..+.. +-+...|+.+..
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~  194 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---CQHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAI  194 (497)
T ss_dssp             ------------------------CCHHHHHH---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHH
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHH
Confidence            34445555555566666666655554443311   12345555556666666666666666666552 333456666666


Q ss_pred             HHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 040261          242 ELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFC  279 (343)
Q Consensus       242 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  279 (343)
                      .+...|+..+|...|.+.+... +|...++..|...+.
T Consensus       195 ~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         195 LASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH
Confidence            6666666666666666666554 445555555555544

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=2.1e-06  Score=56.62  Aligned_cols=98  Identities=12%  Similarity=0.108  Sum_probs=78.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCC-cc-----HHHHH
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFT-PD-----AVTFT   91 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~-----~~~~~   91 (343)
                      ..+..+...+.+.|++++|++.|++.++.+ +.+..++..+..+|.+.|++++|+..++++++.... +.     ..+|.
T Consensus         5 ~~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~   83 (128)
T d1elra_           5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (128)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            346678889999999999999999998876 457888999999999999999999999998864211 11     23566


Q ss_pred             HHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           92 SLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        92 ~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      .+...+...+++++|++.|++....
T Consensus        84 ~lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          84 RIGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            6777778888999999999887765

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=3.1e-06  Score=58.89  Aligned_cols=112  Identities=16%  Similarity=0.008  Sum_probs=78.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCC-CC-------------CHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGL-FP-------------DLYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~-------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      ..+...+..+.+.|++++|+..|++.+..-. .+             ...+|+.+..+|.+.|++++|+..++..+...+
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p   93 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDS   93 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhccc
Confidence            4566677889999999999999998875311 01             023455667777788888888888888877653


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING  131 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  131 (343)
                       .+..++..+..++...|++++|+..|++..+..+. +......+..+
T Consensus        94 -~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~-n~~~~~~l~~~  139 (170)
T d1p5qa1          94 -NNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVC  139 (170)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHH
T ss_pred             -cchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence             26777777888888888888888888888776432 44444444333

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.46  E-value=9.3e-06  Score=56.39  Aligned_cols=79  Identities=6%  Similarity=-0.106  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHH
Q 040261          235 TFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYC  314 (343)
Q Consensus       235 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  314 (343)
                      +|+.+..+|.+.|++++|+..++..++.+ |.+...+..+..+|...|++++|...|+...+.. +.+......+.....
T Consensus        64 ~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~~  141 (170)
T d1p5qa1          64 SHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQ  141 (170)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            56667788888888888888888888875 5578888888888888888999988888888753 224444444444433


Q ss_pred             h
Q 040261          315 K  315 (343)
Q Consensus       315 ~  315 (343)
                      +
T Consensus       142 ~  142 (170)
T d1p5qa1         142 R  142 (170)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.42  E-value=0.00017  Score=55.39  Aligned_cols=270  Identities=11%  Similarity=0.124  Sum_probs=157.3

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHH
Q 040261           15 PPVCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLI   94 (343)
Q Consensus        15 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~   94 (343)
                      ++..-...++..|.+.|.++.|..+|..+.         -|..++..+.+.++++.|.+++.+.      -+..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~---------d~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT---------CHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC---------CHHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHH
Confidence            455556677888889999999999998653         3456777888889999888877653      1566888888


Q ss_pred             HHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261           95 KGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      ..+.+.....-+     .+.......+......++..|-..|.+++...+++......       ..+...++.++..|+
T Consensus        77 ~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-------~~~~~~~~~L~~lya  144 (336)
T d1b89a_          77 FACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-------RAHMGMFTELAILYS  144 (336)
T ss_dssp             HHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-------TCCHHHHHHHHHHHH
T ss_pred             HHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-------ccchHHHHHHHHHHH
Confidence            888877766443     22333334466667788999999999999999999876543       456667888888888


Q ss_pred             hcCChHHHHHHHHHhhhCCCCC--------ChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC
Q 040261          175 KEGFVDKAKELFLKMKDENINP--------DVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN  246 (343)
Q Consensus       175 ~~~~~~~a~~~~~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  246 (343)
                      +.+ .++..+.++..... ..+        ....|..++..|.+.|+++.|..++   .++  .++..-....+..+.+.
T Consensus       145 k~~-~~kl~e~l~~~s~~-y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~---i~~--~~~~~~~~~f~e~~~k~  217 (336)
T d1b89a_         145 KFK-PQKMREHLELFWSR-VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM---MNH--PTDAWKEGQFKDIITKV  217 (336)
T ss_dssp             TTC-HHHHHHHHHHHSTT-SCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH---HHS--TTTTCCHHHHHHHHHHC
T ss_pred             HhC-hHHHHHHHHhcccc-CCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHH---HHc--chhhhhHHHHHHHHHcc
Confidence            864 44444444433211 111        1122344444555555555544332   222  33333344556667777


Q ss_pred             CChhHHHHHHHHHHHcCCCCCHHHHHHH-------------HHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          247 GKMDEASRLLELMIQIGVRPDASVYNTL-------------MDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       247 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      .+++...++.....+.  .|+  ..+.+             +..+.+.+++......++.....|   +....+++...|
T Consensus       218 ~N~e~~~~~i~~yL~~--~p~--~i~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~~n---~~~vn~al~~ly  290 (336)
T d1b89a_         218 ANVELYYRAIQFYLEF--KPL--LLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHN---NKSVNESLNNLF  290 (336)
T ss_dssp             SSTHHHHHHHHHHHHH--CGG--GHHHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTTC---CHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHc--CHH--HHHHHHHHhccCCCHHHHHHHHHhcCCcHHHHHHHHHHHHcC---hHHHHHHHHHHH
Confidence            7777666666655553  232  22333             344444555555555555554443   456888899999


Q ss_pred             HhcCChHHHHHH
Q 040261          314 CKNKEIEGALSL  325 (343)
Q Consensus       314 ~~~~~~~~a~~~  325 (343)
                      ...++++.-.+.
T Consensus       291 ie~~d~~~l~~~  302 (336)
T d1b89a_         291 ITEEDYQALRTS  302 (336)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             hCcchhHHHHHH
Confidence            999987654443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=6.3e-07  Score=74.17  Aligned_cols=134  Identities=10%  Similarity=-0.099  Sum_probs=79.2

Q ss_pred             cCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHH
Q 040261          176 EGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRL  255 (343)
Q Consensus       176 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  255 (343)
                      .+.++.++..+....... +++...+..+...+.+.|+.++|...+.......  | ..++..+...+...|++++|...
T Consensus        99 ~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~~~~~~A~~~  174 (497)
T d1ya0a1          99 SGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYRNQTSQAESY  174 (497)
T ss_dssp             HHHHHHHHHHHTC--------------------------------CCHHHHHH--H-HHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHcccHHHHHHH
Confidence            445566655554443332 2355667777888888999999988877665432  2 35677789999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh
Q 040261          256 LELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCK  315 (343)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  315 (343)
                      |+++.+.. +-+...|+.+...+...|+..+|...|.+..... +|-+.++..|...+.+
T Consensus       175 y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~  232 (497)
T d1ya0a1         175 YRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSK  232 (497)
T ss_dssp             HHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHH
Confidence            99999985 6677899999999999999999999999888754 4556666666666554

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=3.3e-06  Score=55.63  Aligned_cols=95  Identities=15%  Similarity=0.099  Sum_probs=75.0

Q ss_pred             HHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCc------
Q 040261           90 FTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDA------  163 (343)
Q Consensus        90 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~------  163 (343)
                      +..+...+.+.|++++|++.|++.++.++. +...+..+..+|.+.|++++|+..++++.+..       +.+.      
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~-------~~~~~~~~~~   78 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVG-------RENREDYRQI   78 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-------HHSTTCHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhC-------cccHHHHHHH
Confidence            445677888899999999999999988654 68888889999999999999999999987754       2222      


Q ss_pred             -chHHHHHHHHHhcCChHHHHHHHHHhhhC
Q 040261          164 -ITYSTITDGLCKEGFVDKAKELFLKMKDE  192 (343)
Q Consensus       164 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  192 (343)
                       .+|..+...+...+++++|+..|++....
T Consensus        79 a~~~~~lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          79 AKAYARIGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence             35556667777888999999998887654

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.35  E-value=2.2e-05  Score=53.31  Aligned_cols=99  Identities=11%  Similarity=0.047  Sum_probs=72.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHhHhCCC----CCC-----------HHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           18 CSFNILFGCLAKNKHYDTVLSLFKRLNSIGL----FPD-----------LYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        18 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      ..+..-+..+.+.|++++|+..|.+....-.    .++           ..+|..+..+|.+.|++++|++.++.+++..
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~   97 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID   97 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc
Confidence            3466677888999999999999998775211    111           1245567777778888888888888877765


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcC
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFG  117 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  117 (343)
                       +.+..+|..+..++...|++++|+..|++..+..
T Consensus        98 -p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1          98 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             -chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence             3366777778888888888888888888877764

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.30  E-value=8.1e-06  Score=56.68  Aligned_cols=111  Identities=12%  Similarity=0.031  Sum_probs=73.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHhHhCC--------------C-CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCC
Q 040261           19 SFNILFGCLAKNKHYDTVLSLFKRLNSIG--------------L-FPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCF   83 (343)
Q Consensus        19 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   83 (343)
                      .+......+.+.|++++|++.|.+.++..              + +.....|..+..++.+.|++++|+..+.++++..+
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p  108 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDP  108 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhhh
Confidence            35556777888999999999988765310              0 11233456666777777888888888887777643


Q ss_pred             CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 040261           84 TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLING  131 (343)
Q Consensus        84 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  131 (343)
                       .+...|..+..++.+.|++++|++.|++..+..+. +......+..+
T Consensus       109 -~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~-n~~~~~~l~~~  154 (169)
T d1ihga1         109 -SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLKV  154 (169)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             -hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence             35667777777777888888888888877776432 44444444433

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.27  E-value=1.5e-05  Score=55.18  Aligned_cols=118  Identities=9%  Similarity=0.011  Sum_probs=89.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhC---CCCCC-----------HHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSI---GLFPD-----------LYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      ...+...+..+.+.|++++|+..|++....   ....+           ...|..+..++.+.|++++|+..++..++..
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            446777888999999999999999887541   11111           1245667778899999999999999999875


Q ss_pred             CCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 040261           83 FTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTG  136 (343)
Q Consensus        83 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  136 (343)
                       +.+...|..+..++...|++++|...|++..+..+. +......+..+....+
T Consensus        95 -p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~-n~~~~~~l~~~~~~~~  146 (168)
T d1kt1a1          95 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQ-NKAARLQIFMCQKKAK  146 (168)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHHH
T ss_pred             -cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHH
Confidence             347888999999999999999999999999987533 5555555554444433

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.24  E-value=3.7e-05  Score=53.61  Aligned_cols=104  Identities=13%  Similarity=0.094  Sum_probs=79.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhC--CCC-CC------------------HHHHHHHHHHHHhcCCcchHHHHHHHH
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSI--GLF-PD------------------LYTYNILINCFCKMGRVSPGFVVLGRI   78 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~-~~------------------~~~~~~l~~~~~~~~~~~~a~~~~~~~   78 (343)
                      ...........|++++|.+.|......  |.. ++                  ...+..+..++...|++++|+..++++
T Consensus        14 ~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~a   93 (179)
T d2ff4a2          14 EKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEAL   93 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHH
Confidence            344556778899999999999998763  211 11                  134566777888889999999999998


Q ss_pred             HHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHh-----cCCCCCHHH
Q 040261           79 LRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRA-----FGCKPDVFT  124 (343)
Q Consensus        79 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~  124 (343)
                      ++.. +-+...|..++.++.+.|+..+|++.|+++.+     .|+.|...+
T Consensus        94 l~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          94 TFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            8875 34788888899999999999999999888743     588887655

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.24  E-value=3.2e-05  Score=52.50  Aligned_cols=63  Identities=16%  Similarity=0.040  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhC
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESN  297 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  297 (343)
                      .+|..+..+|.+.|++++|+..++.+++.+ +.+..+|..+..++...|++++|...|++..+.
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            356667778888888888888888888775 567788888888888888888888888888775

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.24  E-value=1.6e-05  Score=55.15  Aligned_cols=111  Identities=10%  Similarity=-0.069  Sum_probs=83.9

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHcC--------------C-CccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhcCCCC
Q 040261           56 NILINCFCKMGRVSPGFVVLGRILRSC--------------F-TPDAVTFTSLIKGLCAESRIMEAAALFTKLRAFGCKP  120 (343)
Q Consensus        56 ~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  120 (343)
                      ......+...|+++.|+..|.++++..              . +.....+..+..++.+.|++++|+..+++.++..+. 
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~-  109 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS-  109 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhh-
Confidence            344556678889998888887765320              1 123446677888899999999999999999988644 


Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHH
Q 040261          121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLC  174 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  174 (343)
                      +..+|..+..++...|++++|...|+++.+..       +.+..+...+..+..
T Consensus       110 ~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-------p~n~~~~~~l~~~~~  156 (169)
T d1ihga1         110 NTKALYRRAQGWQGLKEYDQALADLKKAQEIA-------PEDKAIQAELLKVKQ  156 (169)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHH
T ss_pred             hhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHHHH
Confidence            78899999999999999999999999999875       344555555544443

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.23  E-value=6.3e-05  Score=51.93  Aligned_cols=95  Identities=13%  Similarity=0.026  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHH
Q 040261          234 VTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGY  313 (343)
Q Consensus       234 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  313 (343)
                      ..|..+..++.+.|++++|+..++..++.. +.+...|..+..++...|++++|...|+++.+.. +.+......+....
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-P~n~~~~~~l~~~~  142 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQIFMCQ  142 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            356667788888999999999999988876 6678888888889999999999999999988864 23444555444444


Q ss_pred             HhcCChH-HHHHHHHHHH
Q 040261          314 CKNKEIE-GALSLYSEML  330 (343)
Q Consensus       314 ~~~~~~~-~a~~~~~~~~  330 (343)
                      ...+... ...+++..|.
T Consensus       143 ~~~~~~~e~~kk~~~~~f  160 (168)
T d1kt1a1         143 KKAKEHNERDRRTYANMF  160 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHH
Confidence            4443332 3345554444

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.15  E-value=4.6e-05  Score=53.09  Aligned_cols=123  Identities=11%  Similarity=0.070  Sum_probs=84.4

Q ss_pred             HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCC
Q 040261          169 ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGK  248 (343)
Q Consensus       169 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  248 (343)
                      ........|++++|.+.|.+.....  +....     .. ...+.+  +...-..+...    ....+..+..++...|+
T Consensus        17 ~g~~~~~~g~~e~A~~~~~~AL~l~--rG~~l-----~~-~~~~~w--~~~~r~~l~~~----~~~a~~~la~~~~~~g~   82 (179)
T d2ff4a2          17 AGVHAAAAGRFEQASRHLSAALREW--RGPVL-----DD-LRDFQF--VEPFATALVED----KVLAHTAKAEAEIACGR   82 (179)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTC--CSSTT-----GG-GTTSTT--HHHHHHHHHHH----HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhC--ccccc-----cc-CcchHH--HHHHHHHHHHH----HHHHHHHHHHHHHHCCC
Confidence            3456778899999999999887641  11100     00 000111  11111111111    23456778888999999


Q ss_pred             hhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHh-----CCCCccHHHH
Q 040261          249 MDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMES-----NGCMRDVFSY  306 (343)
Q Consensus       249 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  306 (343)
                      +++|...++++++.. +-+...|..++.+|...|+..+|++.|+++.+     .|+.|+..+-
T Consensus        83 ~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          83 ASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             HHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             chHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            999999999999886 67889999999999999999999999988743     5888887653

>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=98.14  E-value=3.6e-06  Score=62.90  Aligned_cols=126  Identities=10%  Similarity=-0.042  Sum_probs=87.9

Q ss_pred             HHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHH
Q 040261           26 CLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIME  105 (343)
Q Consensus        26 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  105 (343)
                      -..+.|++++|+..+++.++.. |.|...+..+...++..|++++|...++...+..+. +...+..+...+...+..++
T Consensus         5 ~aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~-~~~~~~~l~~ll~a~~~~~~   82 (264)
T d1zbpa1           5 NALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKD   82 (264)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHH
Confidence            4567899999999999999876 568889999999999999999999999999987422 34445444444433333333


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCC
Q 040261          106 AAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNG  153 (343)
Q Consensus       106 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  153 (343)
                      +..-.......+.+++...+......+...|+.++|...++++.+..+
T Consensus        83 a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p  130 (264)
T d1zbpa1          83 FAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQ  130 (264)
T ss_dssp             HTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCC
T ss_pred             HHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence            322211111112222334445556778889999999999999888653

>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=98.12  E-value=5.7e-06  Score=61.77  Aligned_cols=123  Identities=12%  Similarity=0.033  Sum_probs=70.4

Q ss_pred             HhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHH
Q 040261          208 FCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       208 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      ..+.|++++|+..+++.++.. +-+...+..+...++..|++++|...++...+.. +-+...+..+...+...+..+++
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~-P~~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF-PEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHhccccHHH
Confidence            345677777777777777763 4456777777777777788888877777777763 22344444444333322222222


Q ss_pred             HHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 040261          288 KELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSK  332 (343)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  332 (343)
                      ..-.......+-+++...+......+...|+.++|.+.++++.+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            211111111111223334444455677778888888888877755

>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=98.10  E-value=1.5e-05  Score=53.60  Aligned_cols=124  Identities=13%  Similarity=0.054  Sum_probs=67.1

Q ss_pred             hcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHH
Q 040261           29 KNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAA  108 (343)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  108 (343)
                      +.+.+++|+..|+...+.. |.+..++..+..++...+++..+.+                         ..+.+++|+.
T Consensus         9 r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e-------------------------~~~~~~~Ai~   62 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISD-------------------------AKQMIQEAIT   62 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHH-------------------------HHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhH-------------------------HHHHHHHHHH
Confidence            4455677777777766654 4455666666666655444333222                         1133456666


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcC-----------ChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcC
Q 040261          109 LFTKLRAFGCKPDVFTYTTLINGLCRTG-----------HTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEG  177 (343)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  177 (343)
                      .|++..+..+. +..+|..+..+|...|           .++.|.+.|++..+.        .|+...+..-+..+    
T Consensus        63 ~~~kAl~l~P~-~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--------~P~~~~~~~~L~~~----  129 (145)
T d1zu2a1          63 KFEEALLIDPK-KDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--------QPDNTHYLKSLEMT----  129 (145)
T ss_dssp             HHHHHHHHCTT-CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--------CTTCHHHHHHHHHH----
T ss_pred             HHHHHHHhcch-hhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc--------CCCHHHHHHHHHHH----
Confidence            66666665433 4556666666555443           346677777777764        35555544444333    


Q ss_pred             ChHHHHHHHHHhhhCC
Q 040261          178 FVDKAKELFLKMKDEN  193 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~  193 (343)
                        .+|.+++.++.+.|
T Consensus       130 --~ka~~~~~e~~k~~  143 (145)
T d1zu2a1         130 --AKAPQLHAEAYKQG  143 (145)
T ss_dssp             --HTHHHHHHHHHHSS
T ss_pred             --HHHHHHHHHHHHHh
Confidence              23445555544443

>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=98.03  E-value=3.8e-05  Score=51.51  Aligned_cols=113  Identities=12%  Similarity=0.039  Sum_probs=61.5

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC----------CChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcC
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKN----------GKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLT  281 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  281 (343)
                      +.+++|...++...+.. +.+...+..+..++...          +.+++|+..|+++++.+ +.+..+|..+..+|...
T Consensus        11 ~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHc
Confidence            34455555555554442 22334444444443322          23455666666666654 44555666666655544


Q ss_pred             C-----------chHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 040261          282 G-----------RVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLSKGI  334 (343)
Q Consensus       282 ~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  334 (343)
                      |           .+++|.+.|++..+.  .|+...+..-+..+      ..|.+++.+..+.|+
T Consensus        89 g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          89 AFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             ccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            3           357788888888775  46655554444333      466677777766654

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.95  E-value=0.002  Score=49.31  Aligned_cols=247  Identities=11%  Similarity=-0.004  Sum_probs=150.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcCCCccHHHHHHHHHHHhh
Q 040261           20 FNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCA   99 (343)
Q Consensus        20 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~   99 (343)
                      |..++..+.+.++++.|.+++.+.      .+..+|..+..++.+......+     .+.......++.....++..|-.
T Consensus        43 ~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~  111 (336)
T d1b89a_          43 FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQD  111 (336)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHH
Confidence            556788888888888888877644      2567888888888877665433     22222333455566778899999


Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCC-CccccCCcchHHHHHHHHHhcCC
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEF-GVVCKPDAITYSTITDGLCKEGF  178 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~  178 (343)
                      .|.+++...+++...... ..+...++.++..|++.+ .++..+.+.......... -...-.....|..++..|.+.|+
T Consensus       112 ~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~-~~kl~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~  189 (336)
T d1b89a_         112 RGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFK-PQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEE  189 (336)
T ss_dssp             TTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTC-HHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             cCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhC-hHHHHHHHHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCC
Confidence            999999999999876542 446777888888888764 344444444332211000 00000012335556666667777


Q ss_pred             hHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHH-------------HHHHHHh
Q 040261          179 VDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNV-------------IMNELCK  245 (343)
Q Consensus       179 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------------l~~~~~~  245 (343)
                      ++.|..+.-.-     +++..-....+..+.+..+.+...+++....+.  .|+  ..+.             ++..+.+
T Consensus       190 ~~~A~~~~i~~-----~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~--~p~--~i~~lL~~v~~~~d~~r~V~~~~k  260 (336)
T d1b89a_         190 YDNAIITMMNH-----PTDAWKEGQFKDIITKVANVELYYRAIQFYLEF--KPL--LLNDLLMVLSPRLDHTRAVNYFSK  260 (336)
T ss_dssp             HHHHHHHHHHS-----TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH--CGG--GHHHHHHHHGGGCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHc-----chhhhhHHHHHHHHHccCChHHHHHHHHHHHHc--CHH--HHHHHHHHhccCCCHHHHHHHHHh
Confidence            76666544221     233444455566666777766666666655543  232  2233             3444555


Q ss_pred             CCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          246 NGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       246 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      .+++.-...+++...+.+   +..+.+++...|...++++.-++..
T Consensus       261 ~~~l~li~p~Le~v~~~n---~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         261 VKQLPLVKPYLRSVQNHN---NKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             TTCTTTTHHHHHHHHTTC---CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCcHHHHHHHHHHHHcC---hHHHHHHHHHHHhCcchhHHHHHHH
Confidence            566666666666655444   4578899999999999976644444

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.70  E-value=0.00038  Score=47.14  Aligned_cols=63  Identities=13%  Similarity=0.141  Sum_probs=35.5

Q ss_pred             hhHHHH--HHHHHhcCChhHHHHHHHHhHhCCC-CCC----------HHHHHHHHHHHHhcCCcchHHHHHHHHHH
Q 040261           18 CSFNIL--FGCLAKNKHYDTVLSLFKRLNSIGL-FPD----------LYTYNILINCFCKMGRVSPGFVVLGRILR   80 (343)
Q Consensus        18 ~~~~~l--~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   80 (343)
                      .+|..+  ...+.+.|++++|++.|++.++... .|+          ...|+.+..++.+.|++++|...+++.++
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~   83 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   83 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhh
Confidence            345555  4455566777777777777664210 011          23455556666666666666665555543

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.63  E-value=0.00047  Score=46.65  Aligned_cols=99  Identities=18%  Similarity=0.122  Sum_probs=74.7

Q ss_pred             HHHHHH--HHHHHhcCCcchHHHHHHHHHHcCCC-c----------cHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc---
Q 040261           53 YTYNIL--INCFCKMGRVSPGFVVLGRILRSCFT-P----------DAVTFTSLIKGLCAESRIMEAAALFTKLRAF---  116 (343)
Q Consensus        53 ~~~~~l--~~~~~~~~~~~~a~~~~~~~~~~~~~-~----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  116 (343)
                      .+|..+  ...+.+.|++++|+..|++.++.... |          ....|+.+..+|...|++++|...+++..+.   
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            455555  45566789999999999999864211 1          2457888999999999999999999887653   


Q ss_pred             --CCCCC-----HHHHHHHHHHHHhcCChHHHHHHHHHHHcc
Q 040261          117 --GCKPD-----VFTYTTLINGLCRTGHTIVALNLFEEMANG  151 (343)
Q Consensus       117 --~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  151 (343)
                        ...++     ...+..+..+|...|++++|+..|++..+.
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l  129 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  129 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence              11222     224677889999999999999999997764

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.55  E-value=0.00025  Score=43.35  Aligned_cols=67  Identities=9%  Similarity=-0.027  Sum_probs=42.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHhHhCC-----CCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           16 PVCSFNILFGCLAKNKHYDTVLSLFKRLNSIG-----LFPD-LYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        16 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      +.+.+..++..+.+.|++++|+..|++..+..     ..++ ..++..+..++.+.|++++|...++++++..
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            44555667777777777777777777665421     0111 3456667777777777777777777776653

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.50  E-value=0.00031  Score=42.96  Aligned_cols=73  Identities=12%  Similarity=-0.024  Sum_probs=53.3

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCC
Q 040261          121 DVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDEN  193 (343)
Q Consensus       121 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  193 (343)
                      +...+-.+...+.+.|+++.|..+|++..+..+...........++..+..++.+.|++++|+..++++.+..
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            4455667888899999999999999988765321111011124568888899999999999999999988754

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=97.44  E-value=0.0053  Score=39.89  Aligned_cols=48  Identities=15%  Similarity=0.072  Sum_probs=21.5

Q ss_pred             chHHHHHHHHHHHhCCCCccHHHHHHHHHHHHh----cCChHHHHHHHHHHHhCC
Q 040261          283 RVNRAKELFVSMESNGCMRDVFSYGILINGYCK----NKEIEGALSLYSEMLSKG  333 (343)
Q Consensus       283 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  333 (343)
                      +.++|.++|++..+.|   ++.....|...|..    ..+.++|.++|++..+.|
T Consensus        74 d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          74 DLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            4455555555555443   22233333333333    234555555555554444

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=97.34  E-value=0.0072  Score=39.24  Aligned_cols=111  Identities=11%  Similarity=-0.013  Sum_probs=81.3

Q ss_pred             CChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----CCChhHH
Q 040261          177 GFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCK----NGKMDEA  252 (343)
Q Consensus       177 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a  252 (343)
                      .|+++|+++|++..+.|.   ......+.  .....+.++|...+++..+.|   +......|...|..    ..+.++|
T Consensus         7 kd~~~A~~~~~kaa~~g~---~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A   78 (133)
T d1klxa_           7 KDLKKAIQYYVKACELNE---MFGCLSLV--SNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   78 (133)
T ss_dssp             HHHHHHHHHHHHHHHTTC---TTHHHHHH--TCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHHCCC---hhhhhhhc--cccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHH
Confidence            367899999999888763   33333333  345568899999999998876   45555566666654    5678999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhc----CCchHHHHHHHHHHHhCC
Q 040261          253 SRLLELMIQIGVRPDASVYNTLMDGFCL----TGRVNRAKELFVSMESNG  298 (343)
Q Consensus       253 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  298 (343)
                      ..+|++..+.|   ++.....|...|..    ..+.++|.++|++..+.|
T Consensus        79 ~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          79 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            99999999987   34455556656654    468999999999998876

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.55  E-value=0.036  Score=34.67  Aligned_cols=137  Identities=12%  Similarity=0.071  Sum_probs=68.0

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCCh
Q 040261          100 ESRIMEAAALFTKLRAFGCKPDVFTYTTLINGLCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFV  179 (343)
Q Consensus       100 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  179 (343)
                      .|..++..+++.+....   .+..-++-++--....-+-+...++++..-....                   ...+++.
T Consensus        15 dG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FD-------------------ls~C~Nl   72 (161)
T d1wy6a1          15 DGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFD-------------------LDKCQNL   72 (161)
T ss_dssp             TTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSC-------------------GGGCSCT
T ss_pred             hhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcC-------------------chhhhcH
Confidence            45556666666555543   1334444444444444455555555554433210                   0122333


Q ss_pred             HHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHH
Q 040261          180 DKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELM  259 (343)
Q Consensus       180 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  259 (343)
                      ......+-.+-.     +...++..+......|.-++..++++.+.+.+ +|++...-.+..+|.+.|+..++-.++.++
T Consensus        73 k~vv~C~~~~n~-----~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~A  146 (161)
T d1wy6a1          73 KSVVECGVINNT-----LNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEA  146 (161)
T ss_dssp             HHHHHHHHHTTC-----CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc-----hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            333333322211     33444555555566666666666666655533 555555566666666666666666666666


Q ss_pred             HHcCC
Q 040261          260 IQIGV  264 (343)
Q Consensus       260 ~~~~~  264 (343)
                      .+.|+
T Consensus       147 Ce~G~  151 (161)
T d1wy6a1         147 CKKGE  151 (161)
T ss_dssp             HHTTC
T ss_pred             HHHhH
Confidence            66554

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.39  E-value=0.047  Score=34.14  Aligned_cols=141  Identities=12%  Similarity=0.064  Sum_probs=91.8

Q ss_pred             HHhcCChHHHHHHHHHHHccCCCCCccccCCcchHHHHHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          132 LCRTGHTIVALNLFEEMANGNGEFGVVCKPDAITYSTITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       132 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                      +.-.|..++..+++.+.....         +..-|+.++--....-+-+...++++.+-+.   .|.          ...
T Consensus        12 ~ildG~ve~Gveii~k~~~ss---------~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~---FDl----------s~C   69 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSS---------TKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKC   69 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---------CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGC
T ss_pred             HHHhhhHHhHHHHHHHHcccC---------CccccceeeeecccccchHHHHHHHHHHhhh---cCc----------hhh
Confidence            344677777777777776532         4555666665555566666666666665442   111          122


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHH
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELF  291 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  291 (343)
                      ++.......+-.+     ..+...+...+......|.-++..++++.+.+.+ ++++...-.+..+|.+.|...++.+++
T Consensus        70 ~Nlk~vv~C~~~~-----n~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell  143 (161)
T d1wy6a1          70 QNLKSVVECGVIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLL  143 (161)
T ss_dssp             SCTHHHHHHHHHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hcHHHHHHHHHHh-----cchHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHH
Confidence            3333333332221     2244556667788888889898888888877755 788888888888999999999999999


Q ss_pred             HHHHhCCCC
Q 040261          292 VSMESNGCM  300 (343)
Q Consensus       292 ~~~~~~~~~  300 (343)
                      .+..+.|+.
T Consensus       144 ~~ACe~G~K  152 (161)
T d1wy6a1         144 IEACKKGEK  152 (161)
T ss_dssp             HHHHHTTCH
T ss_pred             HHHHHHhHH
Confidence            888888753

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.12  E-value=0.032  Score=35.10  Aligned_cols=64  Identities=9%  Similarity=-0.035  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHHHhcCC---chHHHHHHHHHHHhCCCCcc-HHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          267 DASVYNTLMDGFCLTG---RVNRAKELFVSMESNGCMRD-VFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       267 ~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      +..+-.....++++..   +.++++.+++.+.+.+ +.+ ...+..|.-+|.+.|++++|.+.++.+++
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            3334334444444332   3345555555544432 112 13334444455555555555555555553

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=95.93  E-value=0.29  Score=38.96  Aligned_cols=181  Identities=10%  Similarity=-0.013  Sum_probs=114.5

Q ss_pred             CChHHHHHHHHHHHccCCCCCccccCCcchHHH----HHHHHHhcCChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhcc
Q 040261          136 GHTIVALNLFEEMANGNGEFGVVCKPDAITYST----ITDGLCKEGFVDKAKELFLKMKDENINPDVVTYTSLIRGFCYA  211 (343)
Q Consensus       136 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  211 (343)
                      .+.+.+...+........       .+..-...    +.......+..+.+...+......+  .+.......+......
T Consensus       228 ~d~~~a~~~l~~~~~~~~-------~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~  298 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQ-------LNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGT  298 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTT-------CCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHH
T ss_pred             cChhHHHHHHHhhhhccc-------ccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHc
Confidence            467777777777765431       22222222    2222334566777777777766554  2444444455556677


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCChhHHHHHHHHHHHc------------CCCC-----------CH
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIMNELCKNGKMDEASRLLELMIQI------------GVRP-----------DA  268 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------------~~~~-----------~~  268 (343)
                      +++..+...+..+... ........--+..++...|+.+.|...|..+...            |.++           ..
T Consensus       299 ~~~~~~~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~~~~fYG~LAa~~Lg~~~~~~~~~~~~~~~~  377 (450)
T d1qsaa1         299 GDRRGLNTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDS  377 (450)
T ss_dssp             TCHHHHHHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSHHHHHHHHHTTCCCCCCCCCCCSCCCC
T ss_pred             CChHHHHHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhcCCChHHHHHHHHcCCCCCCCcCCCCccHHH
Confidence            8888888888776432 1222334445778888899999999988877531            2110           00


Q ss_pred             H----HHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 040261          269 S----VYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEM  329 (343)
Q Consensus       269 ~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  329 (343)
                      .    .-..-+..+...|....|.+.|..+...   .+......+.....+.|.++.|+....+.
T Consensus       378 ~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~~~---~~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         378 ALTQGPEMARVRELMYWNLDNTARSEWANLVKS---KSKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             HHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHTT---CCHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             hhhcChHHHHHHHHHHcCCchHHHHHHHHHHhC---CCHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            0    0112345667889999999999988764   35556667788888999999999877665

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.73  E-value=0.33  Score=28.60  Aligned_cols=62  Identities=8%  Similarity=0.110  Sum_probs=45.7

Q ss_pred             ChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHHHHHHHHHHhCCCCccHHHHHHHH
Q 040261          248 KMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRAKELFVSMESNGCMRDVFSYGILI  310 (343)
Q Consensus       248 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  310 (343)
                      |.-++.+-++.+......|++.+..+.+++|.+.+++..|.++++..+.+. .++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHH
Confidence            445567777777777788888888888899988999999999888877542 23444555544

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.28  E-value=0.52  Score=29.42  Aligned_cols=67  Identities=12%  Similarity=-0.012  Sum_probs=37.4

Q ss_pred             CCHHHHHHHHHHHHhcC---CcchHHHHHHHHHHcCCCccHHHHHHHHHHHhhcCcHHHHHHHHHHHHhc
Q 040261           50 PDLYTYNILINCFCKMG---RVSPGFVVLGRILRSCFTPDAVTFTSLIKGLCAESRIMEAAALFTKLRAF  116 (343)
Q Consensus        50 ~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  116 (343)
                      ++..+-....-+++++.   +.++++.+++.+.+.+.......+..+.-+|.+.|++++|.+.++.+.+.
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            44444444444444443   34566677776665432111234455666666777777777777777665

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.18  E-value=0.42  Score=28.14  Aligned_cols=62  Identities=11%  Similarity=0.148  Sum_probs=37.8

Q ss_pred             ChHHHHHHHHHhhhCCCCCChhhHHHHHHHHhccCcHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040261          178 FVDKAKELFLKMKDENINPDVVTYTSLIRGFCYANDWNEAKCLFIEMMDQGVQPNVVTFNVIM  240 (343)
Q Consensus       178 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  240 (343)
                      +.=++.+-+..+....+.|++....+.+++|.+.+++..|.++++.+..+. .++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHH
Confidence            334555556666666666777777777777777777777777777666542 23344555444

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=88.74  E-value=4.4  Score=31.76  Aligned_cols=116  Identities=11%  Similarity=0.014  Sum_probs=74.6

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHHHHHHHH----HHHHhCCChhHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcCCchHHH
Q 040261          212 NDWNEAKCLFIEMMDQGVQPNVVTFNVIM----NELCKNGKMDEASRLLELMIQIGVRPDASVYNTLMDGFCLTGRVNRA  287 (343)
Q Consensus       212 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  287 (343)
                      .+.+.+..++....... ..+......+-    ......+..+.+..++......+  .+.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcc-cccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHH
Confidence            46677777777766543 22222222222    22234566777777777666543  3444555555566677899999


Q ss_pred             HHHHHHHHhCCCCccHHHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 040261          288 KELFVSMESNGCMRDVFSYGILINGYCKNKEIEGALSLYSEMLS  331 (343)
Q Consensus       288 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  331 (343)
                      ...+..+... ......-...+.+++...|+.+.|...|..+..
T Consensus       305 ~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         305 NTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            9999887643 122345556788999999999999999998753

>d1bpoa1 a.118.1.4 (A:331-487) Clathrin heavy-chain linker domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy-chain linker domain
domain: Clathrin heavy-chain linker domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=87.03  E-value=2.6  Score=27.17  Aligned_cols=65  Identities=17%  Similarity=0.184  Sum_probs=27.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHhHhCCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Q 040261           17 VCSFNILFGCLAKNKHYDTVLSLFKRLNSIGLFPDLYTYNILINCFCKMGRVSPGFVVLGRILRSC   82 (343)
Q Consensus        17 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   82 (343)
                      ...|..-...+...|++.+|-.+-....+ |+-.+..|.+.+-.+-...|+..-.+.+|..+.+.|
T Consensus        31 d~l~~~~F~~lf~~g~y~eAA~~aA~sP~-giLRt~~Ti~rFk~~~~~pGq~spLL~YF~~Ll~~~   95 (157)
T d1bpoa1          31 EELFARKFNALFAQGNYSEAAKVAANAPK-GILRTPDTIRRFQSVPAQPGQTSPLLQYFGILLDQG   95 (157)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHSGG-GSSCSHHHHHHHTTSCCCTTSCCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHhCCc-ccccCHHHHHHHHcCCCCCCCCCHHHHHHHHHHhcC
Confidence            33444444444455555555444433322 233344444433333333344444444444444443